8PQL: Ubiquitin-conjugating enzyme E2 R2
K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide. Determined by electron microscopy at 3.76 Å resolution. Released 14 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 3.76 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 13,553
- Mol. weight
- 377.62 kDa
- Ligands
- SY8, ZN
- Released
- 14 Feb 2024
Explore 8PQL in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8PQL contains 81 α-helices and 49 β-strands across 8 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: 31 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-25 | 14 | |
| α-helix | 32-38 | 7 | |
| α-helix | 41-46 | 6 | |
| α-helix | 54-78 | 25 | |
| α-helix | 87-104 | 18 | |
| α-helix | 106-110 | 5 | |
| α-helix | 139-152 | 14 | |
| α-helix | 157-167 | 11 | |
| α-helix | 178-189 | 12 | |
| α-helix | 192-194 | 3 | |
| α-helix | 201-203 | 3 | |
| α-helix | 204-208 | 5 | |
| α-helix | 209-228 | 20 | |
| α-helix | 236-251 | 16 | |
| α-helix | 260-272 | 13 | |
| α-helix | 275-287 | 13 | |
| α-helix | 291-301 | 11 | |
| α-helix | 308-328 | 21 | |
| α-helix | 337-357 | 21 | |
| α-helix | 362-376 | 15 | |
| α-helix | 388-399 | 12 | |
| α-helix | 410-422 | 13 | |
| α-helix | 428-444 | 17 | |
| α-helix | 454-464 | 11 | |
| α-helix | 471-490 | 20 | |
| α-helix | 492-495 | 4 | |
| β-strand | 506-512 | 7 | 8 |
| α-helix | 521-523 | 3 | |
| α-helix | 531-547 | 17 | |
| β-strand | 552-555 | 4 | 8 |
| β-strand | 561-566 | 6 | 8 |
| β-strand | 573-578 | 6 | 8 |
| α-helix | 579-590 | 12 | |
| β-strand | 593-595 | 3 | 13 |
| α-helix | 596-601 | 6 | |
| α-helix | 607-620 | 14 | |
| β-strand | 623-625 | 3 | 13 |
| β-strand | 637-640 | 4 | 13 |
Chain C: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-20 | 13 | |
| β-strand | 40 | 1 | 1 |
| β-strand | 44-45 | 2 | 2 |
| β-strand | 58-59 | 2 | 2 |
| β-strand | 60-63 | 4 | 1 |
| β-strand | 74-77 | 4 | 1 |
| β-strand | 86 | 1 | 3 |
| β-strand | 91 | 1 | 1 |
| β-strand | 92 | 1 | 3 |
| α-helix | 95-97 | 3 | |
| α-helix | 120-132 | 13 | |
| α-helix | 142-154 | 13 | |
| α-helix | 160-179 | 20 | |
Chain D: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 14 |
| β-strand | 28-32 | 5 | 14 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-44 | 5 | |
| β-strand | 48 | 1 | 15 |
| β-strand | 50 | 1 | 15 |
| β-strand | 59-61 | 3 | 14 |
| α-helix | 67-82 | 16 | |
| α-helix | 91-94 | 4 | |
| α-helix | 100-109 | 10 | |
Chain E: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 4 |
| β-strand | 6 | 1 | 5 |
| β-strand | 12 | 1 | 5 |
| β-strand | 15-16 | 2 | 4 |
| α-helix | 23-33 | 11 | |
| β-strand | 44-45 | 2 | 5 |
| β-strand | 48-49 | 2 | 5 |
| β-strand | 68 | 1 | 5 |
Chain G: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 14 |
| β-strand | 10 | 1 | 16 |
| β-strand | 12-17 | 6 | 14 |
| β-strand | 23 | 1 | 17 |
| α-helix | 24-35 | 12 | |
| α-helix | 39-41 | 3 | |
| β-strand | 56 | 1 | 17 |
| β-strand | 73-76 | 4 | 14 |
| β-strand | 90 | 1 | 16 |
| α-helix | 91-96 | 6 | |
Chain H: 31 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| β-strand | 39 | 1 | 6 |
| β-strand | 42 | 1 | 6 |
| α-helix | 44-50 | 7 | |
| α-helix | 54-63 | 10 | |
| β-strand | 72-74 | 3 | 7 |
| β-strand | 81-84 | 4 | 7 |
| α-helix | 86-93 | 8 | |
| α-helix | 96-105 | 10 | |
| α-helix | 119-126 | 8 | |
| α-helix | 129-136 | 8 | |
| α-helix | 152-158 | 7 | |
| α-helix | 164-170 | 7 | |
| α-helix | 185-190 | 6 | |
| α-helix | 195-203 | 9 | |
| α-helix | 217-224 | 8 | |
| α-helix | 229-234 | 6 | |
| α-helix | 241-257 | 17 | |
| α-helix | 263-277 | 15 | |
| α-helix | 315-329 | 15 | |
| α-helix | 335-350 | 16 | |
| α-helix | 355-369 | 15 | |
| α-helix | 377-394 | 18 | |
| α-helix | 408-426 | 19 | |
| α-helix | 435-453 | 19 | |
| α-helix | 459-474 | 16 | |
| α-helix | 485-489 | 5 | |
| α-helix | 494-496 | 3 | |
| α-helix | 508-517 | 10 | |
| α-helix | 531-537 | 7 | |
| α-helix | 541-548 | 8 | |
| α-helix | 570-575 | 6 | |
| α-helix | 581-583 | 3 | |
| α-helix | 586-597 | 12 | |
| α-helix | 607-615 | 9 | |
Chain K: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-34 | 9 | 8 |
| β-strand | 41-42 | 2 | 9 |
| β-strand | 47-48 | 2 | 9 |
| α-helix | 54-57 | 4 | |
| α-helix | 82-88 | 7 | |
Chain U: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 10 |
| β-strand | 6 | 1 | 11 |
| β-strand | 13-15 | 3 | 10 |
| β-strand | 22 | 1 | 12 |
| α-helix | 23-34 | 12 | |
| β-strand | 41-44 | 4 | 11 |
| β-strand | 49 | 1 | 11 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 12 |
| α-helix | 56-58 | 3 | |
| β-strand | 68-71 | 4 | 11 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin-conjugating enzyme E2 R2 | C | protein | 238 | Homo sapiens | Q712K3 (AlphaFold model) |
| Polyubiquitin-C,Nucleotide exchange factor SIL1 | E | protein | 704 | Homo sapiens | P0CG48 (AlphaFold model), Q9H173 (AlphaFold model) |
| Protein fem-1 homolog C | H | protein | 617 | Homo sapiens | Q96JP0 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1 | K | protein | 108 | Homo sapiens | P62877 |
| Ubiquitin | U | protein | 685 | Homo sapiens | P0CG48 (AlphaFold model) |
| Cullin-2 | A | protein | 745 | Homo sapiens | Q13617 |
| Elongin-C | D | protein | 112 | Homo sapiens | Q15369 |
| Elongin-B | G | protein | 118 | Homo sapiens | Q15370 |
Sequence of entity 1 (C), FASTA
>8PQL_1 Ubiquitin-conjugating enzyme E2 R2 (chains C)
MAQQQMTSSQKALMLELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYFKA
HIKFPIDYPYSPPTFRFLTKMWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNV
RTILLSVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKEYAEIIRKQVSATKAEAEKDG
VKVPTTLAEYCIKTKVPSNDNSSDLLYDDLYDDDIDDEDEEEEDADCYDDDDSGNEES
Sequence of entity 2 (E), FASTA
>8PQL_2 Polyubiquitin-C,Nucleotide exchange factor SIL1 (chains E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKA
KIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKT
ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
LRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIE
NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL
TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH
LVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLED
GRTLSDYNIQKESTLHLVLRLRGGVEGYFQELLGSVNPTQGRAR
Sequence of entity 3 (H), FASTA
>8PQL_3 Protein fem-1 homolog C (chains H)
MDLKTAVFNAARDGKLRLLTKLLASKSKEEVSSLISEKTNGATPLLMAARYGHLDMVEFL
LEQCSASIEVGGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLNHGASVNNTTLTNSTPL
RAACFDGHLEIVKYLVEHKADLEVSNRHGHTCLMISCYKGHKEIAQYLLEKGADVNRKSV
KGNTALHDCAESGSLDIMKMLLMYCAKMEKDGYGMTPLLSASVTGHTNIVDFLTHHAQTS
KTERINALELLGATFVDKKRDLLGALKYWKKAMNMRYSDRTNIISKPVPQTLIMAYDYAK
EVNSAEELEGLIADPDEMRMQALLIRERILGPSHPDTSYYIRYRGAVYADSGNFKRCINL
WKYALDMQQSNLDPLSPMTASSLLSFAELFSFMLQDRAKGLLGTTVTFDDLMGILCKSVL
EIERAIKQTQCPADPLQLNKALSIILHLICLLEKVPCTLEQDHFKKQTIYRFLKLHPRGK
NNFSPLHLAVDKNTTCVGRYPVCKFPSLQVTAILIECGADVNVRDSDDNSPLHIAALNNH
PDIMNLLIKSGAHFDATNLHKQTASDLLDEKEIAKNLIQPINHTTLQCLAARVIVNHRIY
YKGHIPEKLETFVSLHR
Sequence of entity 4 (K), FASTA
>8PQL_4 E3 ubiquitin-protein ligase RBX1 (chains K)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 5 (U), FASTA
>8PQL_5 Ubiquitin (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKA
KIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKT
ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
LRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIE
NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL
TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH
LVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLED
GRTLSDYNIQKESTLHLVLRLRGGV
Sequence of entity 6 (A), FASTA
>8PQL_6 Cullin-2 (chains A)
MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA
Sequence of entity 7 (D), FASTA
>8PQL_7 Elongin-C (chains D)
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Sequence of entity 8 (G), FASTA
>8PQL_8 Elongin-B (chains G)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SY8 | 5-azanylpentan-2-one | C5 H11 N O | 1 |
| ZN | Zinc ion | Zn | 3 |
Primary citation
Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases. Liwocha, J., Li, J., Purser, N. et al. Nat Struct Mol Biol (2024) 31:378-389. DOI 10.1038/s41594-023-01206-1 · PubMed
Other PDB entries of the same protein (UniProt Q712K3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6NYO 1.5 Å, Crystal structure of a human Cdc34-ubiquitin thioester mimetic
- 8R5H 3.44 Å, Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34:…
- 8Q7R 3.71 Å, Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34:…
Browse structure collections
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