8G7Q

Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the near-cognate AUG codon (Structure II)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance.

Rybak, M.Y., Gagnon, M.G.

(2024) Nat Struct Mol Biol 31: 810-816

  • DOI: https://doi.org/10.1038/s41594-024-01236-3
  • Primary Citation of Related Structures:  
    8G7P, 8G7Q, 8G7R, 8G7S

  • PubMed Abstract: 

    The frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 10 4 codons. In the universal genetic code, the AUN codon box specifies two amino acids, isoleucine and methionine. In bacteria and archaea, decoding specificity of the AUA and AUG codons relies on the wobble avoidance strategy that requires modification of C34 in the anticodon loop of isoleucine transfer RNA Ile CAU (tRNA Ile CAU ). Bacterial tRNA Ile CAU with 2-lysylcytidine (lysidine) at the wobble position deciphers AUA while avoiding AUG. Here we report cryo-electron microscopy structures of the Escherichia coli 70S ribosome complexed with elongation factor thermo unstable (EF-Tu) and isoleucine-tRNA Ile LAU in the process of decoding AUA and AUG. Lysidine in tRNA Ile LAU excludes AUG by promoting the formation of an unusual Hoogsteen purine-pyrimidine nucleobase geometry at the third position of the codon, weakening the interactions with the mRNA and destabilizing the EF-Tu ternary complex. Our findings elucidate the molecular mechanism by which tRNA Ile LAU specifically decodes AUA over AUG.

    • Organizational Affiliation: 

    Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]241Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth c]233Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]167Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]131Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]156Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]130Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]130Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth j]103Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]129Escherichia coliMutation(s): 1 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth l]124Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth m]118Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth n]101Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth o]89Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth p]82Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]84Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]75Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth s]92Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth t]87Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth u]71Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor TuZ [auth z]392Escherichia coliMutation(s): 0 
Gene Names: 
tufA_2, tuf, tufA, tufA_1, tufA_3, tufA_4, tufB, tufB_1, tufB_2, A5U30_004581, A9X72_23960, AAS29_002155, AAS29_004093, ACN68_05365, AM464_13225, AT845_003992, AWP47_16755, B6R15_000408, BANRA_00548, BANRA_05052, BG944_004744, BGM66_002194, BJJ90_25160, BLM69_004391, BMT49_21045, BMT50_08130, BMT91_03325, BTQ06_27310, BvCmsKKP036_03588, BVL39_05405, BZL69_05770, C0P57_003010, C3F40_15505, C9E67_28700, CA593_06065, CCV12_004444, CDC27_21515, CO706_19465, CR538_24255, CR539_01630, CR628_004228, CV83915_02073, CY655_25255, D1H34_004550, D3Y67_20900, D9E49_24235, DAH19_24560, DAH21_23365, DAH22_22865, DAH27_25225, DAH28_23840, DAH32_23225, DAH33_24610, DAH34_21600, DAH37_22525, DAH38_23185, DAH40_23380, DAH41_23505, DAH42_24340, DAH43_24835, DAH45_24780, DAH46_24615, DAH47_25180, DAH48_24880, DAH49_24790, DNQ45_05140, DS732_01505, DU321_23465, E3N34_20940, E5P27_19115, E5P28_08865, E5P29_14360, EC95NR1_03445, EKI52_13985, EL79_4415, ELT25_22120, ELU85_23630, ELU98_01540, ELV02_23595, ELV12_15580, ExPECSC038_04335, FA849_13360, FA849_22895, FE584_21060, FE587_22575, FEL34_21300, FHO90_24295, FOI11_015750, FOI11_24390, FZN31_22945, FZU14_22815, G9448_13515, GAJ12_23515, GJ11_25160, H0O37_04690, H6Y26_004587, HV109_22460, HV146_01010, HV146_21790, HV209_21230, HVV39_13100, HVW04_13870, HVW43_15020, HVX31_01850, HVX31_19145, HVX32_01070, HVX32_19165, HVY77_24410, HVZ29_01065, HVZ29_19215, HVZ30_01935, HVZ30_19855, HVZ71_23905, HX136_23675, I6H00_17205, I6H01_14295, I6H02_15680, JE86ST02C_45170, JE86ST05C_45270, JFD_05085, JNP96_01240, NCTC10082_02089, NCTC10089_04881, NCTC10418_07157, NCTC10764_02980, NCTC10767_00724, NCTC10865_05903, NCTC11112_02273, NCTC11126_05444, NCTC11181_01973, NCTC11341_02766, NCTC12950_05222, NCTC13127_06172, NCTC13148_04399, NCTC13216_02099, NCTC4450_01743, NCTC7927_05257, NCTC7928_03622, NCTC8333_05566, NCTC8500_05333, NCTC8621_04880, NCTC8959_04056, NCTC8960_02348, NCTC9036_04657, NCTC9037_04790, NCTC9044_02296, NCTC9045_05550, NCTC9073_00863, NCTC9075_06435, NCTC9077_05944, NCTC9111_04963, NCTC9117_05912, NCTC9702_05647, NCTC9706_02011, NCTC9775_03134, NCTC9777_01126, RG28_25305, SAMEA3472044_04882, SAMEA3751407_05016, SAMEA3752557_04835, SAMEA3753106_04223, TUM18780_41760, WP4S18E07_42760

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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2CA [auth C]273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3DA [auth D]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4EA [auth E]201Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5FA [auth F]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6GA [auth G]177Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9HA [auth H]149Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11IA [auth J]142Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13JA [auth L]142Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14KA [auth M]123Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15LA [auth N]144Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16MA [auth O]136Escherichia coliMutation(s): 1 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17NA [auth P]127Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18OA [auth Q]117Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19PA [auth R]115Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20QA [auth S]118Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L21RA [auth T]103Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22SA [auth U]110Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23TA [auth V]100Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24UA [auth W]104Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25VA [auth X]94Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27WA [auth Y]85Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28XA [auth Z]78Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29YA [auth 1]63Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30ZA [auth 2]59Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31AB [auth 3]70Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BB [auth 4]57Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CB [auth 5]55Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34DB [auth 6]46Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EB [auth 7]65Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FB [auth 8]38Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S Ribosomal RNAA [auth a]1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
Isoleucine tRNAV [auth w],
X [auth y]		76Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
P-site initiator tRNAW [auth x]77Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
M-M mRNAY [auth v]27Escherichia phage T4
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Entity ID: 26
MoleculeChains LengthOrganismImage
23S Ribosomal RNAAA [auth A]2,904Escherichia coli
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Entity ID: 27
MoleculeChains LengthOrganismImage
5S Ribosomal RNABA [auth B]120Escherichia coli
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR
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GB [auth a]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
GCP
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OM [auth z]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
ILE (Subject of Investigation/LOI)
Query on ILE
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JM [auth w],
KM [auth y]		ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-WHFBIAKZSA-N
ZN
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VLA [auth 3],
ZLA [auth 8]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
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AAA [auth A]
ABA [auth A]
AC [auth a]
ACA [auth A]
AD [auth a]
AAA [auth A],
ABA [auth A],
AC [auth a],
ACA [auth A],
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],
AKA [auth A],
AL [auth a],
ALA [auth B],
AM [auth n],
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 A],
BBA [auth A],
BC [auth a],
BCA [auth A],
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 A],
BL [auth a],
BLA [auth B],
BM [auth n],
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 A],
CBA [auth A],
CC [auth a],
CCA [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 A],
CL [auth a],
CLA [auth B],
CM [auth o],
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 A],
DBA [auth A],
DC [auth a],
DCA [auth A],
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 A],
DL [auth a],
DLA [auth B],
DM [auth p],
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 A],
EBA [auth A],
EC [auth a],
ECA [auth A],
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 A],
EL [auth a],
ELA [auth D],
EM [auth p],
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 A],
FBA [auth A],
FC [auth a],
FCA [auth A],
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 A],
FL [auth a],
FLA [auth E],
FM [auth p],
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 A],
GBA [auth A],
GC [auth a],
GCA [auth A],
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 A],
GL [auth a],
GLA [auth E],
GM [auth q],
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 A],
HB [auth a],
HBA [auth A],
HC [auth a],
HCA [auth A],
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 A],
HL [auth a],
HLA [auth E],
HM [auth r],
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 A],
IB [auth a],
IBA [auth A],
IC [auth a],
ICA [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 A],
IL [auth c],
ILA [auth L],
IM [auth r],
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 A],
JB [auth a],
JBA [auth A],
JC [auth a],
JCA [auth A],
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],
JKA [auth A],
JL [auth c],
JLA [auth N],
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 A],
KB [auth a],
KBA [auth A],
KC [auth a],
KCA [auth A],
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 A],
KL [auth d],
KLA [auth O],
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 A],
LB [auth a],
LBA [auth A],
LC [auth a],
LCA [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 A],
LL [auth d],
LLA [auth O],
LM [auth y],
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 A],
MB [auth a],
MBA [auth A],
MC [auth a],
MCA [auth A],
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 A],
ML [auth d],
MLA [auth S],
MM [auth v],
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 A],
NB [auth a],
NBA [auth A],
NC [auth a],
NCA [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 A],
NL [auth d],
NLA [auth S],
NM [auth v],
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 A],
OB [auth a],
OBA [auth A],
OC [auth a],
OCA [auth A],
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 A],
OL [auth e],
OLA [auth S],
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 A],
PB [auth a],
PBA [auth A],
PC [auth a],
PCA [auth A],
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 A],
PL [auth g],
PLA [auth T],
PM [auth z],
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 A],
QB [auth a],
QBA [auth A],
QC [auth a],
QCA [auth A],
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 A],
QL [auth h],
QLA [auth V],
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 A],
RB [auth a],
RBA [auth A],
RC [auth a],
RCA [auth A],
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 A],
RL [auth i],
RLA [auth W],
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 A],
SB [auth a],
SBA [auth A],
SC [auth a],
SCA [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 A],
SL [auth i],
SLA [auth Y],
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 A],
TB [auth a],
TBA [auth A],
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 B],
TL [auth i],
TLA [auth Z],
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 A],
UB [auth a],
UBA [auth A],
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 B],
UL [auth i],
ULA [auth Z],
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 A],
VB [auth a],
VBA [auth A],
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 B],
VL [auth i],
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 A],
WB [auth a],
WBA [auth A],
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 B],
WL [auth i],
WLA [auth 4],
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 A],
XB [auth a],
XBA [auth A],
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],
XKA [auth B],
XL [auth k],
XLA [auth 6],
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 A],
YB [auth a],
YBA [auth A],
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],
YKA [auth B],
YL [auth l],
YLA [auth 7],
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 A],
ZB [auth a],
ZBA [auth A],
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 A],
ZK [auth a],
ZKA [auth B],
ZL [auth l],
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
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T		L [auth l]L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ		DA [auth D]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4		MA [auth O]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIX1.19.2_4158

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM136936
Welch FoundationUnited StatesH-2032-20200401

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Source and taxonomy
  • Version 1.2: 2024-04-10
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-29
    Changes: Database references