6BY1

E. coli pH03H9 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural evidence for product stabilization by the ribosomal mRNA helicase.

Amiri, H.Noller, H.F.

(2019) RNA 25: 364-375


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
CC, DC
271Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
CD, DD
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
CE, DE
181Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
CF, DF
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
CG, DG
176Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
CH, DH
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
C5
109Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
CI, DI
72Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
CJ, DJ
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
CK, DK
122Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
CL, DL
143Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
CM, DM
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
CN, DN
121Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
CO, DO
116Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
CP, DP
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
CQ, DQ
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
CR, DR
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
CS, DS
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
CT, DT
93Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
CU, DU
102Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rplX
Find proteins for P60625 (Escherichia coli O157:H7)
Go to UniProtKB:  P60625
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
CV, DV
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
CW, DW
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
CX, DX
77Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
CY, DY
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
CZ, DZ
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
C0, D0
39Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
C1, D1
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
C2, D2
50Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
C3, D3
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
C4, D4
62Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
C6, D6
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, BB
225Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, BC
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, BD
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, BE
150Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, BF
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, BG
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, BH
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, BI
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, BJ
98Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, BK
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, BL
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, BM
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN, BN
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, BO
89Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, BP
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, BQ
80Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, BR
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, BS
79Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, BT
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA,BA1541Escherichia coli K-12
Entity ID: 2
MoleculeChainsLengthOrganism
23S ribosomal RNACA,DA2904Escherichia coli K-12
Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNACB,DB118Escherichia coli K-12
Entity ID: 4
MoleculeChainsLengthOrganism
Valine-specific transfer RNAAV,AY,AW,BV,BW76Escherichia coli K-12
Entity ID: 36
MoleculeChainsLengthOrganism
Messenger RNAAX,BX46Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C0, C6, D0, D6
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
AA, BA, C4, CA, CB, CC, CN, CQ, DA, DB, DN, DQ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 211.656α = 90.00
b = 433.909β = 90.00
c = 623.532γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

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 SciencesUnited States17129
National Institutes of Health/National Institute of General Medical SciencesUnited States59140

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release