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Title: Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Avilamycin C, mRNA and P-site tRNA at 3.6A resolution      
dateReleased:
08-17-2016
creators:
Arenz, S.
Juette, M.F.
Graf, M.
Nguyen, F.
Huter, P.
Polikanov, Y.S.
Blanchard, S.C.
Wilson, D.N.
description:
Ribosome
privacy:
not applicable
aggregation:
instance of dataset
ID:
PDB:5KCR
refinement:
curated
keywords:
RIBOSOME
Avilamycin
evernimycin
antibiotic
antimicrobial
ribosome
cryo-EM
smFRET
rRNA
L16
resistance
translation
dateCreated:
06-06-2016
availability:
available
types:
structure
authors:
Arenz, S.
Juette, M.F.
Graf, M.
Nguyen, F.
Huter, P.
Polikanov, Y.S.
Blanchard, S.C.
Wilson, D.N.
alternateID:
doi:10.1073/pnas.1604790113
year:
2016
ID: pmid:27330110
title:
Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome.
formula:
C11 H16 N5 O8 P
name:
1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C11 H16 N5 O7 P
name:
2-METHYLADENOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C11 H16 N5 O8 P
name:
2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C10 H16 N3 O8 P
name:
5-METHYLCYTIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C10 H15 N2 O9 P
name:
5-METHYLURIDINE 5'-MONOPHOSPHATE
roles:
chemical component
formula:
C11 H16 N5 O7 P
name:
N6-METHYLADENOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C61 H90 Cl2 O32
name:
(2R,3S,4R,6S)-4-hydroxy-6-{[(2R,3aR,4R,4'R,5'S,6S,6'R,7aR)-4'-hydroxy-6-{[(2S,3R,4R,5S,6R)-3-hydroxy-2-{[(2R,3S,4S,5S,6S)-4-hydroxy-6-({(2R,3aS,3a'R,6S,6'R,7R,7'R,7aR,7a'R)-7'-hydroxy-7'-[(1S)-1-hydroxyethyl]-6'-methyl-7-[(2-methylpropanoyl)oxy]octahydro-4H-2,4'-spirobi[[1,3]dioxolo[4,5-c]pyran]-6-yl}oxy)-5-methoxy-2-(methoxymethyl)tetrahydro-2H-pyran-3-yl]oxy}-5-methoxy-6-methyltetrahydro-2H-pyran-4-yl]oxy}-4,6',7a-trimethyloctahydro-4H-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-5'-yl]oxy}-2-methyltetrahydro-2H-pyran-3-yl 3,5-dichloro-4-hydroxy-2-methoxy-6-methylbenzoate (non-preferred name)
roles:
chemical component
formula:
C10 H14 N5 O7 P
name:
ADENOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C3 H7 N O2
name:
ALANINE
roles:
chemical component
formula:
C6 H15 N4 O2 1
name:
ARGININE
roles:
chemical component
formula:
C4 H8 N2 O3
name:
ASPARAGINE
roles:
chemical component
formula:
C4 H7 N O4
name:
ASPARTIC ACID
roles:
chemical component
formula:
C9 H14 N3 O8 P
name:
CYTIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C3 H7 N O2 S
name:
CYSTEINE
roles:
chemical component
formula:
C10 H14 N5 O8 P
name:
GUANOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C11 H17 N5 O8 P 1
name:
N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C5 H10 N2 O3
name:
GLUTAMINE
roles:
chemical component
formula:
C5 H9 N O4
name:
GLUTAMIC ACID
roles:
chemical component
formula:
C2 H5 N O2
name:
GLYCINE
roles:
chemical component
formula:
C9 H15 N2 O9 P
name:
5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C6 H10 N3 O2 1
name:
HISTIDINE
roles:
chemical component
formula:
C6 H13 N O2
name:
ISOLEUCINE
roles:
chemical component
formula:
C6 H13 N O2
name:
LEUCINE
roles:
chemical component
formula:
C6 H15 N2 O2 1
name:
LYSINE
roles:
chemical component
formula:
C6 H12 N2 O3
name:
N5-METHYLGLUTAMINE
roles:
chemical component
formula:
C5 H11 N O2 S
name:
METHIONINE
roles:
chemical component
formula:
C10 H16 N3 O8 P
name:
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C11 H16 N5 O8 P
name:
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C10 H15 N2 O9 P
name:
O2'-METHYLURIDINE 5'-MONOPHOSPHATE
roles:
chemical component
formula:
C9 H11 N O2
name:
PHENYLALANINE
roles:
chemical component
formula:
C5 H9 N O2
name:
PROLINE
roles:
chemical component
formula:
C9 H13 N2 O9 P
name:
PSEUDOURIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C3 H7 N O3
name:
SERINE
roles:
chemical component
formula:
C4 H9 N O3
name:
THREONINE
roles:
chemical component
formula:
C11 H12 N2 O2
name:
TRYPTOPHAN
roles:
chemical component
formula:
C9 H11 N O3
name:
TYROSINE
roles:
chemical component
formula:
C9 H13 N2 O9 P
name:
URIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C5 H11 N O2
name:
VALINE
roles:
chemical component
formula:
Zn 2
name:
ZINC ION
roles:
chemical component
name:
ELECTRON MICROSCOPY
ID:
pdb:5KCR
ID:
wwpdb:D_1000221973
ID:
emdb:EMD-8237
accessURL: https://files.rcsb.org/download/5KCR.xml.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
PDBML/XML
accessType:
download
authentication:
none
authorization:
none
accessURL: https://files.rcsb.org/download/5KCR.pdb.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
PDB Format
accessType:
download
authentication:
none
authorization:
none
accessURL: https://files.rcsb.org/download/5KCR.cif.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
PDBx/mmCIF
accessType:
download
authentication:
none
authorization:
none
accessURL: http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=FASTA&compression=NO&structureId=5KCR
storedIn:
Protein Data Bank
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
FASTA
accessType:
download
authentication:
none
authorization:
none
accessURL: https://files.rcsb.org/download/5KCR-sf.cif.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
CIF
accessType:
download
authentication:
none
authorization:
none
accessURL: https://files.rcsb.org/download/5KCR.pdb1.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
PDB Format (A)
accessType:
download
authentication:
none
authorization:
none
accessURL: http://www.rcsb.org/pdb/explore/jmol.do?structureId=5KCR&bionumber=1
storedIn:
Protein Data Bank
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
JSmol
accessType:
view
authentication:
none
authorization:
none
abbreviation:
wwPDB
homePage: http://www.wwpdb.org
ID:
SCR:006555
name:
Worldwide Protein Data Bank
abbreviation:
PDB
homePage: http://www.rcsb.org/pdb/
ID:
SCR:012820
name:
Protein Data Bank