8P16

E167K RF2 on E. coli 70S release complex with UGG (Structure I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The compensatory mechanism of a naturally evolved E167K RF2 counteracting the loss of RF1 in bacteria

Pundir, S.Larsson, D.S.D.Selmer, M.Sanyal, S.

To be published.

Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2B [auth g]241Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3C [auth h]233Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4D [auth i]206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5E [auth j]167Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth k]135Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth l]179Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8H [auth m]130Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9I [auth n]130Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10J [auth o]103Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11K [auth p]129Escherichia coliMutation(s): 1 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12L [auth q]124Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13M [auth r]118Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14N [auth s]101Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15O [auth t]89Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16P [auth u]82Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17Q [auth v]84Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18R [auth w]75Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19S [auth x]92Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20T [auth y]87Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21U [auth z]71Escherichia coliMutation(s): 0 
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Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2Z [auth B]273Escherichia coliMutation(s): 0 
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Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3AA [auth C]209Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4BA [auth D]201Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5CA [auth E]179Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6DA [auth F]177Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13EA [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14FA [auth K]123Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15GA [auth L]144Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16HA [auth M]136Escherichia coliMutation(s): 1 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17IA [auth N]127Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18JA [auth O]117Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19KA [auth P]115Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20LA [auth Q]118Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21MA [auth R]103Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22NA [auth S]110Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23OA [auth T]100Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PA [auth U]104Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25QA [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27RA [auth W]85Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28SA [auth X]78Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29TA [auth Y]63Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30UA [auth Z]59Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32VA [auth b]57Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33WA [auth c]55Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34XA [auth d]46Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35YA [auth e]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36ZA [auth f]38Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31AAB [auth a]70Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11BB [auth I]142Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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UniProt GroupP0A7J7
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor RF2CB [auth 6]365Escherichia coli K-12Mutation(s): 1 
Gene Names: prfBsupKb2891JW5847
UniProt
Find proteins for P07012 (Escherichia coli (strain K12))
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UniProt GroupP07012
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9DB [auth G]149Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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UniProt GroupP0A7R1
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth 2]1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
mRNAV [auth 4]49Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
tRNA(fMet)W [auth 5]76Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
23S rRNAX [auth 1]2,904Escherichia coli
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Entity ID: 25
MoleculeChains LengthOrganismImage
5S rRNAY [auth 3]120Escherichia coli
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download Ideal Coordinates CCD File 
SO [auth 1]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD
Query on SPD

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IO [auth 1]
JO [auth 1]
KO [auth 1]
KT [auth 1]
LO [auth 1]
IO [auth 1],
JO [auth 1],
KO [auth 1],
KT [auth 1],
LO [auth 1],
MO [auth 1],
NO [auth 1],
OO [auth 1],
PE [auth 2],
PO [auth 1],
QE [auth 2],
QO [auth 1],
RO [auth 1]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
PUT
Query on PUT

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AT [auth 1]
BT [auth 1]
CT [auth 1]
DT [auth 1]
EG [auth 2]
AT [auth 1],
BT [auth 1],
CT [auth 1],
DT [auth 1],
EG [auth 2],
ET [auth 1],
FG [auth 2],
FT [auth 1],
GT [auth 1],
HT [auth 1],
IT [auth 1],
JT [auth 1],
LT [auth 1]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

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VT [auth f],
WT [auth a]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AF [auth 2]
AP [auth 1]
AQ [auth 1]
AR [auth 1]
AS [auth 1]
AF [auth 2],
AP [auth 1],
AQ [auth 1],
AR [auth 1],
AS [auth 1],
BF [auth 2],
BP [auth 1],
BQ [auth 1],
BR [auth 1],
BS [auth 1],
CF [auth 2],
CP [auth 1],
CQ [auth 1],
CR [auth 1],
CS [auth 1],
DF [auth 2],
DP [auth 1],
DQ [auth 1],
DR [auth 1],
DS [auth 1],
EF [auth 2],
EP [auth 1],
EQ [auth 1],
ER [auth 1],
ES [auth 1],
FF [auth 2],
FP [auth 1],
FQ [auth 1],
FR [auth 1],
FS [auth 1],
GF [auth 2],
GP [auth 1],
GQ [auth 1],
GR [auth 1],
HF [auth 2],
HP [auth 1],
HQ [auth 1],
HR [auth 1],
IF [auth 2],
IP [auth 1],
IQ [auth 1],
IR [auth 1],
JF [auth 2],
JP [auth 1],
JQ [auth 1],
JR [auth 1],
KF [auth 2],
KP [auth 1],
KQ [auth 1],
KR [auth 1],
LF [auth 2],
LG [auth 1],
LP [auth 1],
LQ [auth 1],
LR [auth 1],
MF [auth 2],
MG [auth 1],
MP [auth 1],
MQ [auth 1],
MR [auth 1],
NF [auth 2],
NG [auth 1],
NP [auth 1],
NQ [auth 1],
NR [auth 1],
OF [auth 2],
OG [auth 1],
OP [auth 1],
OQ [auth 1],
OR [auth 1],
PF [auth 2],
PP [auth 1],
PQ [auth 1],
PR [auth 1],
QF [auth 2],
QP [auth 1],
QQ [auth 1],
QR [auth 1],
RE [auth 2],
RF [auth 2],
RP [auth 1],
RQ [auth 1],
RR [auth 1],
SE [auth 2],
SF [auth 2],
SP [auth 1],
SQ [auth 1],
SR [auth 1],
TE [auth 2],
TF [auth 2],
TP [auth 1],
TQ [auth 1],
TR [auth 1],
UE [auth 2],
UF [auth 2],
UP [auth 1],
UQ [auth 1],
UR [auth 1],
VE [auth 2],
VF [auth 2],
VO [auth 1],
VP [auth 1],
VQ [auth 1],
VR [auth 1],
WE [auth 2],
WF [auth 2],
WO [auth 1],
WP [auth 1],
WQ [auth 1],
WR [auth 1],
XE [auth 2],
XF [auth 2],
XO [auth 1],
XP [auth 1],
XQ [auth 1],
XR [auth 1],
YE [auth 2],
YF [auth 2],
YO [auth 1],
YP [auth 1],
YQ [auth 1],
YR [auth 1],
ZE [auth 2],
ZF [auth 2],
ZO [auth 1],
ZP [auth 1],
ZQ [auth 1],
ZR [auth 1]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth 2]
AD [auth 2]
AE [auth 2]
AG [auth 2]
AH [auth 1]
AC [auth 2],
AD [auth 2],
AE [auth 2],
AG [auth 2],
AH [auth 1],
AI [auth 1],
AJ [auth 1],
AK [auth 1],
AL [auth 1],
AM [auth 1],
AN [auth 1],
AO [auth 1],
BC [auth 2],
BD [auth 2],
BE [auth 2],
BG [auth 2],
BH [auth 1],
BI [auth 1],
BJ [auth 1],
BK [auth 1],
BL [auth 1],
BM [auth 1],
BN [auth 1],
BO [auth 1],
CC [auth 2],
CD [auth 2],
CE [auth 2],
CG [auth 2],
CH [auth 1],
CI [auth 1],
CJ [auth 1],
CK [auth 1],
CL [auth 1],
CM [auth 1],
CN [auth 1],
CO [auth 1],
DC [auth 2],
DD [auth 2],
DE [auth 2],
DG [auth 2],
DH [auth 1],
DI [auth 1],
DJ [auth 1],
DK [auth 1],
DL [auth 1],
DM [auth 1],
DN [auth 1],
DO [auth 1],
EB [auth 2],
EC [auth 2],
ED [auth 2],
EE [auth 2],
EH [auth 1],
EI [auth 1],
EJ [auth 1],
EK [auth 1],
EL [auth 1],
EM [auth 1],
EN [auth 1],
EO [auth 1],
FB [auth 2],
FC [auth 2],
FD [auth 2],
FE [auth 2],
FH [auth 1],
FI [auth 1],
FJ [auth 1],
FK [auth 1],
FL [auth 1],
FM [auth 1],
FN [auth 1],
FO [auth 1],
GB [auth 2],
GC [auth 2],
GD [auth 2],
GE [auth 2],
GG [auth 2],
GH [auth 1],
GI [auth 1],
GJ [auth 1],
GK [auth 1],
GL [auth 1],
GM [auth 1],
GN [auth 1],
GO [auth 1],
GS [auth 1],
HB [auth 2],
HC [auth 2],
HD [auth 2],
HE [auth 2],
HG [auth 2],
HH [auth 1],
HI [auth 1],
HJ [auth 1],
HK [auth 1],
HL [auth 1],
HM [auth 1],
HN [auth 1],
HO [auth 1],
HS [auth 1],
IB [auth 2],
IC [auth 2],
ID [auth 2],
IE [auth 2],
IG [auth s],
IH [auth 1],
II [auth 1],
IJ [auth 1],
IK [auth 1],
IL [auth 1],
IM [auth 1],
IN [auth 1],
IS [auth 1],
JB [auth 2],
JC [auth 2],
JD [auth 2],
JE [auth 2],
JG [auth 5],
JH [auth 1],
JI [auth 1],
JJ [auth 1],
JK [auth 1],
JL [auth 1],
JM [auth 1],
JN [auth 1],
JS [auth 1],
KB [auth 2],
KC [auth 2],
KD [auth 2],
KE [auth 2],
KG [auth 5],
KH [auth 1],
KI [auth 1],
KJ [auth 1],
KK [auth 1],
KL [auth 1],
KM [auth 1],
KN [auth 1],
KS [auth 1],
LB [auth 2],
LC [auth 2],
LD [auth 2],
LE [auth 2],
LH [auth 1],
LI [auth 1],
LJ [auth 1],
LK [auth 1],
LL [auth 1],
LM [auth 1],
LN [auth 1],
LS [auth 1],
MB [auth 2],
MC [auth 2],
MD [auth 2],
ME [auth 2],
MH [auth 1],
MI [auth 1],
MJ [auth 1],
MK [auth 1],
ML [auth 1],
MM [auth 1],
MN [auth 1],
MS [auth 1],
MT [auth 3],
NB [auth 2],
NC [auth 2],
ND [auth 2],
NE [auth 2],
NH [auth 1],
NI [auth 1],
NJ [auth 1],
NK [auth 1],
NL [auth 1],
NM [auth 1],
NN [auth 1],
NS [auth 1],
NT [auth 3],
OB [auth 2],
OC [auth 2],
OD [auth 2],
OE [auth 2],
OH [auth 1],
OI [auth 1],
OJ [auth 1],
OK [auth 1],
OL [auth 1],
OM [auth 1],
ON [auth 1],
OS [auth 1],
OT [auth 3],
PB [auth 2],
PC [auth 2],
PD [auth 2],
PG [auth 1],
PH [auth 1],
PI [auth 1],
PJ [auth 1],
PK [auth 1],
PL [auth 1],
PM [auth 1],
PN [auth 1],
PS [auth 1],
PT [auth 3],
QB [auth 2],
QC [auth 2],
QD [auth 2],
QG [auth 1],
QH [auth 1],
QI [auth 1],
QJ [auth 1],
QK [auth 1],
QL [auth 1],
QM [auth 1],
QN [auth 1],
QS [auth 1],
QT [auth 3],
RB [auth 2],
RC [auth 2],
RD [auth 2],
RG [auth 1],
RH [auth 1],
RI [auth 1],
RJ [auth 1],
RK [auth 1],
RL [auth 1],
RM [auth 1],
RN [auth 1],
RS [auth 1],
RT [auth B],
SB [auth 2],
SC [auth 2],
SD [auth 2],
SG [auth 1],
SH [auth 1],
SI [auth 1],
SJ [auth 1],
SK [auth 1],
SL [auth 1],
SM [auth 1],
SN [auth 1],
SS [auth 1],
ST [auth C],
TB [auth 2],
TC [auth 2],
TD [auth 2],
TG [auth 1],
TH [auth 1],
TI [auth 1],
TJ [auth 1],
TK [auth 1],
TL [auth 1],
TM [auth 1],
TN [auth 1],
TO [auth 1],
TS [auth 1],
TT [auth Q],
UB [auth 2],
UC [auth 2],
UD [auth 2],
UG [auth 1],
UH [auth 1],
UI [auth 1],
UJ [auth 1],
UK [auth 1],
UL [auth 1],
UM [auth 1],
UN [auth 1],
UO [auth 1],
US [auth 1],
UT [auth b],
VB [auth 2],
VC [auth 2],
VD [auth 2],
VG [auth 1],
VH [auth 1],
VI [auth 1],
VJ [auth 1],
VK [auth 1],
VL [auth 1],
VM [auth 1],
VN [auth 1],
VS [auth 1],
WB [auth 2],
WC [auth 2],
WD [auth 2],
WG [auth 1],
WH [auth 1],
WI [auth 1],
WJ [auth 1],
WK [auth 1],
WL [auth 1],
WM [auth 1],
WN [auth 1],
WS [auth 1],
XB [auth 2],
XC [auth 2],
XD [auth 2],
XG [auth 1],
XH [auth 1],
XI [auth 1],
XJ [auth 1],
XK [auth 1],
XL [auth 1],
XM [auth 1],
XN [auth 1],
XS [auth 1],
YB [auth 2],
YC [auth 2],
YD [auth 2],
YG [auth 1],
YH [auth 1],
YI [auth 1],
YJ [auth 1],
YK [auth 1],
YL [auth 1],
YM [auth 1],
YN [auth 1],
YS [auth 1],
ZB [auth 2],
ZC [auth 2],
ZD [auth 2],
ZG [auth 1],
ZH [auth 1],
ZI [auth 1],
ZJ [auth 1],
ZK [auth 1],
ZL [auth 1],
ZM [auth 1],
ZN [auth 1],
ZS [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
AA [auth C]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
HA [auth M]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2
MODEL REFINEMENTPHENIX1.20

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-06264
Swedish Research CouncilSweden2018-05946
Swedish Research CouncilSweden2018-05498
Knut and Alice Wallenberg FoundationSwedenKAW 2017.0055
Carl Trygger FoundationSwedenCTS 18:338
Carl Trygger FoundationSwedenCTS 19:806
Wenner-Gren FoundationUnited StatesUPD2017:0238
Swedish Research CouncilSweden2016-06264
Swedish Research CouncilSweden2017-03827

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release