3JW0: E2~Ubiquitin-HECT
E2~Ubiquitin-HECT. Determined by X-ray diffraction at 3.1 Å resolution. Released 12 Jan 2010.
- Method
- X-ray diffraction
- Resolution
- 3.1 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 9,826
- Mol. weight
- 141.97 kDa
- Released
- 12 Jan 2010
Explore 3JW0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3JW0 contains 65 α-helices and 66 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: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-15 | 13 | |
| β-strand | 21-25 | 5 | 1 |
| β-strand | 32-38 | 7 | 1 |
| β-strand | 49-55 | 7 | 1 |
| α-helix | 56-57 | 2 | |
| 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 | 121-129 | 9 | |
| α-helix | 131-144 | 14 | |
Chain B: 8 helices, 8 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 | 83 | 1 | 3 |
| β-strand | 84 | 1 | 4 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-144 | 14 | |
Chain C: 23 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 576-587 | 12 | |
| β-strand | 597-601 | 5 | 5 |
| α-helix | 604-606 | 3 | |
| α-helix | 607-615 | 9 | |
| α-helix | 621-625 | 5 | |
| β-strand | 627-631 | 5 | 5 |
| α-helix | 643-655 | 13 | |
| β-strand | 663-665 | 3 | 6 |
| β-strand | 672-675 | 4 | 6 |
| α-helix | 686-702 | 17 | |
| β-strand | 710-711 | 2 | 6 |
| α-helix | 713-720 | 8 | |
| α-helix | 722-724 | 3 | |
| α-helix | 726-728 | 3 | |
| α-helix | 734-745 | 12 | |
| α-helix | 749-751 | 3 | |
| β-strand | 754 | 1 | 7 |
| β-strand | 756-761 | 6 | 8 |
| β-strand | 764-769 | 6 | 8 |
| α-helix | 774-776 | 3 | |
| β-strand | 778 | 1 | 7 |
| α-helix | 784-796 | 13 | |
| α-helix | 798-800 | 3 | |
| α-helix | 801-811 | 11 | |
| α-helix | 817-819 | 3 | |
| α-helix | 825-833 | 9 | |
| α-helix | 840-845 | 6 | |
| β-strand | 847-850 | 4 | 9 |
| α-helix | 858-869 | 12 | |
| α-helix | 872-883 | 12 | |
| α-helix | 892-895 | 4 | |
| β-strand | 897-898 | 2 | 10 |
| β-strand | 901-902 | 2 | 10 |
| β-strand | 905-909 | 5 | 9 |
| α-helix | 916-917 | 2 | |
| β-strand | 918-920 | 3 | 9 |
| β-strand | 925-928 | 4 | 9 |
| α-helix | 934-946 | 13 | |
Chain D: 23 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 577-587 | 11 | |
| β-strand | 597-603 | 7 | 11 |
| α-helix | 604-606 | 3 | |
| α-helix | 607-616 | 10 | |
| α-helix | 621-624 | 4 | |
| β-strand | 627-633 | 7 | 11 |
| β-strand | 639-641 | 3 | 11 |
| α-helix | 644-655 | 12 | |
| α-helix | 658-660 | 3 | |
| β-strand | 663-665 | 3 | 12 |
| β-strand | 673-675 | 3 | 12 |
| α-helix | 679-682 | 4 | |
| α-helix | 686-702 | 17 | |
| β-strand | 711 | 1 | 12 |
| α-helix | 713-719 | 7 | |
| α-helix | 729-732 | 4 | |
| α-helix | 734-745 | 12 | |
| α-helix | 749-751 | 3 | |
| β-strand | 754 | 1 | 13 |
| β-strand | 756-761 | 6 | 14 |
| β-strand | 764-769 | 6 | 14 |
| α-helix | 774-776 | 3 | |
| β-strand | 778 | 1 | 13 |
| α-helix | 784-796 | 13 | |
| α-helix | 801-811 | 11 | |
| α-helix | 817-820 | 4 | |
| α-helix | 825-832 | 8 | |
| α-helix | 840-845 | 6 | |
| β-strand | 847-850 | 4 | 15 |
| α-helix | 858-869 | 12 | |
| α-helix | 872-883 | 12 | |
| α-helix | 893-895 | 3 | |
| β-strand | 897-898 | 2 | 16 |
| β-strand | 901-902 | 2 | 16 |
| β-strand | 905-909 | 5 | 15 |
| α-helix | 916-917 | 2 | |
| β-strand | 918-920 | 3 | 15 |
| β-strand | 925-928 | 4 | 15 |
| α-helix | 934-945 | 12 | |
Chain X: 2 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 17 |
| β-strand | 4-7 | 4 | 18 |
| β-strand | 12 | 1 | 18 |
| β-strand | 15-16 | 2 | 17 |
| β-strand | 22 | 1 | 19 |
| α-helix | 23-33 | 11 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-43 | 3 | 18 |
| β-strand | 44-45 | 2 | 20 |
| β-strand | 48-49 | 2 | 20 |
| β-strand | 55 | 1 | 19 |
| β-strand | 66-71 | 6 | 18 |
| β-strand | 74 | 1 | 9 |
Chain Y: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 21 |
| β-strand | 12-16 | 5 | 21 |
| β-strand | 22 | 1 | 22 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 43-45 | 3 | 21 |
| β-strand | 48-49 | 2 | 21 |
| β-strand | 55 | 1 | 22 |
| β-strand | 66-69 | 4 | 21 |
| β-strand | 74 | 1 | 15 |
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
>3JW0_1 Ubiquitin-conjugating enzyme E2 D2 (chains A, B)
ASKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP
FKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALKISKVLLSICSLLCDPNPDDPLVP
EIARIYKTDREKYNRIAREWTQKYAM
Sequence of entity 2 (C, D), FASTA
>3JW0_2 E3 ubiquitin-protein ligase NEDD4-like (chains C, D)
GSPEFEFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWI
EFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYF
TFIGRVAGLAVFHGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTE
LDLMFCIDEENFGQTYQVDLKPNGSEIMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEG
FTELLPIDLIKIFDENELELLMCGLGDVDVNDWRQHSIYKNGYCPNHPVIQWFWKAVLLM
DAEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQLFTIEQWGSPEKLPRAHTSFNRLDLPP
YETFEDLREKLLMAVENAQGFEGVD
Sequence of entity 3 (X, Y), FASTA
>3JW0_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
Browse structure collections
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