All structure family : Ribosomal protein L6, alpha-beta domain
 
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Latest PDB release
Entries released this week  (1)
revised
(4)
 
Entry Information
Entry status  (1)
REL
(103)
 
Experimental methods  (3)
X-ray diffraction
(88)
Electron Microscopy
(14)
Solution NMR
(1)
 
Authors  (174)
Steitz TA
(61)
Moore PB
(47)
Blaha G
(28)
Schmeing TM
(22)
Gurel G
(18)
Gürel G
(18)
Schroeder SJ
(16)
Hansen JL
(14)
Strobel SA
(13)
Ban N
(12)
Bashan A
(12)
Huang KS
(12)
Rozenberg H
(12)
Yonath A
(12)
Zimmerman E
(12)
Krupkin M
(10)
Matzov D
(10)
Kitchen DE
(9)
Eyal Z
(8)
Wekselman I
(8)
Connell SR
(7)
Fucini P
(7)
Tu D
(7)
Wilson DN
(7)
Ippolito JA
(6)
Nissen P
(6)
Boehringer D
(5)
Harms JM
(5)
Leibundgut M
(5)
Paukner S
(5)
Schluenzen F
(5)
Hansen J
(4)
Jomaa A
(4)
Spahn CM
(4)
Spahn CMT
(4)
Stachelhaus T
(4)
Zaborowska Z
(4)
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)
Shanmugasundaram V
(3)
Subashi TA
(3)
Yonath AE
(3)
Ahmed T
(2)
Arakawa K
(2)
Arenz S
(2)
Beckmann R
(2)
Belousoff M
(2)
Belousoff MJ
(2)
Berninghausen O
(2)
Bhushan S
(2)
Brandi L
(2)
Churcher M
(2)
Davidovich C
(2)
Diskin Posner Y
(2)
Duffy EM
(2)
Fabbretti A
(2)
Friedlander G
(2)
Giudice E
(2)
Gualerzi CO
(2)
He CG
(2)
Hilcenko C
(2)
Ingmer H
(2)
Jin L
(2)
Kaminishi T
(2)
Kay RR
(2)
Kinashi H
(2)
Kjeldgaard J
(2)
Klein DJ
(2)
Lindahl L
(2)
Milon P
(2)
Milón P
(2)
Ochoa-Lizarralde B
(2)
Schedlbauer A
(2)
Shapira T
(2)
Simonovic M
(2)
Simonović M
(2)
Starosta AL
(2)
Tirado-Rives J
(2)
Traynor D
(2)
Wang D
(2)
Warren AJ
(2)
Weis F
(2)
Wong CC
(2)
Zengel JM
(2)
Ben Hamou R
(1)
Benhamou RI
(1)
Bhattacharjee A
(1)
Bieri P
(1)
Bischoff L
(1)
Bukau B
(1)
Chang J-Y
(1)
Chang JY
(1)
 
More...
 
Homo / hetero assembly  (2)
hetero
(101)
homo
(2)
 
Assembly composition  (3)
RNA/protein complex
(99)
DNA/RNA hybrid/RNA/protein complex
(2)
protein structure
(2)
 
Assembly polymer count  (13)
31-mer
(38)
30-mer
(19)
32-mer
(19)
28-mer
(7)
33-mer
(5)
35-mer
(4)
36-mer
(3)
monomer
(2)
undecamer
(2)
26-mer
(1)
27-mer
(1)
29-mer
(1)
37-mer
(1)
 
Resolution distribution
1.5 - 2
(1)
2.0 - 2.5
(13)
2.5 - 3
(45)
3.0 - 3.5
(27)
3.5 - 4
(16)
 
Release year distribution
1995 - 2000
(1)
2000 - 2005
(39)
2005 - 2010
(51)
2010 - 2015
(19)
2015 - 2020
(24)
 
Journal  (19)
J Mol Biol
(24)
Mol Cell
(18)
Proc Natl Acad Sci U S A
(14)
Cell
(7)
Nucleic Acids Res
(6)
Bioorg Med Chem Lett
(4)
Nat Commun
(4)
Nature
(4)
RNA
(4)
Antimicrob Agents Chemother
(3)
EMBO J
(3)
Nat Struct Mol Biol
(2)
Sci Rep
(2)
Structure
(2)
Cell Rep
(1)
J Med Chem
(1)
Nat Struct Biol
(1)
Protein Cell
(1)
To be published
(1)
 
Macromolecules
Organism superkingdom  (3)
Archaea
(65)
Bacteria
(30)
Eukaryota
(8)
 
Organism name  (12)
Haloarcula marismortui
(65)
Deinococcus radiodurans
(12)
Staphylococcus aureus subsp. aureus NCTC 8325
(6)
Escherichia coli
(5)
Deinococcus radiodurans R1
(4)
Spinacia oleracea
(4)
Dictyostelium discoideum
(2)
Escherichia coli K-12
(1)
Geobacillus stearothermophilus
(1)
Homo sapiens
(1)
Mycobacterium tuberculosis
(1)
Saccharomyces cerevisiae S288C
(1)
 
Molecule name  (13)
Large ribosomal subunit protein uL6
(98)
50S ribosomal protein L6
(95)
Hl10
(65)
Hmal6
(65)
50S ribosomal protein L6, chloroplastic
(4)
Large ribosomal subunit protein uL6c
(4)
60S ribosomal protein L9
(3)
60S ribosomal protein L9-A
(1)
BL10
(1)
L8
(1)
Large ribosomal subunit protein uL6A
(1)
RP24
(1)
YL11
(1)
 
Molecule type  (1)
Protein
(103)
 
Gene names  (21)
rpl6
(65)
rrnAC1596
(65)
rplF
(30)
DR_2111
(16)
JW3267
(6)
SAOUHSC_02496
(6)
b3305
(6)
RPL6
(4)
SOVF_107200
(4)
DDB_G0278959
(2)
RPL9
(2)
rpl9
(2)
MTCY210.38
(1)
OK/SW-cl.103
(1)
RPL8A
(1)
RPL9A
(1)
RPL9P7
(1)
RPL9P8
(1)
RPL9P9
(1)
Rv0719
(1)
YGL147C
(1)
 
Interacting Molecules  (172)
5S ribosomal RNA
(97)
Large ribosomal subunit protein uL3
(97)
23S ribosomal RNA
(96)
Large ribosomal subunit protein uL14
(96)
Large ribosomal subunit protein uL13
(94)
Large ribosomal subunit protein uL15
(94)
Large ribosomal subunit protein uL16
(94)
Large ribosomal subunit protein uL18
(94)
Large ribosomal subunit protein uL2
(94)
Large ribosomal subunit protein uL22
(94)
Large ribosomal subunit protein uL23
(94)
Large ribosomal subunit protein uL24
(94)
Large ribosomal subunit protein uL29
(94)
Large ribosomal subunit protein uL30
(94)
Large ribosomal subunit protein uL4
(94)
Large ribosomal subunit protein uL5
(94)
Large ribosomal subunit protein uL10
(73)
Large ribosomal subunit protein eL24
(67)
Large ribosomal subunit protein eL32
(66)
Large ribosomal subunit protein eL18
(65)
Large ribosomal subunit protein eL19
(65)
Large ribosomal subunit protein eL21
(65)
Large ribosomal subunit protein eL31
(65)
Large ribosomal subunit protein eL37
(65)
Large ribosomal subunit protein eL39
(65)
Large ribosomal subunit protein eL42
(65)
Large ribosomal subunit protein eL8
(65)
Large ribosomal subunit protein uL11
(65)
Large ribosomal subunit protein eL15
(64)
Large ribosomal subunit protein eL43
(64)
Large ribosomal subunit protein bL17
(29)
Large ribosomal subunit protein bL19
(29)
Large ribosomal subunit protein bL20
(29)
Large ribosomal subunit protein bL21
(29)
Large ribosomal subunit protein bL25
(29)
Large ribosomal subunit protein bL27
(29)
Large ribosomal subunit protein bL32
(29)
Large ribosomal subunit protein bL34
(29)
Large ribosomal subunit protein bL35
(29)
Large ribosomal subunit protein bL28
(27)
Large ribosomal subunit protein bL33
(22)
Large ribosomal subunit protein bL36
(15)
Large ribosomal subunit protein bL9
(7)
Large ribosomal subunit protein bL36A
(6)
Large ribosomal subunit protein bL17c
(4)
Large ribosomal subunit protein bL19c
(4)
Large ribosomal subunit protein bL20c
(4)
Large ribosomal subunit protein bL21c
(4)
Large ribosomal subunit protein bL27c
(4)
Large ribosomal subunit protein bL28c
(4)
Large ribosomal subunit protein bL32c
(4)
Large ribosomal subunit protein bL33c
(4)
Large ribosomal subunit protein bL34c
(4)
Large ribosomal subunit protein bL35c
(4)
Large ribosomal subunit protein bL36c
(4)
Large ribosomal subunit protein bL9c
(4)
Large ribosomal subunit protein cL37 alpha
(4)
Large ribosomal subunit protein cL38
(4)
Large ribosomal subunit protein uL13c
(4)
Large ribosomal subunit protein uL14c
(4)
Large ribosomal subunit protein uL15c
(4)
Large ribosomal subunit protein uL16c
(4)
Large ribosomal subunit protein uL18c
(4)
Large ribosomal subunit protein uL22c
(4)
Large ribosomal subunit protein uL23c
(4)
Large ribosomal subunit protein uL24c
(4)
Large ribosomal subunit protein uL29c
(4)
Large ribosomal subunit protein uL2cz/uL2cy
(4)
Large ribosomal subunit protein uL3c
(4)
Large ribosomal subunit protein uL4c
(4)
Large ribosomal subunit protein uL5c
(4)
Alkaline phosphatase
(3)
Eukaryotic translation initiation factor 6
(3)
Large ribosomal subunit protein bL12
(3)
Large ribosomal subunit protein bL31c
(3)
Signal recognition particle protein
(3)
tRNA CCAend
(3)
26S RIBOSOMAL RNA
(2)
5'-R(*CP*CP*(DA)*(PHE)*(ACA))-3'
(2)
5'-R(*CP*CP*AP*(PHE)*(ACA))-3'
(2)
5'-R(*CP*CP*AP*(PHE)*(ACA)*(BTN))-3'
(2)
CCA
(2)
Large ribosomal subunit protein eL40
(2)
Large ribosomal subunit protein uL1
(2)
RNA (5'-R(*CP*CP*(8AN))-3')
(2)
Ribosome maturation protein SBDS
(2)
SRP 4.5S RNA
(2)
23S rRNA methylase leader peptide
(1)
23S ribosomal RNA, chloroplastic
(1)
25S ribosomal RNA
(1)
4.5S ribosomal RNA
(1)
4.8S rRNA
(1)
4.8S ribosomal RNA, chloroplastic
(1)
5'-D(*(DC)P*(DC)P*(5AA)P*(2OP)P*(PO2)P*AP*C*C)-3')
(1)
5'-R(*(DC)P*(DC)P*(PPU)*(LOF)P*(PO2)P*AP*C*C)-3'
(1)
5'-R(*CP*(5AA)*(HFA))-3'
(1)
5'-R(*CP*CP*(5AA)P*(2OP)P*(PAE)P*AP*C*C)-3')
(1)
5'-R(*CP*CP*(5AA)P*(2OP)P*(PO2)P*(DA)P*C*C)-3')
(1)
5'-R(*CP*CP*(PPU))-3'
(1)
5'-R(*CP*CP*(PPU)*(LOF))-3'
(1)
 
More...
 
Interacting ligands  (2)
CL : CHLORIDE ION
(65)
MG : MAGNESIUM ION
(1)
 
Function and Biology
Biological function  (3)
rRNA binding
(103)
structural constituent of ribosome
(103)
large ribosomal subunit rRNA binding
(6)
 
Biological process  (4)
translation
(103)
cytoplasmic translation
(98)
response to antibiotic
(6)
ribosomal large subunit assembly
(6)
 
Biological cell component  (10)
ribosome
(103)
ribonucleoprotein complex
(100)
cytosolic large ribosomal subunit
(98)
cytoplasm
(7)
cytosol
(7)
chloroplast
(2)
extracellular matrix
(2)
phagocytic vesicle
(2)
peptidoglycan-based cell wall
(1)
plasma membrane
(1)
 
Sequence and Structure classification
SCOP fold  (2)
Ribosomal protein L6
(46)
Ribosome and ribosomal fragments
(1)
 
SCOP family  (2)
Ribosomal protein L6
(46)
Large subunit
(1)
 
CATH class  (1)
Alpha Beta
(103)
 
CATH topology  (1)
Outer Surface Protein A; domain 3
(103)
 
Pfam accession / name  (1)
PF00347 : Ribosomal_L6
(103)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(89)
 
Diffraction radiation source type  (2)
Synchrotron
(87)
Rotating anode
(1)
 
Diffraction source  (13)
NSLS BEAMLINE X25
(25)
APS BEAMLINE 19-ID
(19)
NSLS BEAMLINE X29A
(16)
APS BEAMLINE 24-ID-C
(9)
SLS BEAMLINE X06SA
(8)
ESRF BEAMLINE ID23-2
(6)
ESRF BEAMLINE ID29
(4)
ESRF BEAMLINE ID23-1
(3)
SLS BEAMLINE X10SA
(3)
ALS BEAMLINE 8.2.2
(2)
APS BEAMLINE 8-BM
(2)
ESRF BEAMLINE BM1A
(1)
RIGAKU RU300
(1)
 
Synchrotron site  (5)
NSLS
(41)
APS
(30)
ESRF
(14)
SLS
(11)
ALS
(2)
 
Diffraction detector type  (3)
CCD
(76)
Pixel
(10)
Image plate
(4)
 
Refinement software  (6)
CNS
(68)
PHENIX
(17)
CNX
(3)
autoBUSTER
(3)
REFMAC
(2)
X-PLOR
(1)
 
EM microscope model  (3)
FEI TITAN KRIOS
(12)
FEI TECNAI ARCTICA
(1)
JEOL 3200FSC
(1)
 
EM detector name  (3)
FEI FALCON II (4k x 4k)
(12)
FEI FALCON III (4k x 4k)
(1)
GATAN K2 SUMMIT (4k x 4k)
(1)
 
NMR
NMR software packages  (6)
CYANA
(1)
KUJIRA
(1)
NMRPipe
(1)
NMRView
(1)
Olivia
(1)
XwinNMR
(1)
 
NMR Field Strength
600.0 - 700
(1)
700.0 - 800
(1)
 
Representative Structures
Representative Structures
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Entries 1 to 10 of 103
Entries 1 to 10 of 103
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Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP)
Zhu X, Zhou D, Ye K
Protein Cell (2019) [PMID: 29557065  ]
Assembly composition: RNA/protein complex
PDBe complex ID: PDB-CPX-249981 (Preferred)   search this ID
PDBe-KB: P05738    P36105    P10664    P0CX49    P53136    Q08235    (view 25 more)
Electron Microscopy
3.65Å resolution
Released: 11 Apr 2018
Model geometry
Fit model/data
Data not analysed
5z3g
5z3g
5z3g
Cryo-EM structure of the large ribosomal subunit from Mycobacterium tuberculosis bound with a potent linezolid analog
Yang K, Chang J-Y, Cui Z, Zhang J
Nucleic Acids Res (2017) [PMID: 28977617  ]
Assembly composition: RNA/protein complex
Bound ligands: 917    917   
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-235792 (Preferred)   search this ID
PDBe-KB: P9WH81    P0DV54    P9WH89    P9WH87    P9WHC9    P9WHB5    (view 23 more)
Electron Microscopy
3.7Å resolution
Released: 20 Sep 2017
Model geometry
Fit model/data
Data not analysed
5v7q
5v7q
5v7q
The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with lefamulin
Eyal Z, Matzov D, Krupkin M, Rozenberg H, Zimmerman E, Bashan A, Yonath A
Sci Rep (2016) [PMID: 27958389  ]
Assembly composition: RNA/protein complex
Bound ligands: MPD    SPD    MG    EOH    MN    MG    MN    62B    EPE   
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-140918 (Preferred)   search this ID
PDBe-KB: Q2FW21    Q2FW18    Q2FW13    Q2FXQ1    Q2FXQ0    Q2FW33    (view 20 more)
X-ray diffraction
3.55Å resolution
Released: 21 Dec 2016
Model geometry
Fit model/data
5hl7
5hl7
5hl7
The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin
Yonath A
Proc Natl Acad Sci U S A (2016) [PMID: 27791159  ]
Assembly composition: RNA/protein complex
Bound ligands: MG    6O1    MG    6O1   
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-155888 (Preferred)   search this ID
PDBe-KB: Q9RSL3    Q9RY65    Q9RSL0    Q9RSS4    Q9RSW6    Q9RXY1    (view 20 more)
X-ray diffraction
3.58Å resolution
Released: 9 Nov 2016
Model geometry
Fit model/data
5jvh
5jvh
5jvh
The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin
Krupkin M, Wekselman I, Matzov D, Eyal Z, Diskin Posner Y, Rozenberg H, Zimmerman E, Bashan A, Yonath A
Proc Natl Acad Sci U S A (2016) [PMID: 27791159  ]
Assembly composition: RNA/protein complex
Bound ligands: MPD    SPD    MG    6NO    6NO    MG   
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-155885 (Preferred)   search this ID
PDBe-KB: Q9RSL3    Q9RY65    Q9RSL0    Q9RSS4    Q9RSW6    Q9RXY1    (view 21 more)
X-ray diffraction
3.428Å resolution
Released: 9 Nov 2016
Model geometry
Fit model/data
5jvg
5jvg
5jvg
Structure of the large subunit of the chloro-ribosome
Ahmed T, Yin Z, Bhushan S
Sci Rep (2016) [PMID: 27762343  ]
Source organism: Spinacia oleracea  
Assembly composition: RNA/protein complex
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-249740 (Preferred)   search this ID
PDBe-KB: P82193    P12629    P82190    P82245    P06509    P82191    (view 23 more)
Electron Microscopy
3.5Å resolution
Released: 1 Feb 2017
Model geometry
Fit model/data
Data not analysed
5h1s
5h1s
5h1s
RNC in complex with a translocating SecYEG
Jomaa A, Boehringer D, Leibundgut M, Ban N
Nat Commun (2016) [PMID: 26804923  ]
Source organism: Escherichia coli  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
PDBe complex ID: PDB-CPX-249954 (Preferred)   search this ID
PDBe-KB: P0AG55    P60422    P0A7J7    P0ADY7    P61175    P68919    (view 26 more)
Electron Microscopy
3.33Å resolution
Released: 27 Jan 2016
Model geometry
Fit model/data
Data not analysed
5gae
5gae
5gae
RNC in complex with SRP with detached NG domain
Jomaa A, Boehringer D, Leibundgut M, Ban N
Nat Commun (2016) [PMID: 26804923  ]
Source organism: Escherichia coli  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
PDBe complex ID: PDB-CPX-249769 (Preferred)   search this ID
PDBe-KB: P0AG55    P60422    P0A7J7    P0ADY7    P61175    P68919    (view 26 more)
Electron Microscopy
3.8Å resolution
Released: 27 Jan 2016
Model geometry
Fit model/data
Data not analysed
5gah
5gah
5gah
RNC in complex with SRP-SR in the closed state
Jomaa A, Boehringer D, Leibundgut M, Ban N
Nat Commun (2016) [PMID: 26804923  ]
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
PDBe complex ID: PDB-CPX-249768 (Preferred)   search this ID
PDBe-KB: P0AG55    P60422    P0A7J7    P0ADY7    P61175    P68919    (view 26 more)
Electron Microscopy
3.8Å resolution
Released: 27 Jan 2016
Model geometry
Fit model/data
Data not analysed
5gag
5gag
5gag
Structure of the 50S large subunit of chloroplast ribosome from spinach
Ahmed T, Shi J, Bhushan S
Nucleic Acids Res (2017) [PMID: 28582576  ]
Source organism: Spinacia oleracea  
Assembly composition: RNA/protein complex
Assembly name: Large ribosomal protein and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-129290 (Preferred)   search this ID
PDBe-KB: P82193    P12629    P82190    P82245    P27684    P06509    (view 23 more)
Electron Microscopy
3.3Å resolution
Released: 7 Jun 2017
Model geometry
Fit model/data
Data not analysed
5x8t
5x8t
5x8t
...
Entries 1 to 10 of 103
Entries 1 to 10 of 103