1Y8X: Ubiquitin-conjugating enzyme E2 M

Structural basis for recruitment of Ubc12 by an E2-binding domain in NEDD8's E1. Determined by X-ray diffraction at 2.4 Å resolution. Released 8 Feb 2005.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,114
Mol. weight: 29.34 kDa
Released: 8 Feb 2005

Explore 1Y8X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Y8X contains 10 α-helices and 20 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	29-39	11
β-strand	47-50	4	1
β-strand	59-64	6	1
β-strand	74	1	2
β-strand	76-81	6	1
α-helix	90-91	2
β-strand	92-95	4	1
β-strand	101	1	3
β-strand	104	1	3
β-strand	109	1	1
β-strand	110	1	3
α-helix	113-115	3
α-helix	125-137	13
α-helix	147-154	8
α-helix	157-169	13
β-strand	171-173	3	4
β-strand	176-178	3	4
β-strand	182	1	2

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	353-354	2	5
β-strand	360	1	6
α-helix	361-370	10
β-strand	380-385	6	7
β-strand	388-393	6	7
α-helix	398-409	12
β-strand	411	1	6
α-helix	413-415	3
α-helix	421	1
β-strand	422-426	5	7
β-strand	434-437	4	7
β-strand	438-439	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 M	A	protein	160	Homo sapiens	P61081 (AlphaFold model)
Ubiquitin-activating enzyme E1C	B	protein	98	Homo sapiens	Q8TBC4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1Y8X_1 Ubiquitin-conjugating enzyme E2 M (chains A)
GSMASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLVICPDEGFYKSGKFVFSFKVG
QGYPHDPPKVKCETMVYHPNIDLEGNVCLNILREDWKPVLTINSIIYGLQYLFLEPNPED
PLNKEAAEVLQNNRRLFEQNVQRSMRGGYIGSTYFERCLK

Sequence of entity 2 (B), FASTA

>1Y8X_2 Ubiquitin-activating enzyme E1C (chains B)
GSSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSVTSIEERT
RPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS

Primary citation

Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1. Huang, D.T., Paydar, A., Zhuang, M. et al. Mol Cell (2005) 17:341-350. DOI 10.1016/j.molcel.2004.12.020 · PubMed

Other PDB entries of the same protein (UniProt P61081 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
1TT5 2.6 Å, Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction required for optimal…
2NVU 2.8 Å, Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like…
4P5O 3.11 Å, Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like…
4GAO 3.28 Å, DCNL complex with N-terminally acetylated NEDD8 E2 peptide

Browse structure collections

About this viewer

MolViewer shows 1Y8X directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.