5ZLU

Ribosome Structure bound to ABC-F protein.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 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

Ribosome protection by antibiotic resistance ATP-binding cassette protein.

Su, W.Kumar, V.Ding, Y.Ero, R.Serra, A.Lee, B.S.T.Wong, A.S.W.Shi, J.Sze, S.K.Yang, L.Gao, Y.G.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 5157-5162

  • DOI: 10.1073/pnas.1803313115

  • PubMed Abstract: 
  • The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer resistance to ribosome-targeting antibiotics through a yet u ...

    The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer resistance to ribosome-targeting antibiotics through a yet unknown mechanism. Among them, MsrE has been implicated in macrolide resistance. Here, we report the cryo-EM structure of ATP form MsrE bound to the ribosome. Unlike previously characterized ribosomal protection proteins, MsrE is shown to bind to ribosomal exit site. Our structure reveals that the domain linker forms a unique needle-like arrangement with two crossed helices connected by an extended loop projecting into the peptidyl-transferase center and the nascent peptide exit tunnel, where numerous antibiotics bind. In combination with biochemical assays, our structure provides insight into how MsrE binding leads to conformational changes, which results in the release of the drug. This mechanism appears to be universal for the ABC-F type ribosome protection proteins.


    Organizational Affiliation

    Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305; shannon-au@cuhk.edu.hk wahc@stanford.edu.,Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland thilo.kohler@unige.ch.,Centre for BioImaging Sciences, National University of Singapore, Singapore 117557.,Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Biological Science Imaging facility (BSIR), Department of Biology, 89 Chieftan Way, Florida State University, Tallahassee, FL 32306, USA.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan. Electronic address: titoh@ac.shoyaku.ac.jp.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.,Institute of Chemical Biology and Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. becker@genzentrum.lmu.de.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812.,School of Biological Sciences, Nanyang Technological University, Singapore 637551; ygao@ntu.edu.sg yangliang@ntu.edu.sg rero@ntu.edu.sg.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.,Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beatrix@genzentrum.lmu.de.,Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA hughesst@mail.nih.gov.,Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.,CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551.,Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA e-filippova@northwestern.edu wf-anderson@northwestern.edu.,Jacobs University, Bremen, Germany.,Rega Institute for Medical Research and Department of Microbiology and Immunology, Leuven, Belgium.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA. Electronic address: tgonen@ucla.edu.,School of Life Sciences, Sun Yat-Sen University, 510275 Guangzhou, China.,Department of Biochemistry and Molecular Biology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA.,School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong.,Biozentrum, University of Basel, Basel, Switzerland.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: allain@mol.biol.ethz.ch.,School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong; shannon-au@cuhk.edu.hk wahc@stanford.edu.,School of Biological Sciences, Nanyang Technological University, Singapore 637551.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.,Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 6767 Bertner Avenue, Houston, TX 77225, USA.,Institute of Structural Biology, Nanyang Technological University, Singapore 639798.,National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA.,Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland; Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800 VIC, Australia. Electronic address: fionna.loughlin@monash.edu.,Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305.,Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA. Electronic address: jsuh@rice.edu.,Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673.,Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA.,Keck Biophysics Facility, Northwestern University, Evanston, Illinois, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
A
104Thermus thermophilusMutation(s): 0 
Gene Names: rpsQ (rps17)
Find proteins for P24321 (Thermus thermophilus)
Go to UniProtKB:  P24321
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
B
73Thermus thermophilusMutation(s): 0 
Gene Names: rpsR (rps18)
Find proteins for P80382 (Thermus thermophilus)
Go to UniProtKB:  P80382
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
C
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
D
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
E
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
F
27Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
H
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
I
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
J
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
K
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
L
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
M
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
N
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
O
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
P
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
Q
132Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
R
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
S
61Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
T
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
U
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
Y
229Thermus thermophilusMutation(s): 0 
Gene Names: rplA (rpl1)
Find proteins for P27150 (Thermus thermophilus)
Go to UniProtKB:  P27150
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
Z
276Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
a
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
b
210Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
c
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
d
180Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
e
173Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplJ
Find proteins for Q8VVE3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8VVE3
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
f
147Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplK
Find proteins for Q5SLP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP6
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
g
140Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60488
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
h
122Thermus thermophilusMutation(s): 0 
Gene Names: rplN (rpl14)
Find proteins for P60558 (Thermus thermophilus)
Go to UniProtKB:  P60558
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
i
150Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ7
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
j
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
k
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
l
112Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ4
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
m
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
n
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60491
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
o
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60492
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
p
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
q
96Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP0
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
r
110Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP9
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
s
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHZ1
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
t
85Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
u
67Thermus thermophilusMutation(s): 0 
Gene Names: rpmC (rpl29)
Find proteins for Q9LCY4 (Thermus thermophilus)
Go to UniProtKB:  Q9LCY4
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
v
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
w, CC
71Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJE1
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
x
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
y
54Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P35871
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
z
49Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
AA
65Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKU1
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
BB
37Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHR2
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Macrolide efflux protein
EE
497Pseudomonas aeruginosaMutation(s): 0 
Gene Names: mel
Find proteins for A0A1I9WCL8 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A1I9WCL8
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (25-mer)W25Thermus thermophilus HB8
Entity ID: 8
MoleculeChainsLengthOrganism
16S ribosomal RNAG1514Thermus thermophilus HB8
Entity ID: 23
MoleculeChainsLengthOrganism
23S ribosomal RNAV2875Thermus thermophilus HB8
Entity ID: 24
MoleculeChainsLengthOrganism
5S ribosomal RNAX123Thermus thermophilus HB8
Entity ID: 55
MoleculeChainsLengthOrganism
P-site tRNADD77Thermus thermophilus HB8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
EE
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
i, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
DD
RNA LINKINGC9 H13 N2 O9 PU
OMC
Query on OMC
DD
RNA LINKINGC10 H16 N3 O8 PC
4SU
Query on 4SU
DD
RNA LINKINGC9 H13 N2 O8 P SU
7MG
Query on 7MG
DD
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
DD
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 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
Ministry of Education (Singapore)SingaporeMOE2014-T2-1-083

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Other, Refinement description