Uniprot accession / id : P61082  OR   Uniprot accession / id : P61081  OR   Uniprot accession / id : A0A024R4T4  OR   Uniprot accession / id : M0QYI6
 
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revised
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Entry Information
Entry status  (1)
REL
(7)
 
Experimental methods  (1)
X-ray diffraction
(7)
 
Authors  (22)
Schulman BA
(7)
Harper JW
(4)
Monda JK
(4)
Scott DC
(4)
Bennett EJ
(3)
Holton JM
(3)
Huang DT
(3)
Zhuang M
(2)
Cassell R
(1)
Cho SE
(1)
Hunt HW
(1)
King D
(1)
Lydeard J
(1)
Lydeard JR
(1)
Mathew R
(1)
Miller DJ
(1)
Miller DW
(1)
Ohi MD
(1)
Paydar A
(1)
Roussel MF
(1)
Sviderskiy VO
(1)
Waddell MB
(1)
 
Homo / hetero assembly  (1)
hetero
(7)
 
Assembly composition  (1)
protein/protein complex
(7)
 
Assembly polymer count  (3)
trimer
(3)
dimer
(2)
pentamer
(2)
 
Resolution distribution
1.0 - 1.5
(1)
1.5 - 2
(1)
2.0 - 2.5
(1)
2.5 - 3
(2)
3.0 - 3.5
(2)
 
Release year distribution
2000 - 2005
(2)
2005 - 2010
(2)
2010 - 2015
(4)
 
Journal  (6)
Science
(2)
Cell
(1)
Mol Cell
(1)
Nat Struct Mol Biol
(1)
Nature
(1)
Structure
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(7)
 
Organism name  (1)
Homo sapiens
(7)
 
Molecule name  (3)
NEDD8 carrier protein
(7)
NEDD8-conjugating enzyme Ubc12
(7)
Ubiquitin-conjugating enzyme E2 M
(7)
 
Molecule type  (1)
Protein
(7)
 
Gene names  (2)
UBC12
(7)
UBE2M
(7)
 
Interacting Molecules  (7)
Cullin-1
(3)
DCN1-like protein 1
(3)
NEDD8-activating enzyme E1 catalytic subunit
(3)
NEDD8-activating enzyme E1 regulatory subunit
(2)
Ubiquitin-like protein NEDD8
(2)
DCN1-like protein 2
(1)
E3 ubiquitin-protein ligase RBX1
(1)
 
Function and Biology
EC number / name  (1)
2.3.2.34 : E2 NEDD8-conjugating enzyme
(7)
 
Biological function  (8)
ATP binding
(2)
NEDD8 conjugating enzyme activity
(2)
NEDD8 transferase activity
(2)
nucleotide binding
(2)
protein binding
(2)
transferase activity
(2)
ubiquitin-like protein transferase activity
(2)
ubiquitin-protein transferase activity
(2)
 
Biological process  (5)
post-translational protein modification
(2)
protein modification by small protein conjugation
(2)
protein modification process
(2)
protein neddylation
(2)
regulation of postsynapse assembly
(2)
 
Biological cell component  (6)
cytosol
(2)
glutamatergic synapse
(2)
nucleoplasm
(2)
nucleus
(2)
postsynapse
(2)
presynapse
(2)
 
Sequence and Structure classification
SCOP fold  (1)
UBC-like
(2)
 
SCOP family  (1)
UBC-related
(2)
 
CATH class  (1)
Alpha Beta
(3)
 
CATH topology  (1)
Ubiquitin Conjugating Enzyme
(3)
 
Pfam accession / name  (1)
PF00179 : UQ_con
(3)
 
Experimental Information
Diffraction protocol  (2)
Single wavelength
(6)
MAD
(1)
 
Diffraction radiation source type  (1)
Synchrotron
(7)
 
Diffraction source  (7)
ALS BEAMLINE 8.3.1
(2)
APS BEAMLINE 19-ID
(2)
APS BEAMLINE 22-ID
(2)
APS BEAMLINE 24-ID-E
(2)
NSLS BEAMLINE X25
(2)
ALS BEAMLINE 8.2.2
(1)
NSLS BEAMLINE X12B
(1)
 
Synchrotron site  (3)
APS
(6)
ALS
(3)
NSLS
(2)
 
Refinement software  (3)
REFMAC
(3)
CNS
(2)
PHENIX
(1)
 
Representative Structures
Representative Structures
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Entries 1 to 7 of 7
Entries 1 to 7 of 7
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Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8
Huang DT, Miller DW, Mathew R, Cassell R, Holton JM, Roussel MF, Schulman BA
Nat Struct Mol Biol (2004) [PMID: 15361859  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Bound ligands: ZN    ZN   
Assembly name: NEDD8 E1 activating enzyme complex, NAE1-UBA3 and NEDD8-conjugating enzyme Ubc12 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-158198 (Preferred)   search this ID
PDBe-KB: P61081    Q13564    Q8TBC4   
X-ray diffraction
2.6Å resolution
Released: 14 Sep 2004
Model geometry
Fit model/data
1tt5
1tt5
1tt5
Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex
Huang DT, Hunt HW, Zhuang M, Ohi MD, Holton JM, Schulman BA
Nature (2007) [PMID: 17220875  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Bound ligands: MG    ZN    ZN    ATP    MG    ATP   
Assembly name: NEDD8 E1 activating enzyme complex, NAE1-UBA3 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-158197 (Preferred)   search this ID
PDBe-KB: P61081    Q15843    Q13564    Q8TBC4   
X-ray diffraction
2.8Å resolution
Released: 30 Jan 2007
Model geometry
Fit model/data
2nvu
2nvu
2nvu
Structural basis for recruitment of Ubc12 by an E2-binding domain in NEDD8's E1
Huang DT, Paydar A, Zhuang M, Waddell MB, Holton JM, Schulman BA
Mol Cell (2005) [PMID: 15694336  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Modified residues: MSE    MSE   
Assembly name: NEDD8-conjugating enzyme Ubc12 and NEDD8-activating enzyme E1 catalytic subunit (Preferred)   search this complex
PDBe complex ID: PDB-CPX-158201 (Preferred)   search this ID
PDBe-KB: P61081    Q8TBC4   
X-ray diffraction
2.4Å resolution
Released: 8 Feb 2005
Model geometry
Fit model/data
1y8x
1y8x
1y8x
Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action
Scott DC, Schulman BA
Cell (2014) [PMID: 24949976  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Bound ligands: ZN    ZN   
Modified residues: AME    AME   
PDBe complex ID: PDB-CPX-158196 (Preferred)   search this ID
PDBe-KB: P61081    Q15843    Q96GG9    Q13616    P62877   
X-ray diffraction
3.1071Å resolution
Released: 2 Jul 2014
Model geometry
Fit model/data
4p5o
4p5o
4p5o
N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex
Scott DC, Monda JK, Bennett EJ, Harper JW, Schulman BA
Science (2011) [PMID: 21940857  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Modified residues: ACE    ACE   
PDBe complex ID: PDB-CPX-158199 (Preferred)   search this ID
PDBe-KB: P61081    Q96GG9    Q13616   
X-ray diffraction
1.5Å resolution
Released: 12 Oct 2011
Model geometry
Fit model/data
3tdu
3tdu
3tdu
DCNL complex with N-terminally acetylated NEDD8 E2 peptide
Monda JK, Scott DC, Miller DJ, Harper JW, Bennett EJ, Schulman BA
Structure (2013) [PMID: 23201271  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Bound ligands: BR   
Modified residues: AME    AME   
Assembly name: NEDD8-conjugating enzyme Ubc12 and DCN1-like protein 2 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-158200 (Preferred)   search this ID
PDBe-KB: P61081    Q6PH85   
X-ray diffraction
3.28Å resolution
Released: 28 Nov 2012
Model geometry
Fit model/data
4gao
4gao
4gao
N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-stapled acetylated Ubc12N complex
Scott DC, Monda JK, Bennett EJ, Harper JW, Schulman BA
Science (2011) [PMID: 21940857  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Modified residues: MSE    ACE    MSE    ACE    MK8    MK8   
PDBe complex ID: PDB-CPX-158199 (Preferred)   search this ID
PDBe-KB: P61081    Q96GG9    Q13616   
X-ray diffraction
2Å resolution
Released: 12 Oct 2011
Model geometry
Fit model/data
3tdz
3tdz
3tdz
Entries 1 to 7 of 7
Entries 1 to 7 of 7