6HA8

Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 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

Structural basis for antibiotic resistance mediated by theBacillus subtilisABCF ATPase VmlR.

Crowe-McAuliffe, C.Graf, M.Huter, P.Takada, H.Abdelshahid, M.Novacek, J.Murina, V.Atkinson, G.C.Hauryliuk, V.Wilson, D.N.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 8978-8983


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
277Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplB
Find proteins for P42919 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42919
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplC
Find proteins for P42920 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42920
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
207Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplD
Find proteins for P42921 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42921
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
179Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplE
Find proteins for P12877 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12877
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
179Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplF
Find proteins for P46898 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P46898
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
145Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplM
Find proteins for P70974 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P70974
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplN
Find proteins for P12875 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12875
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
146Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplO
Find proteins for P19946 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P19946
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
144Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplP
Find proteins for P14577 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P14577
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
120Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P20277 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20277
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
120Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplR
Find proteins for P46899 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P46899
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplS
Find proteins for O31742 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31742
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
119Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplT
Find proteins for P55873 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P55873
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
102Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplU
Find proteins for P26908 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P26908
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
113Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplV
Find proteins for P42060 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42060
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
95Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplW
Find proteins for P42924 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42924
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
103Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplX
Find proteins for P0CI78 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P0CI78
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Nucleotide-binding protein ExpZ
V
548Bacillus subtilis (strain 168)Mutation(s): 2 
Gene Names: expZ
Find proteins for P39115 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39115
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
94Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P05657 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P05657
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
62Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmB (yloT)
Find proteins for P37807 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P37807
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
66Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P12873 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12873
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
59Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P19947 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P19947
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
59Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmF
Find proteins for O34687 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34687
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 1
1
49Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmGA (rpmG1)
Find proteins for P56849 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P56849
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
44Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmH
Find proteins for P05647 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P05647
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
66Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P55874 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P55874
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
37Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P20278 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20278
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
6
66Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q03223 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q03223
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
8
232Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplA
Find proteins for Q06797 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q06797
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
246Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P21464 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21464
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
218Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P21465 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21465
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
200Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsD
Find proteins for P21466 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21466
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
166Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsE (spcA)
Find proteins for P21467 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21467
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
95Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P21468 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21468
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
156Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P21469 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21469
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
132Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P12879 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12879
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
130Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P21470 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21470
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
102Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsJ (tetA)
Find proteins for P21471 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21471
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
131Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P04969 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P04969
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
138Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsL (fun, strA)
Find proteins for P21472 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21472
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
121Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P20282 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20282
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
61Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsN1 (rpsN, rpsNA, rpsZ)
Find proteins for P12878 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12878
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsO
Find proteins for P21473 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21473
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
90Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P21474 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21474
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
87Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for P12874 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12874
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
79Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P21475 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21475
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
92Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P21476 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21476
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
88Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsT (yqeO)
Find proteins for P21477 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21477
Entity ID: 1
MoleculeChainsLengthOrganism
23S rRNAA2928Bacillus subtilis subsp. subtilis str. 168
Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNAB112Bacillus subtilis subsp. subtilis str. 168
Entity ID: 31
MoleculeChainsLengthOrganism
mRNA73Bacillus subtilis subsp. subtilis str. 168
Entity ID: 33
MoleculeChainsLengthOrganism
16S rRNAa1554Bacillus subtilis subsp. subtilis str. 168
Entity ID: 53
MoleculeChainsLengthOrganism
P-tRNA(Leu)x75Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
V
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
TEL
Query on TEL

Download SDF File 
Download CCD File 
A
TELITHROMYCIN
(3R,5S,6S,7R,8S,11S,12R,13S,14R,15S)-12- [(4-O-ACETYL-2,6-DIDEOXY-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSYL) OXY] -14-{[2-O-ACETYL-3,4,6-TRIDEOXY-3-(DIMETHYLAMINO) BETA-D-XYLO-HEXOPYRANOSYL]OXY} -5,7,8,11,13,15-HEXAMETHYL-4,10-DIOXO-1,9-DIOXASPIRO[2.13]HEXADEC-6-YL ACETATE
C43 H65 N5 O10
LJVAJPDWBABPEJ-MMEUOAQYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR-1805
German Research FoundationGermanyWI3285/6-1
Ministry of Education (Czech Republic)Czech RepublicCIISB project number LM2015043
European UnionCzech RepubliciNext project number 2992

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references