6U48

E. coli 50S with phazolicin (PHZ) bound in exit tunnel


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Phazolicin - a Novel Thiazole/Oxazole-Modified Peptide Inhibiting the Bacterial Ribosome in a Species-Specific Way

Travin, D.Y.Watson, Z.L.Metelev, M.Ward, F.R.Osterman, I.A.Khven, I.M.Khabibullina, N.F.Serebryakova, M.Mergaert, P.Polikanov, Y.S.Cate, J.H.D.Severinov, K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL2
CC
271Escherichia coli M056Mutation(s): 0 
Gene Names: rplB
Find proteins for A0A1X3I1Y9 (Escherichia coli M056)
Go to UniProtKB:  A0A1X3I1Y9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL3
CD
209Escherichia coli H386Mutation(s): 0 
Gene Names: rplC
Find proteins for A0A1X3JBR5 (Escherichia coli H386)
Go to UniProtKB:  A0A1X3JBR5
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL4
CE
201Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplD
Find proteins for D7Z9F6 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9F6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL5
CF
177Escherichia coli LAU-EC10Mutation(s): 0 
Gene Names: rplE
Find proteins for V8K465 (Escherichia coli LAU-EC10)
Go to UniProtKB:  V8K465
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL6
CG
176Escherichia coli 1-392-07_S4_C3Mutation(s): 0 
Gene Names: rplF
Find proteins for A0A080FKA9 (Escherichia coli 1-392-07_S4_C3)
Go to UniProtKB:  A0A080FKA9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL9
CH
149Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplI
Find proteins for D7ZI15 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZI15
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL11
CJ
134Escherichia coli DEC2CMutation(s): 0 
Gene Names: rplK
Find proteins for H4KQ36 (Escherichia coli DEC2C)
Go to UniProtKB:  H4KQ36
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL13
CK
142Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplM
Find proteins for D7ZET0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZET0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL14
CL
122Escherichia coli (strain B / BL21-DE3)Mutation(s): 0 
Gene Names: rplN
Find proteins for A0A140N3H4 (Escherichia coli (strain B / BL21-DE3))
Go to UniProtKB:  A0A140N3H4
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL15
CM
144Escherichia coliMutation(s): 0 
Gene Names: rplO
Find proteins for A0A037Y8L6 (Escherichia coli)
Go to UniProtKB:  A0A037Y8L6
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL16
CN
136Escherichia coli chi7122Mutation(s): 0 
Gene Names: rplP
Find proteins for J7RVN4 (Escherichia coli chi7122)
Go to UniProtKB:  J7RVN4
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL17
CO
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL18
CP
116Escherichia coli 2.3916Mutation(s): 0 
Gene Names: rplR
Find proteins for I2X628 (Escherichia coli 2.3916)
Go to UniProtKB:  I2X628
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL19
CQ
114Escherichia coli KTE10Mutation(s): 0 
Gene Names: rplS
Find proteins for L2UTN8 (Escherichia coli KTE10)
Go to UniProtKB:  L2UTN8
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL20
CR
117Escherichia coli 1.2741Mutation(s): 0 
Gene Names: rplT
Find proteins for I2RGN4 (Escherichia coli 1.2741)
Go to UniProtKB:  I2RGN4
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL21
CS
103Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplU
Find proteins for D7ZEN7 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZEN7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL22
CT
110Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplV
Find proteins for D7Z9G0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G0
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL23
CU
93Escherichia coli DEC1CMutation(s): 0 
Gene Names: rplW
Find proteins for H4IXX7 (Escherichia coli DEC1C)
Go to UniProtKB:  H4IXX7
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL24
CV
102Escherichia coli PCN033Mutation(s): 0 
Gene Names: rplX
Find proteins for A0A0G3K7Z5 (Escherichia coli PCN033)
Go to UniProtKB:  A0A0G3K7Z5
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL25
CW
94Escherichia coli MS 84-1Mutation(s): 0 
Gene Names: rplY
Find proteins for D7XH79 (Escherichia coli MS 84-1)
Go to UniProtKB:  D7XH79
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL27
CX
75Escherichia coli H386Mutation(s): 0 
Gene Names: rpmA
Find proteins for A0A1X3JCC7 (Escherichia coli H386)
Go to UniProtKB:  A0A1X3JCC7
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL28
CY
77N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL29
CZ
62Escherichia coli MS 119-7Mutation(s): 0 
Gene Names: rpmC
Find proteins for D8E8E5 (Escherichia coli MS 119-7)
Go to UniProtKB:  D8E8E5
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL30
C0
58Escherichia coli 5-366-08_S1_C1Mutation(s): 0 
Gene Names: rpmD
Find proteins for A0A073UEE9 (Escherichia coli 5-366-08_S1_C1)
Go to UniProtKB:  A0A073UEE9
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL32
C1
56Escherichia coli 908573Mutation(s): 0 
Gene Names: rpmF
Find proteins for V0ZMP5 (Escherichia coli 908573)
Go to UniProtKB:  V0ZMP5
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL33
C2
50Escherichia coli KTE112Mutation(s): 0 
Gene Names: rpmG
Find proteins for L4V2B0 (Escherichia coli KTE112)
Go to UniProtKB:  L4V2B0
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL34
C3
46Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmH
Find proteins for B7MGC4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MGC4
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL35
C4
64Escherichia coli 1.2741Mutation(s): 0 
Gene Names: rpmI
Find proteins for I2RJ64 (Escherichia coli 1.2741)
Go to UniProtKB:  I2RJ64
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL36
C5
38Escherichia coli (strain UMEA 3162-1)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
Go to UniProtKB:  A0A0E2L017
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
phazolicin
A
22N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
23S rRNACA2904Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNACB118Escherichia coli
Small Molecules
Modified Residues  18 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
CA
RNA LINKINGC9 H13 N2 O9 PU
4D4
Query on 4D4
CN
L-peptide linkingC6 H14 N4 O3ARG
5MC
Query on 5MC
CA
RNA LINKINGC10 H16 N3 O8 PC
6MZ
Query on 6MZ
CA
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
CA
RNA LINKINGC10 H15 N2 O9 PU
A0G
Query on A0G
A
L-peptide linkingC3 H5 N O3

--

1MG
Query on 1MG
CA
RNA LINKINGC11 H16 N5 O8 PG
BB9
Query on BB9
A
PEPTIDE LINKINGC3 H5 N O2 SCYS
OMC
Query on OMC
CA
RNA LINKINGC10 H16 N3 O8 PC
N
Query on N
CA
RNA LINKINGC5 H11 O7 P

--

2MG
Query on 2MG
CA
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
CA
RNA LINKINGC11 H17 N5 O8 PG
MEQ
Query on MEQ
CD
L-PEPTIDE LINKINGC6 H12 N2 O3GLN
OMG
Query on OMG
CA
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
CA
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
CA
RNA LINKINGC11 H16 N5 O7 PA
3TD
Query on 3TD
CA
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
CA
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM R01-114454
National Science Foundation (NSF, United States)United States1106400

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 2.0: 2019-11-27
    Type: Author supporting evidence, Polymer sequence