9PIJ | pdb_00009pij

E. coli 70S ribosome bound to Minocycline


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.0 of the entry. See complete history

Literature

Dual site targeting of the bacterial 70S ribosome by tetracyclines

Devarkar, S.C.Lomakin, I.B.Bunick, C.G.

(2026) Nat Commun 

Macromolecule Content 

  • Total Structure Weight: 2,186.88 kDa 
  • Atom Count: 141,677 
  • Modeled Residue Count: 10,044 
  • Deposited Residue Count: 10,576 
  • Unique protein chains: 49
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33A [auth 0]55Escherichia coliMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34B [auth 1]46Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35C [auth 2]65Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36D [auth 3]38Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L31E [auth 4]70Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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UniProt GroupP0A7M9
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S2G [auth B]241Escherichia coliMutation(s): 0 
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Find proteins for C3TPN2 (Escherichia coli)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3H [auth C]233Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4I [auth D]206Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5J [auth E]167Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6K [auth F]135Escherichia coliMutation(s): 0 
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Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7L [auth G]179Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8M [auth H]130Escherichia coliMutation(s): 0 
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Find proteins for C3SR12 (Escherichia coli)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9N [auth I]130Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10O [auth J]103Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S11P [auth K]129Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12Q [auth L]124Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A0F1AUC4 (Enterobacter sichuanensis)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13R [auth M]118Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A7U9IV78 (Escherichia coli HVH 36)
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14S [auth N]101Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A2X1PQW4 (Escherichia coli)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15T [auth O]89Escherichia coliMutation(s): 0 
UniProt
Find proteins for C3SSQ7 (Escherichia coli)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16U [auth P]82Escherichia coliMutation(s): 0 
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Find proteins for C3SYP2 (Escherichia coli)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17V [auth Q]84Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18W [auth R]75Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A0E2KXL3 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19X [auth S]92Escherichia coliMutation(s): 0 
UniProt
Find proteins for C3SQW2 (Escherichia coli)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20Y [auth T]87Escherichia coliMutation(s): 0 
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Find proteins for C3TRH7 (Escherichia coli)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21Z [auth U]71Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A0E2L2J1 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2EA [auth c]273Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3FA [auth d]209Escherichia coliMutation(s): 0 
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Find proteins for C3SQU2 (Escherichia coli)
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4GA [auth e]201Escherichia coliMutation(s): 0 
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Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5HA [auth f]179Escherichia coliMutation(s): 0 
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Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6IA [auth g]177Escherichia coliMutation(s): 0 
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Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9JA [auth h]149Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13KA [auth i]142Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14LA [auth j]123Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15MA [auth k]144Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16NA [auth l]136Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17OA [auth m]127Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18PA [auth n]117Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19QA [auth o]115Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20RA [auth p]118Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L21SA [auth q]103Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22TA [auth r]110Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23UA [auth s]100Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24VA [auth t]104Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25WA [auth u]94Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27XA [auth v]85Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L28YA [auth w]78Escherichia coliMutation(s): 0 
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Find proteins for A0A1X3JA73 (Escherichia coli H386)
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29ZA [auth x]63Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AB [auth y]59Escherichia coliMutation(s): 0 
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Find proteins for C3SR32 (Escherichia coli)
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BB [auth z]57Escherichia coliMutation(s): 0 
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Find proteins for C3TE02 (Escherichia coli)
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Entity ID: 6
MoleculeChains LengthOrganismImage
16S rRNAF [auth A]1,542Escherichia coli
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Entity ID: 27
MoleculeChains LengthOrganismImage
mRNAAA [auth X]22Escherichia coli
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Entity ID: 28
MoleculeChains LengthOrganismImage
P-site tRNABA [auth Z]75Escherichia coli
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Entity ID: 29
MoleculeChains LengthOrganismImage
23S rRNACA [auth a]2,904Escherichia coli
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 30
MoleculeChains LengthOrganismImage
5S rRNADA [auth b]120Escherichia coli
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MIY
(Subject of Investigation/LOI)

Query on MIY



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AG [auth a],
LC [auth A]
(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE
C23 H27 N3 O7
DYKFCLLONBREIL-KVUCHLLUSA-N
ZN

Query on ZN



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CB [auth 3]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K



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AD [auth A]
AF [auth A]
AJ [auth a]
AK [auth a]
AL [auth a]
AD [auth A],
AF [auth A],
AJ [auth a],
AK [auth a],
AL [auth a],
AP [auth a],
BE [auth A],
BG [auth a],
BH [auth a],
BK [auth a],
BP [auth a],
CG [auth a],
CT [auth a],
DC [auth A],
DE [auth A],
DF [auth A],
DG [auth a],
EB [auth A],
EC [auth A],
EG [auth a],
EP [auth a],
EQ [auth a],
ER [auth a],
FD [auth A],
FE [auth A],
FG [auth a],
FP [auth a],
FR [auth a],
FS [auth a],
GC [auth A],
GE [auth A],
GG [auth a],
GK [auth a],
GQ [auth a],
GR [auth a],
GS [auth a],
HC [auth A],
HD [auth A],
HG [auth a],
HL [auth a],
HO [auth a],
HP [auth a],
HR [auth a],
IC [auth A],
IG [auth a],
II [auth a],
IK [auth a],
IL [auth a],
IP [auth a],
IR [auth a],
JB [auth A],
JC [auth A],
JD [auth A],
JG [auth a],
JK [auth a],
JL [auth a],
JR [auth a],
KG [auth a],
KM [auth a],
KP [auth a],
KQ [auth a],
LB [auth A],
LD [auth A],
LG [auth a],
LJ [auth a],
LK [auth a],
LN [auth a],
LO [auth a],
LQ [auth a],
MC [auth A],
MG [auth a],
MJ [auth a],
MK [auth a],
MO [auth a],
MR [auth a],
NG [auth a],
NI [auth a],
NJ [auth a],
NP [auth a],
NQ [auth a],
OD [auth A],
OG [auth a],
OJ [auth a],
OK [auth a],
OM [auth a],
OO [auth a],
OP [auth a],
OQ [auth a],
PB [auth A],
PF [auth A],
PK [auth a],
PL [auth a],
PO [auth a],
QC [auth A],
QF [auth A],
QJ [auth a],
QK [auth a],
QL [auth a],
QP [auth a],
QQ [auth a],
RC [auth A],
RD [auth A],
RK [auth a],
RL [auth a],
RP [auth a],
RQ [auth a],
SF [auth A],
SK [auth a],
SQ [auth a],
ST [auth b],
TG [auth a],
TH [auth a],
TO [auth a],
TQ [auth a],
UC [auth A],
UG [auth a],
UJ [auth a],
UO [auth a],
VB [auth A],
VC [auth A],
VG [auth a],
VI [auth a],
VJ [auth a],
VN [auth a],
WF [auth a],
WG [auth a],
WL [auth a],
WO [auth a],
WT [auth c],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth a],
XG [auth a],
XI [auth a],
XJ [auth a],
XN [auth a],
XO [auth a],
YC [auth A],
YF [auth a],
YG [auth a],
YJ [auth a],
YO [auth a],
YQ [auth a],
ZC [auth A],
ZF [auth a],
ZJ [auth a],
ZK [auth a]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



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AC [auth A]
AE [auth A]
AH [auth a]
AI [auth a]
AM [auth a]
AC [auth A],
AE [auth A],
AH [auth a],
AI [auth a],
AM [auth a],
AN [auth a],
AO [auth a],
AQ [auth a],
AR [auth a],
AS [auth a],
AT [auth a],
BC [auth A],
BD [auth A],
BF [auth A],
BI [auth a],
BJ [auth a],
BL [auth a],
BM [auth a],
BN [auth a],
BO [auth a],
BQ [auth a],
BR [auth a],
BS [auth a],
BT [auth a],
CC [auth A],
CD [auth A],
CE [auth A],
CF [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],
DB [auth A],
DD [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],
ED [auth A],
EE [auth A],
EF [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],
ES [auth a],
ET [auth a],
FB [auth A],
FC [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],
FQ [auth a],
FT [auth a],
GB [auth A],
GD [auth A],
GF [auth A],
GH [auth a],
GI [auth a],
GJ [auth a],
GL [auth a],
GM [auth a],
GN [auth a],
GO [auth a],
GP [auth a],
GT [auth a],
HB [auth A],
HE [auth A],
HF [auth A],
HH [auth a],
HI [auth a],
HJ [auth a],
HK [auth a],
HM [auth a],
HN [auth a],
HQ [auth a],
HS [auth a],
HT [auth a],
IB [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IH [auth a],
IJ [auth a],
IM [auth a],
IN [auth a],
IO [auth a],
IQ [auth a],
IS [auth a],
IT [auth a],
JE [auth A],
JF [auth A],
JH [auth a],
JI [auth a],
JJ [auth a],
JM [auth a],
JN [auth a],
JO [auth a],
JP [auth a],
JQ [auth a],
JS [auth a],
JT [auth a],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KH [auth a],
KI [auth a],
KJ [auth a],
KK [auth a],
KL [auth a],
KN [auth a],
KO [auth a],
KR [auth a],
KS [auth a],
KT [auth a],
LE [auth A],
LF [auth A],
LH [auth a],
LI [auth a],
LL [auth a],
LM [auth a],
LP [auth a],
LR [auth a],
LS [auth a],
LT [auth a],
MB [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MH [auth a],
MI [auth a],
ML [auth a],
MM [auth a],
MN [auth a],
MP [auth a],
MQ [auth a],
MS [auth a],
MT [auth a],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NH [auth a],
NK [auth a],
NL [auth a],
NM [auth a],
NN [auth a],
NO [auth a],
NR [auth a],
NS [auth a],
NT [auth a],
OB [auth A],
OC [auth A],
OE [auth A],
OF [auth A],
OH [auth a],
OI [auth a],
OL [auth a],
ON [auth a],
OR [auth a],
OS [auth a],
OT [auth a],
PC [auth A],
PD [auth A],
PE [auth A],
PG [auth a],
PH [auth a],
PI [auth a],
PJ [auth a],
PM [auth a],
PN [auth a],
PP [auth a],
PQ [auth a],
PR [auth a],
PS [auth a],
PT [auth a],
QB [auth A],
QD [auth A],
QE [auth A],
QG [auth a],
QH [auth a],
QI [auth a],
QM [auth a],
QN [auth a],
QO [auth a],
QR [auth a],
QS [auth a],
QT [auth b],
RB [auth A],
RE [auth A],
RF [auth A],
RG [auth a],
RH [auth a],
RI [auth a],
RJ [auth a],
RM [auth a],
RN [auth a],
RO [auth a],
RR [auth a],
RS [auth a],
RT [auth b],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SG [auth a],
SH [auth a],
SI [auth a],
SJ [auth a],
SL [auth a],
SM [auth a],
SN [auth a],
SO [auth a],
SP [auth a],
SR [auth a],
SS [auth a],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TI [auth a],
TJ [auth a],
TK [auth a],
TL [auth a],
TM [auth a],
TN [auth a],
TP [auth a],
TR [auth a],
TS [auth a],
TT [auth b],
UB [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UH [auth a],
UI [auth a],
UK [auth a],
UL [auth a],
UM [auth a],
UN [auth a],
UP [auth a],
UQ [auth a],
UR [auth a],
US [auth a],
UT [auth b],
VD [auth A],
VE [auth A],
VF [auth A],
VH [auth a],
VK [auth a],
VL [auth a],
VM [auth a],
VO [auth a],
VP [auth a],
VQ [auth a],
VR [auth a],
VS [auth a],
VT [auth b],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WH [auth a],
WI [auth a],
WJ [auth a],
WK [auth a],
WM [auth a],
WN [auth a],
WP [auth a],
WQ [auth a],
WR [auth a],
WS [auth a],
XB [auth A],
XH [auth a],
XK [auth a],
XL [auth a],
XM [auth a],
XP [auth a],
XQ [auth a],
XR [auth a],
XS [auth a],
XT [auth p],
YB [auth A],
YD [auth A],
YE [auth A],
YH [auth a],
YI [auth a],
YK [auth a],
YL [auth a],
YM [auth a],
YN [auth a],
YP [auth a],
YR [auth a],
YS [auth a],
YT [auth p],
ZB [auth A],
ZD [auth A],
ZE [auth A],
ZG [auth a],
ZH [auth a],
ZI [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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
Q [auth L]L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
FA [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-13
    Type: Initial release