All structure family : Ribosomal protein L13
 
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Latest PDB release
Entries released this week  (1)
revised
(1)
 
Entry Information
Entry status  (1)
REL
(88)
 
Experimental methods  (2)
X-ray diffraction
(78)
Electron Microscopy
(10)
 
Authors  (156)
Steitz TA
(62)
Moore PB
(48)
Blaha G
(28)
Schmeing TM
(22)
Gurel G
(18)
Gürel G
(18)
Schroeder SJ
(16)
Hansen JL
(14)
Strobel SA
(13)
Huang KS
(12)
Ban N
(10)
Kitchen DE
(9)
Nissen P
(7)
Tu D
(7)
Fucini P
(6)
Harms JM
(6)
Ippolito JA
(6)
Schluenzen F
(6)
Connell SR
(5)
Hansen J
(5)
Wilson DN
(5)
Spahn CM
(4)
Spahn CMT
(4)
Stachelhaus T
(4)
Zaborowska Z
(4)
Amunts A
(3)
Bai XC
(3)
Brown A
(3)
Chen JM
(3)
Granskog K
(3)
Han S
(3)
Huband MD
(3)
Kanyo ZF
(3)
Magee TV
(3)
Maguire BA
(3)
Marr ES
(3)
McCurdy SP
(3)
Nguyen TT
(3)
Ramakrishnan V
(3)
Shanmugasundaram V
(3)
Subashi TA
(3)
Yonath A
(3)
Aibara S
(2)
Arakawa K
(2)
Bashan A
(2)
Beckmann R
(2)
Belousoff MJ
(2)
Duffy EM
(2)
Kimanius D
(2)
Kinashi H
(2)
Klein DJ
(2)
Rathore S
(2)
Rorbach J
(2)
Rozenberg H
(2)
Shapira T
(2)
Simonovic M
(2)
Simonović M
(2)
Sinning I
(2)
Tirado-Rives J
(2)
Wang D
(2)
Zimmerman E
(2)
Abrahams JP
(1)
Aebersold R
(1)
Ahmed YL
(1)
Bange G
(1)
Barandun J
(1)
Barrio-Garcia C
(1)
Becker T
(1)
Berninghausen O
(1)
Bhattacharjee A
(1)
Bieri P
(1)
Bingel-Erlenmeyer R
(1)
Blau M
(1)
Boehringer D
(1)
Bukau B
(1)
Chait BT
(1)
Chaker-Margot M
(1)
Chen S
(1)
Chen Y
(1)
Cheng J
(1)
Deuerling E
(1)
Dong MQ
(1)
Duffy E
(1)
Edwards PC
(1)
Ehrenberg M
(1)
Farmer J
(1)
Ferbitz L
(1)
Franceschi FJ
(1)
Frank J
(1)
Freeborn B
(1)
Gao N
(1)
Goldberg J
(1)
Greber BJ
(1)
Halic M
(1)
Hanselmann R
(1)
Hunziker M
(1)
Hurt E
(1)
Ismail S
(1)
Jiang L
(1)
Johnson G
(1)
 
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Homo / hetero assembly  (2)
hetero
(87)
homo
(1)
 
Assembly composition  (3)
RNA/protein complex
(85)
DNA/RNA hybrid/RNA/protein complex
(2)
protein structure
(1)
 
Assembly polymer count  (12)
31-mer
(38)
30-mer
(18)
32-mer
(17)
33-mer
(6)
34-mer
(2)
29-mer
(1)
35-mer
(1)
43-mer
(1)
51-mer
(1)
55-mer
(1)
56-mer
(1)
monomer
(1)
 
Resolution distribution
1.5 - 2
(1)
2.0 - 2.5
(14)
2.5 - 3
(43)
3.0 - 3.5
(23)
3.5 - 4
(4)
9.0 - 9.5
(2)
9.5 - 10
(1)
 
Release year distribution
1995 - 2000
(1)
2000 - 2005
(41)
2005 - 2010
(54)
2010 - 2015
(10)
2015 - 2020
(5)
 
Journal  (16)
J Mol Biol
(26)
Mol Cell
(17)
Cell
(8)
Proc Natl Acad Sci U S A
(8)
Nature
(7)
Bioorg Med Chem Lett
(4)
RNA
(4)
Antimicrob Agents Chemother
(3)
Nat Struct Mol Biol
(2)
Science
(2)
EMBO J
(1)
J Med Chem
(1)
Mol Microbiol
(1)
Nat Struct Biol
(1)
Protein Cell
(1)
To be published
(1)
 
Macromolecules
Organism superkingdom  (3)
Archaea
(67)
Bacteria
(14)
Eukaryota
(7)
 
Organism name  (9)
Haloarcula marismortui
(66)
Deinococcus radiodurans
(11)
Homo sapiens
(3)
Escherichia coli
(2)
Saccharomyces cerevisiae S288C
(2)
Escherichia coli K-12
(1)
Pyrococcus horikoshii
(1)
Saccharomyces cerevisiae BY4741
(1)
Sus scrofa
(1)
 
Molecule name  (14)
50S ribosomal protein L13
(81)
Large ribosomal subunit protein uL13
(81)
Hmal13
(66)
39S ribosomal protein L13, mitochondrial
(3)
60S ribosomal protein L16-A
(3)
L13a
(3)
L13mt
(3)
L21
(3)
Large ribosomal subunit protein uL13A
(3)
Large ribosomal subunit protein uL13m
(3)
MRP-L13
(3)
RP22
(3)
YL15
(3)
MITORIBOSOMAL PROTEIN UL13M, MRPL13
(1)
 
Molecule type  (1)
Protein
(88)
 
Gene names  (12)
rpl13
(67)
rrnAC0065
(66)
rplM
(14)
DR_0174
(11)
JW3200
(3)
MRPL13
(3)
RPL13
(3)
RPL16A
(3)
RPL21A
(3)
YIL133C
(3)
b3231
(3)
PH1634
(1)
 
Interacting Molecules  (205)
Large ribosomal subunit protein uL3
(82)
5S ribosomal RNA
(80)
Large ribosomal subunit protein uL14
(80)
Large ribosomal subunit protein uL15
(80)
Large ribosomal subunit protein uL18
(80)
Large ribosomal subunit protein uL2
(80)
Large ribosomal subunit protein uL22
(80)
Large ribosomal subunit protein uL23
(80)
Large ribosomal subunit protein uL24
(80)
Large ribosomal subunit protein uL29
(80)
Large ribosomal subunit protein uL30
(80)
Large ribosomal subunit protein uL4
(80)
Large ribosomal subunit protein uL5
(80)
Large ribosomal subunit protein uL6
(80)
23S ribosomal RNA
(79)
Large ribosomal subunit protein uL16
(78)
Large ribosomal subunit protein eL32
(69)
Large ribosomal subunit protein eL18
(66)
Large ribosomal subunit protein eL19
(66)
Large ribosomal subunit protein eL21
(66)
Large ribosomal subunit protein eL24
(66)
Large ribosomal subunit protein eL31
(66)
Large ribosomal subunit protein eL37
(66)
Large ribosomal subunit protein eL39
(66)
Large ribosomal subunit protein eL42
(66)
Large ribosomal subunit protein eL8
(66)
Large ribosomal subunit protein eL15
(65)
Large ribosomal subunit protein eL43
(65)
Large ribosomal subunit protein uL10
(65)
Large ribosomal subunit protein uL11
(57)
Large ribosomal subunit protein bL17
(14)
Large ribosomal subunit protein bL19
(14)
Large ribosomal subunit protein bL20
(14)
Large ribosomal subunit protein bL21
(14)
Large ribosomal subunit protein bL25
(14)
Large ribosomal subunit protein bL27
(14)
Large ribosomal subunit protein bL32
(14)
Large ribosomal subunit protein bL33
(14)
Large ribosomal subunit protein bL34
(14)
Large ribosomal subunit protein bL35
(14)
Large ribosomal subunit protein bL36
(11)
Large ribosomal subunit protein bL28
(10)
Large ribosomal subunit protein bL17m
(4)
Large ribosomal subunit protein bL19m
(4)
Large ribosomal subunit protein bL21m
(4)
Large ribosomal subunit protein bL31
(4)
Large ribosomal subunit protein bL32m
(4)
Large ribosomal subunit protein bL34m
(4)
Large ribosomal subunit protein bL35m
(4)
Large ribosomal subunit protein bL9
(4)
Large ribosomal subunit protein bL9m
(4)
Large ribosomal subunit protein uL10m
(4)
Large ribosomal subunit protein uL11m
(4)
Large ribosomal subunit protein uL14m
(4)
Large ribosomal subunit protein uL16m
(4)
Large ribosomal subunit protein uL24m
(4)
Large ribosomal subunit protein uL29m
(4)
Large ribosomal subunit protein uL30m
(4)
16S ribosomal RNA
(3)
5.8S ribosomal RNA
(3)
ATP-dependent RNA helicase HAS1
(3)
Large ribosomal subunit protein bL20m
(3)
Large ribosomal subunit protein bL27m
(3)
Large ribosomal subunit protein bL28m
(3)
Large ribosomal subunit protein bL33m
(3)
Large ribosomal subunit protein bL36A
(3)
Large ribosomal subunit protein eL13A
(3)
Large ribosomal subunit protein eL14A
(3)
Large ribosomal subunit protein eL15A
(3)
Large ribosomal subunit protein eL18A
(3)
Large ribosomal subunit protein eL20A
(3)
Large ribosomal subunit protein eL33A
(3)
Large ribosomal subunit protein eL37A
(3)
Large ribosomal subunit protein eL6A
(3)
Large ribosomal subunit protein eL8A
(3)
Large ribosomal subunit protein mL37
(3)
Large ribosomal subunit protein mL38
(3)
Large ribosomal subunit protein mL39
(3)
Large ribosomal subunit protein mL40
(3)
Large ribosomal subunit protein mL41
(3)
Large ribosomal subunit protein mL42
(3)
Large ribosomal subunit protein mL43
(3)
Large ribosomal subunit protein mL44
(3)
Large ribosomal subunit protein mL45
(3)
Large ribosomal subunit protein mL46
(3)
Large ribosomal subunit protein mL48
(3)
Large ribosomal subunit protein mL49
(3)
Large ribosomal subunit protein mL50
(3)
Large ribosomal subunit protein mL51
(3)
Large ribosomal subunit protein mL52
(3)
Large ribosomal subunit protein mL53
(3)
Large ribosomal subunit protein mL62
(3)
Large ribosomal subunit protein mL63
(3)
Large ribosomal subunit protein mL64
(3)
Large ribosomal subunit protein mL65
(3)
Large ribosomal subunit protein mL66
(3)
Large ribosomal subunit protein uL15m
(3)
Large ribosomal subunit protein uL18m
(3)
Large ribosomal subunit protein uL22A
(3)
Large ribosomal subunit protein uL22m
(3)
 
More...
 
Interacting ligands  (4)
CL : CHLORIDE ION
(65)
NA : SODIUM ION
(64)
SR : STRONTIUM ION
(29)
MG : MAGNESIUM ION
(1)
 
Function and Biology
Biological function  (8)
structural constituent of ribosome
(88)
mRNA binding
(87)
rRNA binding
(77)
RNA binding
(6)
large ribosomal subunit rRNA binding
(3)
mRNA 5'-UTR binding
(3)
protein binding
(3)
zinc ion binding
(3)
 
Biological process  (5)
translation
(88)
negative regulation of translation
(87)
cytoplasmic translation
(6)
maturation of LSU-rRNA
(3)
mitochondrial translation
(3)
 
Biological cell component  (11)
ribosome
(88)
ribonucleoprotein complex
(87)
cytosolic large ribosomal subunit
(84)
large ribosomal subunit
(70)
cytoplasm
(20)
cytosol
(6)
mitochondrial inner membrane
(3)
mitochondrial large ribosomal subunit
(3)
mitochondrial ribosome
(3)
mitochondrion
(3)
nucleolus
(3)
 
Sequence and Structure classification
SCOP fold  (2)
Ribosomal protein L13
(50)
Ribosome and ribosomal fragments
(19)
 
SCOP family  (2)
Ribosomal protein L13
(50)
Large subunit
(19)
 
CATH class  (2)
Alpha Beta
(83)
Mainly Alpha
(3)
 
CATH topology  (2)
Ribosomal Protein L13p; Chain: A;
(83)
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(3)
 
Pfam accession / name  (1)
PF00572 : Ribosomal_L13
(87)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(79)
 
Diffraction radiation source type  (1)
Synchrotron
(78)
 
Diffraction source  (13)
NSLS BEAMLINE X25
(26)
APS BEAMLINE 19-ID
(20)
NSLS BEAMLINE X29A
(16)
APS BEAMLINE 24-ID-C
(9)
SLS BEAMLINE X06SA
(6)
ESRF BEAMLINE ID29
(3)
SLS BEAMLINE X10SA
(3)
ALS BEAMLINE 8.2.2
(2)
APS BEAMLINE 8-BM
(2)
ESRF BEAMLINE BM1A
(1)
ESRF BEAMLINE ID14-4
(1)
ESRF BEAMLINE ID23-2
(1)
PHOTON FACTORY BEAMLINE BL-18B
(1)
 
Synchrotron site  (6)
NSLS
(42)
APS
(31)
SLS
(9)
ESRF
(6)
ALS
(2)
Photon Factory
(1)
 
Diffraction detector type  (3)
CCD
(73)
Image plate
(4)
Pixel
(4)
 
Refinement software  (6)
CNS
(71)
PHENIX
(4)
CNX
(3)
autoBUSTER
(3)
REFMAC
(2)
TNT
(1)
 
EM microscope model  (3)
FEI TITAN KRIOS
(7)
FEI TECNAI F20
(2)
FEI TECNAI F30
(1)
 
EM detector name  (4)
FEI FALCON II (4k x 4k)
(5)
KODAK SO-163 FILM
(3)
FEI FALCON III (4k x 4k)
(1)
GATAN K2 SUMMIT (4k x 4k)
(1)
 
Representative Structures
Representative Structures
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Entries 1 to 10 of 88
Entries 1 to 10 of 88
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50S subunit with EF-G(GDPNP) and RRF bound
Gao N, Zavialov AV, Ehrenberg M, Frank J
J Mol Biol (2007) [PMID: 17996252  ]
Source organism: Escherichia coli  
Assembly composition: RNA/protein complex
PDBe complex ID: PDB-CPX-249951 (Preferred)   search this ID
PDBe-KB: P0AA10    P0A805    P60422    P0A7J7    P0ADY7    P61175    (view 26 more)
Electron Microscopy
9.1Å resolution
Released: 4 Mar 2008
Model geometry
Fit model/data
Data not analysed
2rdo
2rdo
2rdo
CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI AT 2.4 ANGSTROM RESOLUTION
Ban N, Nissen P, Hansen J, Moore PB, Steitz TA
Science (2000) [PMID: 10937989  ]
Assembly composition: RNA/protein complex
Bound ligands: K    K    MG    CD    MG    CD   
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-145603 (Preferred)   search this ID
PDBe-KB: P29198    P14123    P10971    P32410    P12737    P12733    (view 21 more)
X-ray diffraction
2.4Å resolution
Released: 14 Aug 2000
Model geometry
Fit model/data
Data not analysed
1ffk
1ffk
1ffk
MODEL OF E. COLI SRP BOUND TO 70S RNCS
Halic M, Blau M, Becker T, Mielke T, Pool MR, Wild K, Sinning I, Beckmann R
Nature (2006) [PMID: 17086193  ]
Source organism: Escherichia coli K-12  
Assembly composition: RNA/protein complex
Bound ligands: MG    MG   
PDBe complex ID: PDB-CPX-130261 (Preferred)   search this ID
PDBe-KB: P0AA10    O62798    P60422    P0A7J7    P0ADY7    P61175    (view 25 more)
Electron Microscopy
9.5Å resolution
Released: 8 Nov 2006
Model geometry
Fit model/data
Data not analysed
2j28
2j28
2j28
Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin
Schluenzen F, Pyetan E, Fucini P, Yonath A, Harms JM
Mol Microbiol (2004) [PMID: 15554968  ]
Assembly composition: RNA/protein complex
Bound ligands: MUL   
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-155895 (Preferred)   search this ID
PDBe-KB: Q9RXY1    Q9RY65    Q9RSL0    Q9RSS4    Q9RSW6    Q9RSK9    (view 23 more)
X-ray diffraction
3.5Å resolution
Released: 1 Mar 2005
Model geometry
Fit model/data
Data not deposited
1xbp
1xbp
1xbp
The Hsp15 protein fitted into the low resolution Cryo-EM map of the 50S.nc-tRNA.Hsp15 complex
Jiang L, Abrahams JP
J Mol Biol (2009) [PMID: 19013177  ]
Source organism: Escherichia coli  
Assembly composition: RNA/protein complex
Bound ligands: MG    MG   
Assembly name: Large ribosomal protein (Preferred)   search this complex
PDBe complex ID: PDB-CPX-249965 (Preferred)   search this ID
PDBe-KB: P0AA10    P60422    P0ADY7    P61175    P68919    P0A7P5    (view 22 more)
Electron Microscopy
10Å resolution
Released: 21 Oct 2008
Model geometry
Fit model/data
Data not analysed
3bbx
3bbx
3bbx
Structure of chloramphenicol bound to the 50S ribosomal subunit
Hansen JL, Moore PB, Steitz TA
J Mol Biol (2003) [PMID: 12860128  ]
Assembly composition: RNA/protein complex
Bound ligands: CLM    K    K    MG    CLM    NA    CD    CL    MG    CD    NA   
Assembly name: Large ribosomal protein (Preferred)   search this complex
PDBe complex ID: PDB-CPX-250165 (Preferred)   search this ID
PDBe-KB: P29198    P14123    P10971    P32410    P12737    P12733    (view 22 more)
X-ray diffraction
3Å resolution
Released: 22 Jul 2003
Model geometry
Fit model/data
1nji
1nji
1nji
Co-crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit
Hansen JL, Ban N, Nissen P, Moore PB, Steitz TA
J Mol Biol (2003) [PMID: 12860128  ]
Assembly composition: RNA/protein complex
Bound ligands: K    K    MG    BLS    BLS    NA    CD    CL    MG    CD    NA   
Assembly name: Large ribosomal protein (Preferred)   search this complex
PDBe complex ID: PDB-CPX-250165 (Preferred)   search this ID
PDBe-KB: P29198    P14123    P10971    P32410    P12737    P12733    (view 22 more)
X-ray diffraction
3.01Å resolution
Released: 22 Jul 2003
Model geometry
Fit model/data
1kc8
1kc8
1kc8
The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortui
Schmeing TM, Steitz TA
Nature (2005) [PMID: 16306996  ]
Source organisms: Synthetic construct, Haloarcula marismortui  
Assembly composition: RNA/protein complex
Bound ligands: K    K    MG    SR    SR    NA    CD    CL    MG    CD    NA   
Modified residues: OMG    OMU    ACA    BTN    PPU    PPU    UR3    1MA    BTN    1MA    HFA    PSU    PSU    HFA    OMG    OMU    UR3   
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-238722 (Preferred)   search this ID
PDBe-KB: P29198    P14123    P10971    P32410    P12737    P12733    (view 23 more)
X-ray diffraction
2.4Å resolution
Released: 29 Nov 2005
Model geometry
Fit model/data
1vqn
1vqn
1vqn
Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans
Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CMT, Fucini P
Mol Cell (2008) [PMID: 18406324  ]
Assembly composition: RNA/protein complex
Bound ligands: MG    MG   
Modified residues: DBU    BB9    DCY    MH6    BB9    DBU    DHA    QUA    TS9    TS9    NH2    QUA    DCY    MH6    NH2   
PDBe complex ID: PDB-CPX-143180 (Preferred)   search this ID
PDBe-KB: Q9RXY1    P0C8P8    Q9RY65    Q9RSL0    Q9RSS4    Q9RSW6    (view 23 more)
X-ray diffraction
3.3Å resolution
Released: 17 Jun 2008
Model geometry
Fit model/data
3cf5
3cf5
3cf5
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
Wilson DN, Schluenzen F, Harms JM, Starosta AL, Connell SR, Fucini P
Proc Natl Acad Sci U S A (2008) [PMID: 18757750  ]
Assembly composition: RNA/protein complex
Bound ligands: MG    ZLD    ZN    ZLD    ZN    MG   
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-155877 (Preferred)   search this ID
PDBe-KB: Q9RXY1    Q9RY65    Q9RSL0    Q9RSS4    Q9RSW6    Q9RSK9    (view 22 more)
X-ray diffraction
3.5Å resolution
Released: 16 Sep 2008
Model geometry
Fit model/data
3dll
3dll
3dll
...
Entries 1 to 10 of 88
Entries 1 to 10 of 88