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 1.2 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

  • DOI: 10.1073/pnas.1808535115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In <i>Bacillus subtilis </i>, the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (S ...

    Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In Bacillus subtilis , the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (S A ) antibiotic virginiamycin M (VgM). VmlR is an ATP-binding cassette (ABC) protein of the F type, which, like other antibiotic resistance (ARE) ABCF proteins, is thought to bind to antibiotic-stalled ribosomes and promote dissociation of the drug from its binding site. To investigate the molecular mechanism by which VmlR confers antibiotic resistance, we have determined a cryo-electron microscopy (cryo-EM) structure of an ATPase-deficient B. subtilis VmlR-EQ 2 mutant in complex with a B. subtilis ErmDL-stalled ribosomal complex (SRC). The structure reveals that VmlR binds within the E site of the ribosome, with the antibiotic resistance domain (ARD) reaching into the peptidyltransferase center (PTC) of the ribosome and a C-terminal extension (CTE) making contact with the small subunit (SSU). To access the PTC, VmlR induces a conformational change in the P-site tRNA, shifting the acceptor arm out of the PTC and relocating the CCA end of the P-site tRNA toward the A site. Together with microbiological analyses, our study indicates that VmlR allosterically dissociates the drug from its ribosomal binding site and exhibits specificity to dislodge VgM, Lnc, and the pleuromutilin tiamulin (Tia), but not chloramphenicol (Cam), linezolid (Lnz), nor the macrolide erythromycin (Ery).


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea. Electronic address: chahong@korea.ac.kr.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands.,Helmholtz Centre for Infection Research , 38124 Braunschweig , Germany.,Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC206, La Jolla, CA 92037, USA.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 106, Taiwan. andyhsu@ntu.edu.tw.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand.,Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133, Milano, Italy. emilio.parisini@iit.it.,Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.,School of Biological Sciences , Nanyang Technological University , 639798 Singapore.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy. alfonso.gautieri@polimi.it.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands.,Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.,Department of Chemistry and Biochemistry, University of Lethbridge, Alberta T1K 3M4, Canada.,Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy.,Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA. Electronic address: qunliu@bnl.gov.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, The Netherlands.,Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133, Milano, Italy.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.,Institute of Molecular Systems Biology and Department of Health Sciences and Technology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Université Paris-Saclay , Gif-sur-Yvette 91190 , France.,SAXS/WAXS, Australian Synchrotron/ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. kwmiller@mgh.harvard.edu.,Department of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand emily.parker@vuw.ac.nz g.b.jameson@massey.ac.nz.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Technical University Darmstadt , Alarich-Weiss-Straße 4 , 64287 Darmstadt , Germany.,Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,NeCEN, Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, Netherlands.,MOH Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.,Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.,National Institute of Biological Sciences, Beijing, China.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 106, Taiwan.,Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institute , 5232 Villigen , Switzerland.,Instituto de Bionanotecnología del NOA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, G4206XCP Santiago del Estero, Argentina.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany goerlich@mpibpc.mpg.de.,Department of Infectious Diseases and Microbiology , University of Lübeck , 23562 Lübeck , Germany.,Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea.,AbbVie Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, United States.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. nisimasu@bs.s.u-tokyo.ac.jp nureki@bs.s.u-tokyo.ac.jp.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Max Planck Institute of Biochemistry , 82152 Martinsried , Germany.,College of Animal Science and Technology, China Agricultural University, Beijing, China.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA.,Dipartimento di Scienze della Terra , Università di Pisa , via Santa Maria 53 , 56126 Pisa , Italy.,Division of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudangiro Ochang, Cheongwongu, Cheongju, Chungbuk 28119, South Korea.,Laboratory Molecular and Cellular Signaling, Department Cellular and Molecular Medicine, Campus Gasthuisberg O/N-I Bus 802, Herestraat 49 3000 Leuven, Belgium.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica., Taipei, 115, Taiwan.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK. s.s.virdee@dundee.ac.uk.,D3-PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.,Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan. bmchinp@ibms.sinica.edu.tw.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand.,RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.,Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.,Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , 80804 Munich , Germany.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. simonasm@mrc-lmb.cam.ac.uk.,Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. radu@mrc-lmb.cam.ac.uk.,Institute of Fundamental Sciences and the Riddet Institute, Massey University, Palmerston North 4442, New Zealand.,Institute of Technology, University of Tartu, 50411 Tartu, Estonia.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.,NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China. yonghenc@163.com.,Institute of Neuropathology, University of Zurich, Switzerland.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA mr@purdue.edu.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Institute for Genetics, University of Cologne, Cologne, Germany.,Dipartimento di Farmacia , Università di Pisa , Via Bonanno 6 , 56126 Pisa , Italy.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 90187 Umeå, Sweden.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China. shaofeng@nibs.ac.cn.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Institute for Advanced Biosciences, Keio University, 14-1 Baba-cho, Tsuruoka, Yamagata 997-0035, Japan.,University of Lübeck , 23562 Lübeck , Germany.,Centro de Química Estrutural, Instituto Superior Técnico , Universidade de Lisboa , Av. Rovisco Pais 1 , 1049-001 Lisboa , Portugal.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Synchrotron SOLEIL , L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette , France.,Structural Genomics Consortium, University of Toronto , 101 College Street, Toronto, ON M5G 1L7, Canada.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA. Electronic address: lei.shi2@nih.gov.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. radu@mrc-lmb.cam.ac.uk.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Technische Universität Braunschweig , 38106 Braunschweig , Germany.,Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany; daniel.wilson@chemie.uni-hamburg.de.,Department of Agricultural Chemistry, National Taiwan University, Taipei, 106, Taiwan. andyhsu@ntu.edu.tw.,McGovern Institute for Brain Research, Cambridge, MA 02139, USA.,Beijing Mingde Zhengkang Technologies Co., Ltd., Beijing, China.,New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA.,Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan.,Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA. Electronic address: mq2102@cumc.columbia.edu.




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
  • Version 1.2: 2019-12-18
    Type: Other