7MT7

Mtb 70S with P and E site tRNAs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Interplay between an ATP-binding cassette F protein and the ribosome from Mycobacterium tuberculosis.

Cui, Z.Li, X.Shin, J.Gamper, H.Hou, Y.M.Sacchettini, J.C.Zhang, J.

(2022) Nat Commun 13: 432-432

  • DOI: https://doi.org/10.1038/s41467-022-28078-1
  • Primary Citation of Related Structures:  
    7MSC, 7MSH, 7MSM, 7MSZ, 7MT2, 7MT3, 7MT7, 7MU0

  • PubMed Abstract: 

    EttA, energy-dependent translational throttle A, is a ribosomal factor that gates ribosome entry into the translation elongation cycle. A detailed understanding of its mechanism of action is limited due to the lack of high-resolution structures along its ATPase cycle. Here we present the cryo-electron microscopy (cryo-EM) structures of EttA from Mycobacterium tuberculosis (Mtb), referred to as MtbEttA, in complex with the Mtb 70S ribosome initiation complex (70SIC) at the pre-hydrolysis (ADPNP) and transition (ADP-VO 4 ) states, and the crystal structure of MtbEttA alone in the post-hydrolysis (ADP) state. We observe that MtbEttA binds the E-site of the Mtb 70SIC, remodeling the P-site tRNA and the ribosomal intersubunit bridge B7a during the ribosomal ratcheting. In return, the rotation of the 30S causes conformational changes in MtbEttA, forcing the two nucleotide-binding sites (NBSs) to alternate to engage each ADPNP in the pre-hydrolysis states, followed by complete engagements of both ADP-VO 4 molecules in the ATP-hydrolysis transition states. In the post-hydrolysis state, the conserved ATP-hydrolysis motifs of MtbEttA dissociate from both ADP molecules, leaving two nucleotide-binding domains (NBDs) in an open conformation. These structures reveal a dynamic interplay between MtbEttA and the Mtb ribosome, providing insights into the mechanism of translational regulation by EttA-like proteins.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 2B [auth 1]55Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34C [auth 2]47Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35D [auth 3]64Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36E [auth 4]37Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31F [auth 6]80Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37G [auth 7]24Mycobacterium tuberculosis H37RvMutation(s): 0 
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Find proteins for A0A0U0UFA0 (Mycobacterium tuberculosis)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1H [auth 8]235Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2K [auth C]280Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3L [auth D]217Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4M [auth E]223Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5N [auth F]187Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6O [auth G]179Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9P [auth H]152Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13Q [auth J]195Mycobacterium tuberculosis H37RvMutation(s): 0 
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Find proteins for A0A0T9D5H2 (Mycobacterium tuberculosis)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14R [auth K]122Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15S [auth L]146Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16T [auth M]138Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17U [auth N]180Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18V [auth O]122Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19W [auth P]113Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20X [auth Q]129Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Y [auth R]104Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Z [auth S]197Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23AA [auth T]100Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24BA [auth U]105Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25CA [auth V]215Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27DA [auth W]86Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28EA [auth X]64Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29FA [auth Y]77Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30GA [auth Z]65Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3IA [auth c]274Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4JA [auth d]201Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5KA [auth e]220Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6LA [auth f]96Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7MA [auth g]156Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8NA [auth h]132Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9OA [auth i]151Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10PA [auth j]101Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11QA [auth k]139Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12RA [auth l]124Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13SA [auth m]124Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZTA [auth n]61Mycobacterium tuberculosis H37RvMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15UA [auth o]89Mycobacterium tuberculosis H37RvMutation(s): 0 
UniProt
Find proteins for P9WH55 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16VA [auth p]162Mycobacterium tuberculosis H37RvMutation(s): 0 
UniProt
Find proteins for P9WH53 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17WA [auth q]135Mycobacterium tuberculosis H37RvMutation(s): 0 
UniProt
Find proteins for P9WH51 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18 1XA [auth r]84Mycobacterium tuberculosis H37RvMutation(s): 0 
UniProt
Find proteins for P9WH49 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19YA [auth s]93Mycobacterium tuberculosis H37RvMutation(s): 0 
UniProt
Find proteins for P9WH45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20ZA [auth t]86Mycobacterium tuberculosis H37RvMutation(s): 0 
UniProt
Find proteins for P9WH41 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 9
MoleculeChains LengthOrganismImage
23S rRNAI [auth A]3,138Mycobacterium tuberculosis H37Rv
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Entity ID: 10
MoleculeChains LengthOrganismImage
5S rRNAJ [auth B]115Mycobacterium tuberculosis H37Rv
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Entity ID: 34
MoleculeChains LengthOrganismImage
16S rRNAHA [auth a]1,537Mycobacterium tuberculosis H37Rv
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Entity ID: 53
MoleculeChains LengthOrganismImage
tRNA (Met)AB [auth x],
BB [auth y]
77Escherichia coli
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Entity ID: 54
MoleculeChains LengthOrganismImage
mRNACB [auth z]26Mycobacterium tuberculosis
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download Ideal Coordinates CCD File 
IS [auth y]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DB [auth 1]
EB [auth 4]
EN [auth X]
ES [auth n]
FS [auth r]
DB [auth 1],
EB [auth 4],
EN [auth X],
ES [auth n],
FS [auth r],
HB [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth A]
AC [auth A],
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 D],
AO [auth a],
AP [auth a],
AQ [auth a],
AR [auth a],
AS [auth a],
BC [auth A],
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 E],
BO [auth a],
BP [auth a],
BQ [auth a],
BR [auth a],
BS [auth a],
CC [auth A],
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 L],
CO [auth a],
CP [auth a],
CQ [auth a],
CR [auth a],
CS [auth a],
DC [auth A],
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 U],
DO [auth a],
DP [auth a],
DQ [auth a],
DR [auth a],
DS [auth a],
EC [auth A],
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],
EO [auth a],
EP [auth a],
EQ [auth a],
ER [auth a],
FB [auth 4],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [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],
GB [auth 4],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
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 r],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
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 t],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
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],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [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 y],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
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 y],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
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],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
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],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
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],
OB [auth A],
OC [auth A],
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],
PB [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],
QB [auth A],
QC [auth A],
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],
RB [auth A],
RC [auth A],
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],
SB [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],
TB [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 B],
TN [auth a],
TO [auth a],
TP [auth a],
TQ [auth a],
TR [auth a],
UB [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 B],
UN [auth a],
UO [auth a],
UP [auth a],
UQ [auth a],
UR [auth a],
VB [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 B],
VN [auth a],
VO [auth a],
VP [auth a],
VQ [auth a],
VR [auth a],
WB [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 B],
WN [auth a],
WO [auth a],
WP [auth a],
WQ [auth a],
WR [auth a],
XB [auth A],
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 B],
XN [auth a],
XO [auth a],
XP [auth a],
XQ [auth a],
XR [auth a],
YB [auth A],
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 C],
YN [auth a],
YO [auth a],
YP [auth a],
YQ [auth a],
YR [auth a],
ZB [auth A],
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 C],
ZN [auth a],
ZO [auth a],
ZP [auth a],
ZQ [auth a],
ZR [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI095208
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU24GM116787

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references