1VQP

The structure of the transition state analogue "RAP" bound to the large ribosomal subunit of haloarcula marismortui

• PDB DOI: https://doi.org/10.2210/pdb1VQP/pdb
• NAKB: 1VQP

• Classification: RIBOSOME
• Organism(s): Haloarcula marismortui
• Mutation(s): Yes 


• Deposited: 2004-12-16 Released: 2005-11-29 
• Deposition Author(s): Schmeing, T.M., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 

Starting Model: experimental

Literature

Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.

Schmeing, T.M., Huang, K.S., Kitchen, D.E., Strobel, S.A., Steitz, T.A.

(2005) Mol Cell 20: 437-448

• PubMed: 16285925 
• DOI: https://doi.org/10.1016/j.molcel.2005.09.006
• Primary Citation of Related Structures:  
  1VQ4, 1VQ5, 1VQ8, 1VQ9, 1VQK, 1VQL, 1VQM, 1VQO, 1VQP


• PubMed Abstract: 
  

  Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 29-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1,491.01 kDa 
• Atom Count: 99,070 
• Modelled Residue Count: 6,659 
• Deposited Residue Count: 7,483 
• Unique protein chains: 29
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2P	D [auth A]	240	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P20276  Go to UniProtKB:  P20276

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3P	E [auth B]	338	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P20279  Go to UniProtKB:  P20279

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4E	F [auth C]	246	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12735  Go to UniProtKB:  P12735

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5P	G [auth D]	177	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14124  Go to UniProtKB:  P14124

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6P	H [auth E]	178	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14135  Go to UniProtKB:  P14135

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L7AE	I [auth F]	120	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12743  Go to UniProtKB:  P12743

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG	J [auth G]	348	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P15825  Go to UniProtKB:  P15825

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L10E	K [auth H]	171	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P60617  Go to UniProtKB:  P60617

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13P	L [auth J]	145	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P29198  Go to UniProtKB:  P29198

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14P	M [auth K]	132	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P22450  Go to UniProtKB:  P22450

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15P	N [auth L]	165	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12737  Go to UniProtKB:  P12737

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L15E	O [auth M]	195	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P60618  Go to UniProtKB:  P60618

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18P	P [auth N]	187	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14123  Go to UniProtKB:  P14123

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18e	Q [auth O]	116	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12733  Go to UniProtKB:  P12733

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19E	R [auth P]	149	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14119  Go to UniProtKB:  P14119

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21e	S [auth Q]	96	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12734  Go to UniProtKB:  P12734

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22P	T [auth R]	155	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P10970  Go to UniProtKB:  P10970

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23P	U [auth S]	85	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12732  Go to UniProtKB:  P12732

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24P	V [auth T]	120	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P10972  Go to UniProtKB:  P10972

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24E	W [auth U]	66	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14116  Go to UniProtKB:  P14116

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29P	X [auth V]	71	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P10971  Go to UniProtKB:  P10971

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30P	Y [auth W]	154	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14121  Go to UniProtKB:  P14121

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31e	Z [auth X]	92	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P18138  Go to UniProtKB:  P18138

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32E	AA [auth Y]	241	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12736  Go to UniProtKB:  P12736

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L37Ae	BA [auth Z]	83	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P60619  Go to UniProtKB:  P60619

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L37e	CA [auth 1]	57	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P32410  Go to UniProtKB:  P32410

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L39e	DA [auth 2]	50	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P22452  Go to UniProtKB:  P22452

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L44E	EA [auth 3]	92	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P32411  Go to UniProtKB:  P32411

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L11P	FA [auth I]	162	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14122 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14122  Go to UniProtKB:  P14122

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S ribosomal rna	A [auth 0]	2,922	Haloarcula marismortui

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	B [auth 9]	122	Haloarcula marismortui

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-R(*(DC)P*(DC)P*(PPU)*(LOF)P*(PO2)P*AP*C*C)-3'	C [auth 4]	8	N/A

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	AM [auth Z], BM [auth 1], EM [auth 3], ML [auth O], XL [auth U]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SR	AH [auth 0], AI [auth 0], AJ [auth 0], AK [auth 0], BH [auth 0], BI [auth 0], BJ [auth 0], BK [auth 0], BL [auth H], CH [auth 0], CI [auth 0], CJ [auth 0], CK [auth 0], CM [auth 1], DH [auth 0], DI [auth 0], DJ [auth 0], DK [auth 0], DM [auth 1], EH [auth 0], EI [auth 0], EJ [auth 0], EK [auth 0], FH [auth 0], FI [auth 0], FJ [auth 0], FK [auth 0], GH [auth 0], GI [auth 0], GJ [auth 0], GK [auth 0], GM [auth 3], HH [auth 0], HI [auth 0], HJ [auth 0], HK [auth 0], IH [auth 0], II [auth 0], IJ [auth 0], IK [auth 0], IL [auth L], JH [auth 0], JI [auth 0], JJ [auth 0], KH [auth 0], KI [auth 0], KJ [auth 0], LH [auth 0], LI [auth 0], LJ [auth 0], LK [auth 9], MH [auth 0], MI [auth 0], MJ [auth 0], MK [auth 9], NH [auth 0], NI [auth 0], NJ [auth 0], NK [auth 9], OH [auth 0], OI [auth 0], OJ [auth 0], PG [auth 0], PH [auth 0], PI [auth 0], PJ [auth 0], QG [auth 0], QH [auth 0], QI [auth 0], QJ [auth 0], RG [auth 0], RH [auth 0], RI [auth 0], RJ [auth 0], RK [auth A], SG [auth 0], SH [auth 0], SI [auth 0], SJ [auth 0], SK [auth A], TG [auth 0], TH [auth 0], TI [auth 0], TJ [auth 0], TK [auth A], TL [auth R], UG [auth 0], UH [auth 0], UI [auth 0], UJ [auth 0], VG [auth 0], VH [auth 0], VI [auth 0], VJ [auth 0], VK [auth B], VL [auth S], WG [auth 0], WH [auth 0], WI [auth 0], WJ [auth 0], WK [auth B], XG [auth 0], XH [auth 0], XI [auth 0], XJ [auth 0], YG [auth 0], YH [auth 0], YI [auth 0], YJ [auth 0], ZG [auth 0], ZH [auth 0], ZI [auth 0], ZJ [auth 0], ZK [auth F]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N
K	QD [auth 0], RD [auth 0], SD [auth 0]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	DL [auth J], EL [auth J], FG [auth 0], FL [auth J], FM [auth 3], GG [auth 0], HG [auth 0], HL [auth L], IG [auth 0], JG [auth 0], KG [auth 0], KL [auth M], LG [auth 0], LL [auth N], MG [auth 0], NG [auth 0], NL [auth O], OG [auth 0], QK [auth A], SL [auth R], UK [auth B], ZL [auth Y]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	AB [auth 0], AC [auth 0], AD [auth 0], BB [auth 0], BC [auth 0], BD [auth 0], CB [auth 0], CC [auth 0], CD [auth 0], DB [auth 0], DC [auth 0], DD [auth 0], EB [auth 0], EC [auth 0], ED [auth 0], FB [auth 0], FC [auth 0], FD [auth 0], GA [auth 0], GB [auth 0], GC [auth 0], GD [auth 0], GL [auth K], HA [auth 0], HB [auth 0], HC [auth 0], HD [auth 0], IA [auth 0], IB [auth 0], IC [auth 0], ID [auth 0], JA [auth 0], JB [auth 0], JC [auth 0], JD [auth 0], JK [auth 9], KA [auth 0], KB [auth 0], KC [auth 0], KD [auth 0], LA [auth 0], LB [auth 0], LC [auth 0], LD [auth 0], MA [auth 0], MB [auth 0], MC [auth 0], MD [auth 0], NA [auth 0], NB [auth 0], NC [auth 0], ND [auth 0], OA [auth 0], OB [auth 0], OC [auth 0], OD [auth 0], OK [auth A], PA [auth 0], PB [auth 0], PC [auth 0], PD [auth 0], PK [auth A], QA [auth 0], QB [auth 0], QC [auth 0], RA [auth 0], RB [auth 0], RC [auth 0], SA [auth 0], SB [auth 0], SC [auth 0], TA [auth 0], TB [auth 0], TC [auth 0], UA [auth 0], UB [auth 0], UC [auth 0], VA [auth 0], VB [auth 0], VC [auth 0], WA [auth 0], WB [auth 0], WC [auth 0], WL [auth T], XA [auth 0], XB [auth 0], XC [auth 0], YA [auth 0], YB [auth 0], YC [auth 0], YL [auth Y], ZA [auth 0], ZB [auth 0], ZC [auth 0]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	AE [auth 0], AF [auth 0], AG [auth 0], AL [auth H], BE [auth 0], BF [auth 0], BG [auth 0], CE [auth 0], CF [auth 0], CG [auth 0], CL [auth J], DE [auth 0], DF [auth 0], DG [auth 0], EE [auth 0], EF [auth 0], EG [auth 0], FE [auth 0], FF [auth 0], GE [auth 0], GF [auth 0], HE [auth 0], HF [auth 0], IE [auth 0], IF [auth 0], JE [auth 0], JF [auth 0], JL [auth M], KE [auth 0], KF [auth 0], KK [auth 9], LE [auth 0], LF [auth 0], ME [auth 0], MF [auth 0], NE [auth 0], NF [auth 0], OE [auth 0], OF [auth 0], OL [auth Q], PE [auth 0], PF [auth 0], PL [auth R], QE [auth 0], QF [auth 0], QL [auth R], RE [auth 0], RF [auth 0], RL [auth R], SE [auth 0], SF [auth 0], TD [auth 0], TE [auth 0], TF [auth 0], UD [auth 0], UE [auth 0], UF [auth 0], UL [auth S], VD [auth 0], VE [auth 0], VF [auth 0], WD [auth 0], WE [auth 0], WF [auth 0], XD [auth 0], XE [auth 0], XF [auth 0], XK [auth C], YD [auth 0], YE [auth 0], YF [auth 0], YK [auth D], ZD [auth 0], ZE [auth 0], ZF [auth 0]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.61	α = 90
b = 298.189	β = 90
c = 574.98	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-29 
Deposition Author(s): Schmeing, T.M., Steitz, T.A.

Revision History  

• Version 1.0: 2005-11-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description