4V64

Crystal structure of the bacterial ribosome from Escherichia coli in complex with hygromycin B.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for hygromycin B inhibition of protein biosynthesis

Borovinskaya, M.A.Shoji, S.Fredrick, K.Cate, J.H.D.

(2008) Rna 14: 1590-1599

  • DOI: 10.1261/rna.1076908
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminoglycosides are one of the most widely used and clinically important classes of antibiotics that target the ribosome. Hygromycin B is an atypical aminoglycoside antibiotic with unique structural and functional properties. Here we describe the str ...

    Aminoglycosides are one of the most widely used and clinically important classes of antibiotics that target the ribosome. Hygromycin B is an atypical aminoglycoside antibiotic with unique structural and functional properties. Here we describe the structure of the intact Escherichia coli 70S ribosome in complex with hygromycin B. The antibiotic binds to the mRNA decoding center in the small (30S) ribosomal subunit of the 70S ribosome and induces a localized conformational change, in contrast to its effects observed in the structure of the isolated 30S ribosomal subunit in complex with the drug. The conformational change in the ribosome caused by hygromycin B binding differs from that induced by other aminoglycosides. Also, in contrast to other aminoglycosides, hygromycin B potently inhibits spontaneous reverse translocation of tRNAs and mRNA on the ribosome in vitro. These structural and biochemical results help to explain the unique mode of translation inhibition by hygromycin B.


    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, CC
232Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, CD
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: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, CE
166Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, CF
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, CG
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, CH
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, CI
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, CJ
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, CK
128Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, CL
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: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, CM
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN, CN
100Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG61 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AG61
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, CO
89Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsO
Find proteins for P0ADZ5 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0ADZ5
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, CP
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, CQ
83Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for P0AG64 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0AG64
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, CR
74Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, CS
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, CT
86Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, CB
240Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU, CU
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BV, 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: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BC, DC
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BD, 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: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BE, DE
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BF, DF
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BG, DG
176Shigella flexneriMutation(s): 0 
Gene Names: rplF
Find proteins for P0AG58 (Shigella flexneri)
Go to UniProtKB:  P0AG58
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BH, 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: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BJ, DJ
142Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA11 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0AA11
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BK, DK
123Shigella flexneriMutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY6 (Shigella flexneri)
Go to UniProtKB:  P0ADY6
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BL, DL
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BM, 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: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BN, DN
127Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG46 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AG46
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BO, DO
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BP, 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: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BQ, 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: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BR, 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: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BS, 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: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BT, DT
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BU, DU
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BW, DW
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BX, DX
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BY, DY
58Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG53 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AG53
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BZ, DZ
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B0, D0
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B1, D1
54Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B2, D2
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: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B3, D3
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B4, D4
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BI, DI
141Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA,CA1542Escherichia coli
Entity ID: 22
MoleculeChainsLengthOrganism
5S ribosomal RNABA,DA120Escherichia coli
Entity ID: 23
MoleculeChainsLengthOrganism
23S ribosomal RNABB,DB2904Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B4, D4
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
AA, AE, AN, BB, CA, CE, DB
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HYG
Query on HYG

Download SDF File 
Download CCD File 
AA, CA
HYGROMYCIN B
HYGROMIX, ANTIHELMYCIN, HYDROMYCIN B, DESTOMYSIN, ANTIBIOTIC A-396-II
C20 H37 N3 O13
GRRNUXAQVGOGFE-WRWUMOMGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.269 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 208.700α = 90.00
b = 379.500β = 90.00
c = 739.300γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CNSrefinement
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2017-11-22
    Type: Refinement description