3JVZ: E2~Ubiquitin-HECT

E2~Ubiquitin-HECT. Determined by X-ray diffraction at 3.3 Å resolution. Released 12 Jan 2010.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,814
Mol. weight: 141.94 kDa
Released: 12 Jan 2010

Explore 3JVZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JVZ contains 70 α-helices and 61 β-strands across 6 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
α-helix	13-15	3
β-strand	21-25	5	1
β-strand	32-38	7	1
β-strand	49-55	7	1
α-helix	64-65	2
β-strand	66-69	4	1
β-strand	75	1	2
β-strand	78	1	2
β-strand	83	1	1
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-128	8
α-helix	131-141	11
α-helix	142-146	5

Chain B: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	17-18	2
β-strand	21-25	5	3
β-strand	32-38	7	3
α-helix	39-40	2
β-strand	49-55	7	3
α-helix	64-65	2
β-strand	66-69	4	3
β-strand	75	1	4
β-strand	78	1	4
β-strand	84	1	4
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-128	8
α-helix	131-141	11
α-helix	142-146	5

Chain C: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	575-587	13
β-strand	597-601	5	5
α-helix	604-606	3
α-helix	607-615	9
α-helix	623-625	3
β-strand	627-631	5	5
α-helix	643-655	13
β-strand	663-665	3	6
β-strand	673-675	3	6
α-helix	686-702	17
β-strand	711	1	6
α-helix	713-720	8
α-helix	726-728	3
α-helix	729-732	4
α-helix	734-745	12
β-strand	754	1	7
β-strand	756-758	3	8
β-strand	761	1	9
β-strand	764	1	9
β-strand	767-769	3	8
β-strand	778	1	7
α-helix	784-792	9
α-helix	793-797	5
α-helix	798-800	3
α-helix	801-811	11
α-helix	817-820	4
α-helix	825-833	9
α-helix	840-844	5
β-strand	848-850	3	10
α-helix	858-869	12
α-helix	872-883	12
α-helix	893-895	3
β-strand	897-899	3	11
β-strand	901-902	2	11
β-strand	906-909	4	10
α-helix	916-917	2
β-strand	918-920	3	10
β-strand	925-928	4	10
α-helix	934-946	13

Chain D: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	577-587	11
β-strand	597-603	7	12
α-helix	604-606	3
α-helix	607-616	10
α-helix	621-624	4
β-strand	627-633	7	12
β-strand	639-641	3	12
α-helix	644-655	12
α-helix	658-660	3
β-strand	663-665	3	13
β-strand	673-675	3	13
α-helix	679-682	4
α-helix	686-703	18
β-strand	711	1	13
α-helix	713-720	8
α-helix	726-728	3
α-helix	729-732	4
α-helix	734-745	12
α-helix	749-751	3
β-strand	754	1	14
β-strand	756-761	6	15
β-strand	764-769	6	15
α-helix	774-776	3
β-strand	778	1	14
α-helix	784-796	13
α-helix	798-800	3
α-helix	801-811	11
α-helix	817-820	4
α-helix	827-832	6
α-helix	840-845	6
β-strand	848-850	3	16
α-helix	858-869	12
α-helix	872-883	12
α-helix	893-895	3
β-strand	897-899	3	17
β-strand	901-902	2	17
β-strand	906-909	4	16
α-helix	916-917	2
β-strand	918-920	3	16
β-strand	925-928	4	16
α-helix	937-945	9

Chain X: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	18
β-strand	12-16	5	18
β-strand	22	1	19
α-helix	23-30	8
α-helix	38-40	3
β-strand	43-44	2	18
β-strand	49	1	18
β-strand	55	1	19
β-strand	66-69	4	18

Chain Y: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	20
β-strand	12-15	4	20
α-helix	23-29	7
α-helix	31-34	4
α-helix	38-40	3
β-strand	41-44	4	21
β-strand	49	1	21
α-helix	50-51	2
β-strand	65-66	2	20
β-strand	68-71	4	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	A, B	protein	146	Homo sapiens	P62837 (AlphaFold model)
E3 ubiquitin-protein ligase NEDD4-like	C, D	protein	385	Homo sapiens	Q96PU5 (AlphaFold model)
Ubiquitin	X, Y	protein	81	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3JVZ_1 Ubiquitin-conjugating enzyme E2 D2 (chains A, B)
ASKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP
FKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALKISKVLLSICSLLCDPNPDDPLVP
EIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 2 (C, D), FASTA

>3JVZ_2 E3 ubiquitin-protein ligase NEDD4-like (chains C, D)
GSPEFEFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWI
EFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYF
TFIGRVAGLAVFHGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTE
LDLMFCIDEENFGQTYQVDLKPNGSEIMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEG
FTELLPIDLIKIFDENELELLMCGLGDVDVNDWRQHSIYKNGYCPNHPVIQWFWKAVLLM
DAEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQLFTIEQWGSPEKLPRAHTAFNRLDLPP
YETFEDLREKLLMAVENAQGFEGVD

Sequence of entity 3 (X, Y), FASTA

>3JVZ_3 Ubiquitin (chains X, Y)
GSGGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGG

Primary citation

Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. Kamadurai, H.B., Souphron, J., Scott, D.C. et al. Mol Cell (2009) 36:1095-1102. DOI 10.1016/j.molcel.2009.11.010 · PubMed

Other PDB entries of the same protein (UniProt P62837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GLS 1.25 Å, Crystal Structure of Human UBCH5B C85E
2ESK 1.36 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
2ESQ 1.44 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
2ESO 1.5 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
2ESP 1.52 Å, Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
7AI0 1.56 Å, Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal…
5D1M 1.58 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
3L1Y 1.6 Å, Crystal structure of human UBC4 E2 conjugating enzyme
5D1L 1.62 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub

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