2GJD: Ubiquitin-conjugating enzyme E2-18 kDa

Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic stress. Determined by X-ray diffraction at 1.75 Å resolution. Released 4 Jul 2006.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 5,493
Mol. weight: 71.75 kDa
Released: 4 Jul 2006

Explore 2GJD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2GJD contains 33 α-helices and 34 β-strands across 4 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: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
β-strand	25-30	6	1
β-strand	36-46	11	1
α-helix	47-48	2
β-strand	56	1	2
β-strand	57-63	7	1
α-helix	72-73	2
β-strand	74-76	3	1
α-helix	77-78	2
β-strand	86	1	3
β-strand	91	1	1
β-strand	92	1	3
α-helix	95-97	3
α-helix	109-120	12
α-helix	131-139	9
α-helix	141-154	14
β-strand	156	1	2

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
β-strand	25-30	6	4
β-strand	36-46	11	4
α-helix	47-48	2
β-strand	56	1	5
β-strand	57-63	7	4
α-helix	72-73	2
β-strand	74-76	3	4
α-helix	77-78	2
β-strand	86	1	6
β-strand	91	1	4
β-strand	92	1	6
α-helix	95-97	3
α-helix	109-121	13
α-helix	131-139	9
α-helix	141-154	14
β-strand	156	1	5

Chain C: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-19	16
α-helix	20-21	2
β-strand	25-30	6	7
β-strand	36-46	11	7
α-helix	47-48	2
β-strand	57-63	7	7
α-helix	72-73	2
β-strand	74-76	3	7
α-helix	77-78	2
β-strand	86	1	8
β-strand	91	1	7
β-strand	92	1	8
α-helix	93	1
α-helix	95-97	3
α-helix	109-121	13
α-helix	131-139	9
α-helix	141-154	14

Chain D: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
β-strand	25-30	6	9
β-strand	36-46	11	9
α-helix	47-48	2
β-strand	56	1	10
β-strand	57-63	7	9
α-helix	72-73	2
β-strand	74-76	3	9
β-strand	86	1	11
β-strand	91	1	9
β-strand	92	1	11
α-helix	95-97	3
α-helix	109-120	12
α-helix	131-139	9
α-helix	141-154	14
β-strand	156	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2-18 kDa	A, B, C, D	protein	157	Saccharomyces cerevisiae	P50623 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>2GJD_1 Ubiquitin-conjugating enzyme E2-18 kDa (chains A, B, C, D)
MSSLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPI
TVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLL
DSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK

Primary citation

Distinct functional domains of ubc9 dictate cell survival and resistance to genotoxic stress. van Waardenburg, R.C., Duda, D.M., Lancaster, C.S. et al. Mol Cell Biol (2006) 26:4958-4969. DOI 10.1128/MCB.00160-06 · PubMed

Other PDB entries of the same protein (UniProt P50623 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2EKE 1.9 Å, Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a…
3ONG 2.3 Å, Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways
5JNE 2.85 Å, E2-SUMO-Siz1 E3-SUMO-PCNA complex
7P47 3.31 Å, Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic
6Q83 4.53 Å, Crystal structure of the biportin Pdr6 in complex with UBC9

Browse structure collections

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