7N2C

Elongating 70S ribosome complex in a fusidic acid-stalled intermediate state of translocation bound to EF-G(GDP) (INT2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of early translocation events on the ribosome.

Rundlet, E.J.Holm, M.Schacherl, M.Natchiar, S.K.Altman, R.B.Spahn, C.M.T.Myasnikov, A.G.Blanchard, S.C.

(2021) Nature 595: 741-745

  • DOI: https://doi.org/10.1038/s41586-021-03713-x
  • Primary Citation of Related Structures:  
    7N1P, 7N2C, 7N2U, 7N2V, 7N30, 7N31

  • PubMed Abstract: 

    Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around 10 -3  to 10 -5 at each step) over thousands of cycles 1 . The cadence and fidelity of ribosome transit through mRNA templates in discrete codon increments is a paradigm for movement in biological systems that must hold for diverse mRNA and tRNA substrates across domains of life. Here we use single-molecule fluorescence methods to guide the capture of structures of early translocation events on the bacterial ribosome. Our findings reveal that the bacterial GTPase elongation factor G specifically engages spontaneously achieved ribosome conformations while in an active, GTP-bound conformation to unlock and initiate peptidyl-tRNA translocation. These findings suggest that processes intrinsic to the pre-translocation ribosome complex can regulate the rate of protein synthesis, and that energy expenditure is used later in the translocation mechanism than previously proposed.


  • Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth SB]241Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth SC]233Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth SD]206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth SE]167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth SF]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth SG]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth SH]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth SI]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth SJ]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth SK]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth SL]124Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth SM]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth SN]101Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth SO]89Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth SP]82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth SQ]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth SR]75Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth SS]92Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth ST]87Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth SU]71Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1Y [auth LA]234Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2Z [auth LB]273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3AA [auth LC]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4BA [auth LD]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5CA [auth LE]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6DA [auth LF]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12EA [auth LG]121Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth LI]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10GA [auth LJ]165Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11HA [auth LK]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13IA [auth LM]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14JA [auth LN]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15KA [auth LO]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth LP]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17MA [auth LQ]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18NA [auth LR]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19OA [auth LS]115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20PA [auth LT]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21QA [auth LU]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22RA [auth LV]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23SA [auth LW]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth LX]104Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25UA [auth LY]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27VA [auth La]85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28WA [auth Lb]78Escherichia coli K-12Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29XA [auth Lc]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30YA [auth Ld]59Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31ZA [auth Le]70Escherichia coli K-12Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AB [auth Lf]57Escherichia coli K-12Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33BB [auth Lg]55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CB [auth Lh]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DB [auth Li]65Escherichia coli K-12Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36EB [auth Lj]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor GFB [auth EF]704Escherichia coli K-12Mutation(s): 1 
Gene Names: fusAfarfusb3340JW3302
EC: 3.6.5
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
PolypeptideGB [auth Pp]3Escherichia coli K-12Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth 16]1,534Escherichia coli K-12
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Entity ID: 22
MoleculeChains LengthOrganismImage
Chains: mRV [auth mR]60Escherichia coli K-12
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Entity ID: 23
MoleculeChains LengthOrganismImage
23S rRNAW [auth 23]2,904Escherichia coli K-12
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Entity ID: 24
MoleculeChains LengthOrganismImage
5S rRNAX [auth 5]120Escherichia coli K-12
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Entity ID: 60
MoleculeChains LengthOrganismImage
Chains: PtHB [auth Pt]76Escherichia coli
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Entity ID: 61
MoleculeChains LengthOrganismImage
tRNAIB [auth Dt]76Escherichia coli
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FUA (Subject of Investigation/LOI)
Query on FUA

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BK [auth EF]FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
ATP (Subject of Investigation/LOI)
Query on ATP

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CD [auth 23],
DD [auth 23]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

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CK [auth EF]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SPD (Subject of Investigation/LOI)
Query on SPD

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WD [auth 23],
XD [auth 23],
YD [auth 23]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
PUT (Subject of Investigation/LOI)
Query on PUT

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ED [auth 23]
FD [auth 23]
GD [auth 23]
HD [auth 23]
ID [auth 23]
ED [auth 23],
FD [auth 23],
GD [auth 23],
HD [auth 23],
ID [auth 23],
JB [auth 16],
JD [auth 23],
KB [auth 16],
KD [auth 23],
LD [auth 23],
MD [auth 23],
ND [auth 23],
OD [auth 23],
PD [auth 23],
QD [auth 23],
RD [auth 23],
SD [auth 23],
SJ [auth LC],
TD [auth 23],
UD [auth 23],
VD [auth 23]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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XJ [auth Le],
ZC [auth SB],
ZJ [auth Lj]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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AC [auth 16]
AD [auth SN]
AE [auth 23]
AF [auth 23]
AG [auth 23]
AC [auth 16],
AD [auth SN],
AE [auth 23],
AF [auth 23],
AG [auth 23],
AH [auth 23],
AI [auth 23],
AJ [auth 23],
AK [auth EF],
BC [auth 16],
BD [auth SN],
BE [auth 23],
BF [auth 23],
BG [auth 23],
BH [auth 23],
BI [auth 23],
BJ [auth 23],
CC [auth 16],
CE [auth 23],
CF [auth 23],
CG [auth 23],
CH [auth 23],
CI [auth 23],
CJ [auth 23],
DC [auth 16],
DE [auth 23],
DF [auth 23],
DG [auth 23],
DH [auth 23],
DI [auth 23],
DJ [auth 23],
EC [auth 16],
EE [auth 23],
EF [auth 23],
EG [auth 23],
EH [auth 23],
EI [auth 23],
EJ [auth 23],
FC [auth 16],
FE [auth 23],
FF [auth 23],
FG [auth 23],
FH [auth 23],
FI [auth 23],
FJ [auth 23],
GC [auth 16],
GE [auth 23],
GF [auth 23],
GG [auth 23],
GH [auth 23],
GI [auth 23],
GJ [auth 23],
HC [auth 16],
HE [auth 23],
HF [auth 23],
HG [auth 23],
HH [auth 23],
HI [auth 23],
HJ [auth 23],
IC [auth 16],
IE [auth 23],
IF [auth 23],
IG [auth 23],
IH [auth 23],
II [auth 23],
IJ [auth 23],
JC [auth 16],
JE [auth 23],
JF [auth 23],
JG [auth 23],
JH [auth 23],
JI [auth 23],
JJ [auth 23],
KC [auth 16],
KE [auth 23],
KF [auth 23],
KG [auth 23],
KH [auth 23],
KI [auth 23],
KJ [auth 23],
LB [auth 16],
LC [auth 16],
LE [auth 23],
LF [auth 23],
LG [auth 23],
LH [auth 23],
LI [auth 23],
LJ [auth 23],
MB [auth 16],
MC [auth 16],
ME [auth 23],
MF [auth 23],
MG [auth 23],
MH [auth 23],
MI [auth 23],
MJ [auth 23],
NB [auth 16],
NC [auth 16],
NE [auth 23],
NF [auth 23],
NG [auth 23],
NH [auth 23],
NI [auth 23],
NJ [auth 5],
OB [auth 16],
OC [auth 16],
OE [auth 23],
OF [auth 23],
OG [auth 23],
OH [auth 23],
OI [auth 23],
OJ [auth 5],
PB [auth 16],
PC [auth 16],
PE [auth 23],
PF [auth 23],
PG [auth 23],
PH [auth 23],
PI [auth 23],
PJ [auth 5],
QB [auth 16],
QC [auth 16],
QE [auth 23],
QF [auth 23],
QG [auth 23],
QH [auth 23],
QI [auth 23],
QJ [auth 5],
RB [auth 16],
RC [auth 16],
RE [auth 23],
RF [auth 23],
RG [auth 23],
RH [auth 23],
RI [auth 23],
RJ [auth LB],
SB [auth 16],
SC [auth 16],
SE [auth 23],
SF [auth 23],
SG [auth 23],
SH [auth 23],
SI [auth 23],
TB [auth 16],
TC [auth 16],
TE [auth 23],
TF [auth 23],
TG [auth 23],
TH [auth 23],
TI [auth 23],
TJ [auth LC],
UB [auth 16],
UC [auth 16],
UE [auth 23],
UF [auth 23],
UG [auth 23],
UH [auth 23],
UI [auth 23],
UJ [auth LD],
VB [auth 16],
VC [auth 16],
VE [auth 23],
VF [auth 23],
VG [auth 23],
VH [auth 23],
VI [auth 23],
VJ [auth LQ],
WB [auth 16],
WC [auth 16],
WE [auth 23],
WF [auth 23],
WG [auth 23],
WH [auth 23],
WI [auth 23],
WJ [auth LW],
XB [auth 16],
XC [auth 16],
XE [auth 23],
XF [auth 23],
XG [auth 23],
XH [auth 23],
XI [auth 23],
YB [auth 16],
YC [auth 16],
YE [auth 23],
YF [auth 23],
YG [auth 23],
YH [auth 23],
YI [auth 23],
YJ [auth Lf],
ZB [auth 16],
ZD [auth 23],
ZE [auth 23],
ZF [auth 23],
ZG [auth 23],
ZH [auth 23],
ZI [auth 23]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L [auth SL]L-PEPTIDE LINKINGC5 H9 N O4 SASP
4D4
Query on 4D4
LA [auth LP]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2021-08-11
    Changes: Database references