5J8B

Crystal structure of Elongation Factor 4 (EF-4/LepA) in complex with GDPCP bound to the Thermus thermophilus 70S ribosome

• PDB DOI: https://doi.org/10.2210/pdb5J8B/pdb
• NAKB: 5J8B

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-07 Released: 2016-05-25 
• Deposition Author(s): Gagnon, M.G., Lin, J., Steitz, T.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.261 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Elongation factor 4 remodels the A-site tRNA on the ribosome.

Gagnon, M.G., Lin, J., Steitz, T.A.

(2016) Proc Natl Acad Sci U S A 113: 4994-4999

• PubMed: 27092003 
• DOI: https://doi.org/10.1073/pnas.1522932113
• Primary Citation of Related Structures:  
  5J8B


• PubMed Abstract: 
  

  During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. The structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114;

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 52-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1z1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 52-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2,391.37 kDa 
• Atom Count: 155,465 
• Modelled Residue Count: 11,372 
• Deposited Residue Count: 11,953 
• Unique protein chains: 52
• Unique nucleic acid chains: 7

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	C	228	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P27150 (Thermus thermophilus) Explore P27150  Go to UniProtKB:  P27150

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	D	276	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60405 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60405  Go to UniProtKB:  P60405

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	E	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN8  Go to UniProtKB:  Q5SHN8

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	F	210	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN9  Go to UniProtKB:  Q5SHN9

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	G	182	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ0  Go to UniProtKB:  Q5SHQ0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	H	180	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	I [auth J]	173	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q8VVE3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8VVE3  Go to UniProtKB:  Q8VVE3

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	J [auth K]	147	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP6  Go to UniProtKB:  Q5SLP6

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	K [auth N]	140	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60488 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60488  Go to UniProtKB:  P60488

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	L [auth O]	122	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP8  Go to UniProtKB:  Q5SHP8

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	M [auth P]	150	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ7  Go to UniProtKB:  Q5SHQ7

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	N [auth Q]	141	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60489  Go to UniProtKB:  P60489

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	O [auth R]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q9Z9H5  Go to UniProtKB:  Q9Z9H5

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	P [auth S]	112	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ4  Go to UniProtKB:  Q5SHQ4

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	Q [auth T]	146	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60490  Go to UniProtKB:  P60490

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	R [auth U]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60491  Go to UniProtKB:  P60491

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	S [auth V]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60492  Go to UniProtKB:  P60492

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	T [auth W]	113	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP3  Go to UniProtKB:  Q5SHP3

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	U [auth X]	96	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP0  Go to UniProtKB:  Q5SHP0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	V [auth Y]	110	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP9  Go to UniProtKB:  Q5SHP9

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	W [auth Z]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ1  Go to UniProtKB:  Q5SHZ1

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	X [auth 0]	85	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60493  Go to UniProtKB:  P60493

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	Y [auth 1]	98	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60494  Go to UniProtKB:  P60494

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	Z [auth 2]	72	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP6  Go to UniProtKB:  Q5SHP6

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	AA [auth 3]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ6  Go to UniProtKB:  Q5SHQ6

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	BA [auth 4]	71	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJE1  Go to UniProtKB:  Q5SJE1

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	CA [auth 5]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80339  Go to UniProtKB:  P80339

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	DA [auth 6]	54	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P35871  Go to UniProtKB:  P35871

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	EA [auth 7]	49	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80340 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80340  Go to UniProtKB:  P80340

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	FA [auth 8]	65	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKU1  Go to UniProtKB:  Q5SKU1

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	GA [auth 9]	37	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHR2  Go to UniProtKB:  Q5SHR2

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	IA [auth b]	256	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371  Go to UniProtKB:  P80371

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	JA [auth c]	239	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372  Go to UniProtKB:  P80372

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	KA [auth d]	209	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373  Go to UniProtKB:  P80373

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	LA [auth e]	162	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5  Go to UniProtKB:  Q5SHQ5

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	MA [auth f]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8  Go to UniProtKB:  Q5SLP8

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	NA [auth g]	156	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291  Go to UniProtKB:  P17291

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	OA [auth h]	138	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	PA [auth i]	128	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374  Go to UniProtKB:  P80374

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	QA [auth j]	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7  Go to UniProtKB:  Q5SHN7

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	RA [auth k]	129	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376  Go to UniProtKB:  P80376

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	SA [auth l]	132	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3  Go to UniProtKB:  Q5SHN3

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	TA [auth m]	126	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377  Go to UniProtKB:  P80377

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14 type Z	UA [auth n]	61	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	VA [auth o]	89	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76  Go to UniProtKB:  Q5SJ76

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	WA [auth p]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3  Go to UniProtKB:  Q5SJH3

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	XA [auth q]	105	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	YA [auth r]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0  Go to UniProtKB:  Q5SLQ0

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	ZA [auth s]	93	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2  Go to UniProtKB:  Q5SHP2

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	AB [auth t]	106	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380  Go to UniProtKB:  P80380

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein Thx	BB [auth u]	27	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3  Go to UniProtKB:  Q5SIH3

Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
GDPCP fused to the N-terminus of the ribosomal protein L9,Elongation factor 4	GB [auth z]	679	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: rplI, TTHA0242, lepA, TTHA0741 EC: 3.6.5
UniProt
Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ1  Go to UniProtKB:  Q5SLQ1
Find proteins for Q5SKA7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKA7  Go to UniProtKB:  Q5SKA7
UniProt Groups	Q5SLQ1Q5SKA7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S Ribosomal RNA	A	2,915	Thermus thermophilus HB8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5S Ribosomal RNA	B	121	Thermus thermophilus HB8

Entity ID: 34
Molecule	Chains	Length	Organism	Image
16S Ribosomal RNA	HA [auth a]	1,521	Thermus thermophilus HB8

Entity ID: 55
Molecule	Chains	Length	Organism	Image
mRNA	CB [auth v]	24	Thermus thermophilus HB8

Entity ID: 56
Molecule	Chains	Length	Organism	Image
A-site tRNA	DB [auth w]	76	Thermus thermophilus HB8

Entity ID: 57
Molecule	Chains	Length	Organism	Image
P-site tRNA	EB [auth x]	77	Thermus thermophilus HB8

Entity ID: 58
Molecule	Chains	Length	Organism	Image
E-site tRNA	FB [auth y]	76	Thermus thermophilus HB8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCP	XKA [auth z]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C11 H18 N5 O13 P3 PHBDHXOBFUBCJD-KQYNXXCUSA-N
SF4	AKA [auth d]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN	CCA [auth Y], ICA [auth 4], JKA [auth n], LCA [auth 5], NCA [auth 6], SCA [auth 9]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AAA [auth A], ABA [auth E], AC [auth A], ACA [auth W], AD [auth A], ADA [auth a], AE [auth A], AEA [auth a], AF [auth A], AFA [auth a], AG [auth A], AGA [auth a], AH [auth A], AHA [auth a], AI [auth A], AIA [auth a], AJ [auth A], AJA [auth a], AK [auth A], AL [auth A], AM [auth A], AN [auth A], AO [auth A], AP [auth A], AQ [auth A], AR [auth A], AS [auth A], AT [auth A], AU [auth A], AV [auth A], AW [auth A], AX [auth A], AY [auth A], AZ [auth A], BAA [auth B], BBA [auth E], BC [auth A], BCA [auth X], BD [auth A], BDA [auth a], BE [auth A], BEA [auth a], BF [auth A], BFA [auth a], BG [auth A], BGA [auth a], BH [auth A], BHA [auth a], BI [auth A], BIA [auth a], BJ [auth A], BJA [auth a], BK [auth A], BKA [auth e], BL [auth A], BM [auth A], BN [auth A], BO [auth A], BP [auth A], BQ [auth A], BR [auth A], BS [auth A], BT [auth A], BU [auth A], BV [auth A], BW [auth A], BX [auth A], BY [auth A], BZ [auth A], CAA [auth B], CBA [auth E], CC [auth A], CD [auth A], CDA [auth a], CE [auth A], CEA [auth a], CF [auth A], CFA [auth a], CG [auth A], CGA [auth a], CH [auth A], CHA [auth a], CI [auth A], CIA [auth a], CJ [auth A], CJA [auth a], CK [auth A], CKA [auth f], CL [auth A], CM [auth A], CN [auth A], CO [auth A], CP [auth A], CQ [auth A], CR [auth A], CS [auth A], CT [auth A], CU [auth A], CV [auth A], CW [auth A], CX [auth A], CY [auth A], CZ [auth A], DAA [auth B], DBA [auth E], DC [auth A], DCA [auth Z], DD [auth A], DDA [auth a], DE [auth A], DEA [auth a], DF [auth A], DFA [auth a], DG [auth A], DGA [auth a], DH [auth A], DHA [auth a], DI [auth A], DIA [auth a], DJ [auth A], DJA [auth a], DK [auth A], DKA [auth l], DL [auth A], DM [auth A], DN [auth A], DO [auth A], DP [auth A], DQ [auth A], DR [auth A], DS [auth A], DT [auth A], DU [auth A], DV [auth A], DW [auth A], DX [auth A], DY [auth A], DZ [auth A], EAA [auth B], EBA [auth F], EC [auth A], ECA [auth 0], ED [auth A], EDA [auth a], EE [auth A], EEA [auth a], EF [auth A], EFA [auth a], EG [auth A], EGA [auth a], EH [auth A], EHA [auth a], EI [auth A], EIA [auth a], EJ [auth A], EJA [auth a], EK [auth A], EKA [auth m], EL [auth A], EM [auth A], EN [auth A], EO [auth A], EP [auth A], EQ [auth A], ER [auth A], ES [auth A], ET [auth A], EU [auth A], EV [auth A], EW [auth A], EX [auth A], EY [auth A], EZ [auth A], FAA [auth B], FBA [auth F], FC [auth A], FCA [auth 0], FD [auth A], FDA [auth a], FE [auth A], FEA [auth a], FF [auth A], FFA [auth a], FG [auth A], FGA [auth a], FH [auth A], FHA [auth a], FI [auth A], FIA [auth a], FJ [auth A], FJA [auth a], FK [auth A], FKA [auth m], FL [auth A], FM [auth A], FN [auth A], FO [auth A], FP [auth A], FQ [auth A], FR [auth A], FS [auth A], FT [auth A], FU [auth A], FV [auth A], FW [auth A], FX [auth A], FY [auth A], FZ [auth A], GAA [auth B], GBA [auth F], GC [auth A], GCA [auth 0], GD [auth A], GDA [auth a], GE [auth A], GEA [auth a], GF [auth A], GFA [auth a], GG [auth A], GGA [auth a], GH [auth A], GHA [auth a], GI [auth A], GIA [auth a], GJ [auth A], GJA [auth a], GK [auth A], GKA [auth n], GL [auth A], GM [auth A], GN [auth A], GO [auth A], GP [auth A], GQ [auth A], GR [auth A], GS [auth A], GT [auth A], GU [auth A], GV [auth A], GW [auth A], GX [auth A], GY [auth A], GZ [auth A], HAA [auth B], HB [auth A], HBA [auth F], HC [auth A], HCA [auth 0], HD [auth A], HDA [auth a], HE [auth A], HEA [auth a], HF [auth A], HFA [auth a], HG [auth A], HGA [auth a], HH [auth A], HHA [auth a], HI [auth A], HIA [auth a], HJ [auth A], HJA [auth a], HK [auth A], HKA [auth n], HL [auth A], HM [auth A], HN [auth A], HO [auth A], HP [auth A], HQ [auth A], HR [auth A], HS [auth A], HT [auth A], HU [auth A], HV [auth A], HW [auth A], HX [auth A], HY [auth A], HZ [auth A], IAA [auth B], IB [auth A], IBA [auth F], IC [auth A], ID [auth A], IDA [auth a], IE [auth A], IEA [auth a], IF [auth A], IFA [auth a], IG [auth A], IGA [auth a], IH [auth A], IHA [auth a], II [auth A], IIA [auth a], IJ [auth A], IJA [auth a], IK [auth A], IKA [auth n], IL [auth A], IM [auth A], IN [auth A], IO [auth A], IP [auth A], IQ [auth A], IR [auth A], IS [auth A], IT [auth A], IU [auth A], IV [auth A], IW [auth A], IX [auth A], IY [auth A], IZ [auth A], JAA [auth B], JB [auth A], JBA [auth F], JC [auth A], JCA [auth 5], JD [auth A], JDA [auth a], JE [auth A], JEA [auth a], JF [auth A], JFA [auth a], JG [auth A], JGA [auth a], JH [auth A], JHA [auth a], JI [auth A], JIA [auth a], JJ [auth A], JJA [auth a], JK [auth A], JL [auth A], JM [auth A], JN [auth A], JO [auth A], JP [auth A], JQ [auth A], JR [auth A], JS [auth A], JT [auth A], JU [auth A], JV [auth A], JW [auth A], JX [auth A], JY [auth A], JZ [auth A], KAA [auth B], KB [auth A], KBA [auth G], KC [auth A], KCA [auth 5], KD [auth A], KDA [auth a], KE [auth A], KEA [auth a], KF [auth A], KFA [auth a], KG [auth A], KGA [auth a], KH [auth A], KHA [auth a], KI [auth A], KIA [auth a], KJ [auth A], KJA [auth a], KK [auth A], KKA [auth v], KL [auth A], KM [auth A], KN [auth A], KO [auth A], KP [auth A], KQ [auth A], KR [auth A], KS [auth A], KT [auth A], KU [auth A], KV [auth A], KW [auth A], KX [auth A], KY [auth A], KZ [auth A], LAA [auth B], LB [auth A], LBA [auth G], LC [auth A], LD [auth A], LDA [auth a], LE [auth A], LEA [auth a], LF [auth A], LFA [auth a], LG [auth A], LGA [auth a], LH [auth A], LHA [auth a], LI [auth A], LIA [auth a], LJ [auth A], LJA [auth a], LK [auth A], LKA [auth v], LL [auth A], LM [auth A], LN [auth A], LO [auth A], LP [auth A], LQ [auth A], LR [auth A], LS [auth A], LT [auth A], LU [auth A], LV [auth A], LW [auth A], LX [auth A], LY [auth A], LZ [auth A], MAA [auth B], MB [auth A], MBA [auth H], MC [auth A], MCA [auth 6], MD [auth A], MDA [auth a], ME [auth A], MEA [auth a], MF [auth A], MFA [auth a], MG [auth A], MGA [auth a], MH [auth A], MHA [auth a], MI [auth A], MIA [auth a], MJ [auth A], MJA [auth a], MK [auth A], MKA [auth x], ML [auth A], MM [auth A], MN [auth A], MO [auth A], MP [auth A], MQ [auth A], MR [auth A], MS [auth A], MT [auth A], MU [auth A], MV [auth A], MW [auth A], MX [auth A], MY [auth A], MZ [auth A], NAA [auth B], NB [auth A], NBA [auth N], NC [auth A], ND [auth A], NDA [auth a], NE [auth A], NEA [auth a], NF [auth A], NFA [auth a], NG [auth A], NGA [auth a], NH [auth A], NHA [auth a], NI [auth A], NIA [auth a], NJ [auth A], NJA [auth a], NK [auth A], NKA [auth x], NL [auth A], NM [auth A], NN [auth A], NO [auth A], NP [auth A], NQ [auth A], NR [auth A], NS [auth A], NT [auth A], NU [auth A], NV [auth A], NW [auth A], NX [auth A], NY [auth A], NZ [auth A], OAA [auth B], OB [auth A], OBA [auth O], OC [auth A], OCA [auth 6], OD [auth A], ODA [auth a], OE [auth A], OEA [auth a], OF [auth A], OFA [auth a], OG [auth A], OGA [auth a], OH [auth A], OHA [auth a], OI [auth A], OIA [auth a], OJ [auth A], OJA [auth a], OK [auth A], OKA [auth x], OL [auth A], OM [auth A], ON [auth A], OO [auth A], OP [auth A], OQ [auth A], OR [auth A], OS [auth A], OT [auth A], OU [auth A], OV [auth A], OW [auth A], OX [auth A], OY [auth A], OZ [auth A], PAA [auth B], PB [auth A], PBA [auth O], PC [auth A], PCA [auth 7], PD [auth A], PDA [auth a], PE [auth A], PEA [auth a], PF [auth A], PFA [auth a], PG [auth A], PGA [auth a], PH [auth A], PHA [auth a], PI [auth A], PIA [auth a], PJ [auth A], PJA [auth a], PK [auth A], PKA [auth x], PL [auth A], PM [auth A], PN [auth A], PO [auth A], PP [auth A], PQ [auth A], PR [auth A], PS [auth A], PT [auth A], PU [auth A], PV [auth A], PW [auth A], PX [auth A], PY [auth A], PZ [auth A], QAA [auth B], QB [auth A], QBA [auth P], QC [auth A], QCA [auth 8], QD [auth A], QDA [auth a], QE [auth A], QEA [auth a], QF [auth A], QFA [auth a], QG [auth A], QGA [auth a], QH [auth A], QHA [auth a], QI [auth A], QIA [auth a], QJ [auth A], QJA [auth a], QK [auth A], QKA [auth x], QL [auth A], QM [auth A], QN [auth A], QO [auth A], QP [auth A], QQ [auth A], QR [auth A], QS [auth A], QT [auth A], QU [auth A], QV [auth A], QW [auth A], QX [auth A], QY [auth A], QZ [auth A], RAA [auth B], RB [auth A], RBA [auth P], RC [auth A], RCA [auth 9], RD [auth A], RDA [auth a], RE [auth A], REA [auth a], RF [auth A], RFA [auth a], RG [auth A], RGA [auth a], RH [auth A], RHA [auth a], RI [auth A], RIA [auth a], RJ [auth A], RJA [auth a], RK [auth A], RKA [auth x], RL [auth A], RM [auth A], RN [auth A], RO [auth A], RP [auth A], RQ [auth A], RR [auth A], RS [auth A], RT [auth A], RU [auth A], RV [auth A], RW [auth A], RX [auth A], RY [auth A], RZ [auth A], SAA [auth B], SB [auth A], SBA [auth P], SC [auth A], SD [auth A], SDA [auth a], SE [auth A], SEA [auth a], SF [auth A], SFA [auth a], SG [auth A], SGA [auth a], SH [auth A], SHA [auth a], SI [auth A], SIA [auth a], SJ [auth A], SJA [auth a], SK [auth A], SKA [auth x], SL [auth A], SM [auth A], SN [auth A], SO [auth A], SP [auth A], SQ [auth A], SR [auth A], SS [auth A], ST [auth A], SU [auth A], SV [auth A], SW [auth A], SX [auth A], SY [auth A], SZ [auth A], TAA [auth D], TB [auth A], TBA [auth Q], TC [auth A], TCA [auth a], TD [auth A], TDA [auth a], TE [auth A], TEA [auth a], TF [auth A], TFA [auth a], TG [auth A], TGA [auth a], TH [auth A], THA [auth a], TI [auth A], TIA [auth a], TJ [auth A], TJA [auth a], TK [auth A], TKA [auth x], TL [auth A], TM [auth A], TN [auth A], TO [auth A], TP [auth A], TQ [auth A], TR [auth A], TS [auth A], TT [auth A], TU [auth A], TV [auth A], TW [auth A], TX [auth A], TY [auth A], TZ [auth A], UAA [auth D], UB [auth A], UBA [auth Q], UC [auth A], UCA [auth a], UD [auth A], UDA [auth a], UE [auth A], UEA [auth a], UF [auth A], UFA [auth a], UG [auth A], UGA [auth a], UH [auth A], UHA [auth a], UI [auth A], UIA [auth a], UJ [auth A], UJA [auth a], UK [auth A], UKA [auth x], UL [auth A], UM [auth A], UN [auth A], UO [auth A], UP [auth A], UQ [auth A], UR [auth A], US [auth A], UT [auth A], UU [auth A], UV [auth A], UW [auth A], UX [auth A], UY [auth A], UZ [auth A], VAA [auth D], VB [auth A], VBA [auth R], VC [auth A], VCA [auth a], VD [auth A], VDA [auth a], VE [auth A], VEA [auth a], VF [auth A], VFA [auth a], VG [auth A], VGA [auth a], VH [auth A], VHA [auth a], VI [auth A], VIA [auth a], VJ [auth A], VJA [auth a], VK [auth A], VKA [auth z], VL [auth A], VM [auth A], VN [auth A], VO [auth A], VP [auth A], VQ [auth A], VR [auth A], VS [auth A], VT [auth A], VU [auth A], VV [auth A], VW [auth A], VX [auth A], VY [auth A], VZ [auth A], WAA [auth D], WB [auth A], WBA [auth R], WC [auth A], WCA [auth a], WD [auth A], WDA [auth a], WE [auth A], WEA [auth a], WF [auth A], WFA [auth a], WG [auth A], WGA [auth a], WH [auth A], WHA [auth a], WI [auth A], WIA [auth a], WJ [auth A], WJA [auth a], WK [auth A], WKA [auth z], WL [auth A], WM [auth A], WN [auth A], WO [auth A], WP [auth A], WQ [auth A], WR [auth A], WS [auth A], WT [auth A], WU [auth A], WV [auth A], WW [auth A], WX [auth A], WY [auth A], WZ [auth A], XAA [auth D], XB [auth A], XBA [auth U], XC [auth A], XCA [auth a], XD [auth A], XDA [auth a], XE [auth A], XEA [auth a], XF [auth A], XFA [auth a], XG [auth A], XGA [auth a], XH [auth A], XHA [auth a], XI [auth A], XIA [auth a], XJ [auth A], XJA [auth a], XK [auth A], XL [auth A], XM [auth A], XN [auth A], XO [auth A], XP [auth A], XQ [auth A], XR [auth A], XS [auth A], XT [auth A], XU [auth A], XV [auth A], XW [auth A], XX [auth A], XY [auth A], XZ [auth A], YAA [auth D], YB [auth A], YBA [auth V], YC [auth A], YCA [auth a], YD [auth A], YDA [auth a], YE [auth A], YEA [auth a], YF [auth A], YFA [auth a], YG [auth A], YGA [auth a], YH [auth A], YHA [auth a], YI [auth A], YIA [auth a], YJ [auth A], YJA [auth a], YK [auth A], YL [auth A], YM [auth A], YN [auth A], YO [auth A], YP [auth A], YQ [auth A], YR [auth A], YS [auth A], YT [auth A], YU [auth A], YV [auth A], YW [auth A], YX [auth A], YY [auth A], YZ [auth A], ZAA [auth E], ZB [auth A], ZBA [auth V], ZC [auth A], ZCA [auth a], ZD [auth A], ZDA [auth a], ZE [auth A], ZEA [auth a], ZF [auth A], ZFA [auth a], ZG [auth A], ZGA [auth a], ZH [auth A], ZHA [auth a], ZI [auth A], ZIA [auth a], ZJ [auth A], ZJA [auth d], ZK [auth A], ZL [auth A], ZM [auth A], ZN [auth A], ZO [auth A], ZP [auth A], ZQ [auth A], ZR [auth A], ZS [auth A], ZT [auth A], ZU [auth A], ZV [auth A], ZW [auth A], ZX [auth A], ZY [auth A], ZZ [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.261 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.124	α = 90
b = 271.723	β = 90
c = 436.83	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Gagnon, M.G., Lin, J., Steitz, T.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM022778

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations
• Version 2.0: 2019-07-03
  Changes: Data collection, Non-polymer description, Structure summary
• Version 2.1: 2019-12-25
  Changes: Author supporting evidence
• Version 2.2: 2024-03-06
  Changes: Advisory, Data collection, Database references, Derived calculations