8EKC

Escherichia coli 70S ribosome bound to thermorubin, deacylated P-site tRNAfMet and aminoacylated A-site Phe-tRNA

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history. 


Literature

Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin.

Paranjpe, M.N., Marina, V.I., Grachev, A.A., Maviza, T.P., Tolicheva, O.A., Paleskava, A., Osterman, I.A., Sergiev, P.V., Konevega, A.L., Polikanov, Y.S., Gagnon, M.G.

(2023) Nucleic Acids Res 51: 449-462

  • DOI: https://doi.org/10.1093/nar/gkac1189
  • Primary Citation of Related Structures:  
    8EKB, 8EKC

  • PubMed Abstract: 

    Thermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and was thought to inhibit factor-dependent initiation of translation and obstruct the accommodation of tRNAs into the A site. Here, we show that thermorubin causes ribosomes to stall in vivo and in vitro at internal and termination codons, thereby allowing the ribosome to initiate protein synthesis and translate at least a few codons before stalling. Our biochemical data show that THR affects multiple steps of translation elongation with a significant impact on the binding stability of the tRNA in the A site, explaining premature cessation of translation. Our high-resolution crystal and cryo-EM structures of the 70S-THR complex show that THR can co-exist with P- and A-site tRNAs, explaining how ribosomes can elongate in the presence of the drug. Remarkable is the ability of THR to arrest ribosomes at the stop codons. Our data suggest that by causing structural re-arrangements in the decoding center, THR interferes with the accommodation of tRNAs or release factors into the ribosomal A site.

    • Organizational Affiliation: 

    Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, 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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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]129Escherichia coliMutation(s): 0 
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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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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: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2AA [auth C]273Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3BA [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4CA [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5DA [auth F]179Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6EA [auth G]177Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth H]149Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13GA [auth L]142Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14HA [auth M]123Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L15IA [auth N]144Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16JA [auth O]136Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17KA [auth P]127Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18LA [auth Q]117Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19MA [auth R]115Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20NA [auth S]118Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L21OA [auth T]103Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PA [auth U]110Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23QA [auth V]100Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24RA [auth W]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25SA [auth X]94Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27TA [auth Y]85Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28UA [auth Z]78Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29VA [auth 1]63Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30WA [auth 2]59Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31XA [auth 3]70Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32YA [auth 4]57Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33ZA [auth 5]55Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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UniProt GroupP0A7N9
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth 6]46Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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UniProt GroupP0A7P5
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth 7]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth 8]38Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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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
A-site phenylalanine tRNAV [auth w]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-F-Stop mRNAX [auth v]24Escherichia phage T4
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S Ribosomal RNAY [auth A]2,904Escherichia coli
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S Ribosomal RNAZ [auth B]120Escherichia coli
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T8B (Subject of Investigation/LOI)
Query on T8B
Download Ideal Coordinates CCD File 
FG [auth a]Thermorubin
C32 H24 O12
GGEDVBUCHDZLTH-MOSHPQCFSA-N
PHE
Query on PHE
Download Ideal Coordinates CCD File 
JG [auth w]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
PCA [auth 3],
SCA [auth 8]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
AAA [auth A]
ABA [auth A]
AC [auth a]
ACA [auth B]
AD [auth a]
AAA [auth A],
ABA [auth A],
AC [auth a],
ACA [auth B],
AD [auth a],
AE [auth a],
AF [auth a],
AG [auth a],
AH [auth A],
AI [auth A],
AJ [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 A],
BBA [auth A],
BC [auth a],
BCA [auth B],
BD [auth a],
BE [auth a],
BF [auth a],
BG [auth a],
BH [auth A],
BI [auth A],
BJ [auth A],
BK [auth A],
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 A],
CBA [auth A],
CC [auth a],
CCA [auth B],
CD [auth a],
CE [auth a],
CF [auth a],
CG [auth a],
CH [auth A],
CI [auth A],
CJ [auth A],
CK [auth A],
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 A],
DB [auth a],
DBA [auth A],
DC [auth a],
DCA [auth B],
DD [auth a],
DE [auth a],
DF [auth a],
DG [auth a],
DH [auth A],
DI [auth A],
DJ [auth A],
DK [auth A],
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 A],
EB [auth a],
EBA [auth A],
EC [auth a],
ECA [auth B],
ED [auth a],
EE [auth a],
EF [auth a],
EG [auth a],
EH [auth A],
EI [auth A],
EJ [auth A],
EK [auth A],
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 A],
FB [auth a],
FBA [auth A],
FC [auth a],
FCA [auth B],
FD [auth a],
FE [auth a],
FF [auth a],
FH [auth A],
FI [auth A],
FJ [auth A],
FK [auth A],
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 A],
GB [auth a],
GBA [auth A],
GC [auth a],
GCA [auth B],
GD [auth a],
GE [auth a],
GF [auth a],
GG [auth l],
GH [auth A],
GI [auth A],
GJ [auth A],
GK [auth A],
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 A],
HB [auth a],
HBA [auth A],
HC [auth a],
HCA [auth C],
HD [auth a],
HE [auth a],
HF [auth a],
HG [auth n],
HH [auth A],
HI [auth A],
HJ [auth A],
HK [auth A],
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 A],
IB [auth a],
IBA [auth A],
IC [auth a],
ICA [auth C],
ID [auth a],
IE [auth a],
IF [auth a],
IG [auth w],
IH [auth A],
II [auth A],
IJ [auth A],
IK [auth A],
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 A],
JB [auth a],
JBA [auth A],
JC [auth a],
JCA [auth C],
JD [auth a],
JE [auth a],
JF [auth a],
JH [auth A],
JI [auth A],
JJ [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 A],
KB [auth a],
KBA [auth A],
KC [auth a],
KCA [auth D],
KD [auth a],
KE [auth a],
KF [auth a],
KG [auth x],
KH [auth A],
KI [auth A],
KJ [auth A],
KK [auth A],
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 A],
LB [auth a],
LBA [auth A],
LC [auth a],
LCA [auth N],
LD [auth a],
LE [auth a],
LF [auth a],
LG [auth x],
LH [auth A],
LI [auth A],
LJ [auth A],
LK [auth A],
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 A],
MB [auth a],
MBA [auth A],
MC [auth a],
MCA [auth P],
MD [auth a],
ME [auth a],
MF [auth a],
MG [auth v],
MH [auth A],
MI [auth A],
MJ [auth A],
MK [auth A],
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 A],
NB [auth a],
NBA [auth A],
NC [auth a],
NCA [auth S],
ND [auth a],
NE [auth a],
NF [auth a],
NG [auth v],
NH [auth A],
NI [auth A],
NJ [auth A],
NK [auth A],
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 A],
OB [auth a],
OBA [auth A],
OC [auth a],
OCA [auth V],
OD [auth a],
OE [auth a],
OF [auth a],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth A],
OK [auth A],
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 A],
PB [auth a],
PBA [auth A],
PC [auth a],
PD [auth a],
PE [auth a],
PF [auth a],
PG [auth A],
PH [auth A],
PI [auth A],
PJ [auth A],
PK [auth A],
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 A],
QB [auth a],
QBA [auth A],
QC [auth a],
QCA [auth 4],
QD [auth a],
QE [auth a],
QF [auth a],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth A],
QK [auth A],
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 A],
RB [auth a],
RBA [auth A],
RC [auth a],
RCA [auth 7],
RD [auth a],
RE [auth a],
RF [auth a],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth A],
RK [auth A],
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 A],
SB [auth a],
SBA [auth A],
SC [auth a],
SD [auth a],
SE [auth a],
SF [auth a],
SG [auth A],
SH [auth A],
SI [auth A],
SJ [auth A],
SK [auth A],
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 A],
TB [auth a],
TBA [auth A],
TC [auth a],
TD [auth a],
TE [auth a],
TF [auth a],
TG [auth A],
TH [auth A],
TI [auth A],
TJ [auth A],
TK [auth A],
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 A],
UB [auth a],
UBA [auth A],
UC [auth a],
UD [auth a],
UE [auth a],
UF [auth a],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth A],
UK [auth A],
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 A],
VB [auth a],
VBA [auth A],
VC [auth a],
VD [auth a],
VE [auth a],
VF [auth a],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth A],
VK [auth A],
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 A],
WB [auth a],
WBA [auth A],
WC [auth a],
WD [auth a],
WE [auth a],
WF [auth a],
WG [auth A],
WH [auth A],
WI [auth A],
WJ [auth A],
WK [auth A],
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 A],
XB [auth a],
XBA [auth B],
XC [auth a],
XD [auth a],
XE [auth a],
XF [auth a],
XG [auth A],
XH [auth A],
XI [auth A],
XJ [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 A],
YB [auth a],
YBA [auth B],
YC [auth a],
YD [auth a],
YE [auth a],
YF [auth a],
YG [auth A],
YH [auth A],
YI [auth A],
YJ [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 A],
ZB [auth a],
ZBA [auth B],
ZC [auth a],
ZD [auth a],
ZE [auth a],
ZF [auth a],
ZG [auth A],
ZH [auth A],
ZI [auth A],
ZJ [auth A],
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
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		BA [auth D]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4		JA [auth O]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIX1.19.2

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 StatesGM136936
Welch FoundationUnited StatesH-2032-20200401

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2023-01-25
    Changes: Database references
  • Version 2.0: 2023-07-26
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description