9T7V: LRRC58-EloB/C-CDO1
Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub. Determined by electron microscopy at 2.95 Å resolution. Released 20 May 2026.
- Method
- Electron microscopy
- Resolution
- 2.95 Å
- Organism
- Homo sapiens
- Chains
- 9
- Atoms
- 15,047
- Mol. weight
- 268 kDa
- Ligands
- FE, SY8, ZN
- Released
- 20 May 2026
Explore 9T7V in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9T7V contains 85 α-helices and 80 β-strands across 9 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: 4 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-22 | 11 | |
| α-helix | 30-39 | 10 | |
| α-helix | 41-42 | 2 | |
| β-strand | 61-64 | 4 | 1 |
| α-helix | 66-68 | 3 | |
| β-strand | 71-77 | 7 | 1 |
| β-strand | 82 | 1 | 2 |
| β-strand | 86 | 1 | 2 |
| β-strand | 92-99 | 8 | 1 |
| β-strand | 102-107 | 6 | 2 |
| β-strand | 122-125 | 4 | 2 |
| β-strand | 130-133 | 4 | 1 |
| β-strand | 139-143 | 5 | 2 |
| β-strand | 151-158 | 8 | 1 |
| β-strand | 164-167 | 4 | 2 |
| β-strand | 174-177 | 4 | 2 |
| β-strand | 183-184 | 2 | 1 |
| β-strand | 187-188 | 2 | 1 |
Chain B: 8 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 48-52 | 5 | 20 |
| β-strand | 72-76 | 5 | 20 |
| β-strand | 95-99 | 5 | 20 |
| β-strand | 124-126 | 3 | 20 |
| α-helix | 138-141 | 4 | |
| β-strand | 147-149 | 3 | 20 |
| α-helix | 160-164 | 5 | |
| β-strand | 171-172 | 2 | 20 |
| α-helix | 183-187 | 5 | |
| β-strand | 194-195 | 2 | 20 |
| α-helix | 206-210 | 5 | |
| β-strand | 216-218 | 3 | 20 |
| β-strand | 227-228 | 2 | 21 |
| α-helix | 229-233 | 5 | |
| β-strand | 239-241 | 3 | 20 |
| α-helix | 259-261 | 3 | |
| α-helix | 262-273 | 12 | |
| α-helix | 284-291 | 8 | |
| β-strand | 295 | 1 | 22 |
| β-strand | 304 | 1 | 22 |
| β-strand | 310-316 | 7 | 21 |
| β-strand | 324-330 | 7 | 21 |
Chain C: 40 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-30 | 12 | |
| α-helix | 37-51 | 15 | |
| α-helix | 57-80 | 24 | |
| α-helix | 86-102 | 17 | |
| α-helix | 103-105 | 3 | |
| α-helix | 113-117 | 5 | |
| α-helix | 135-143 | 9 | |
| α-helix | 144-148 | 5 | |
| α-helix | 149-168 | 20 | |
| α-helix | 175-187 | 13 | |
| α-helix | 203-224 | 22 | |
| α-helix | 227-248 | 22 | |
| α-helix | 258-269 | 12 | |
| α-helix | 271-273 | 3 | |
| α-helix | 274-278 | 5 | |
| α-helix | 281-285 | 5 | |
| α-helix | 292-300 | 9 | |
| α-helix | 308-328 | 21 | |
| α-helix | 337-359 | 23 | |
| α-helix | 363-377 | 15 | |
| α-helix | 404-416 | 13 | |
| β-strand | 417 | 1 | 11 |
| α-helix | 420-423 | 4 | |
| α-helix | 427-440 | 14 | |
| α-helix | 441-443 | 3 | |
| α-helix | 447-464 | 18 | |
| β-strand | 467 | 1 | 11 |
| α-helix | 470-483 | 14 | |
| α-helix | 487-513 | 27 | |
| α-helix | 523-525 | 3 | |
| β-strand | 526-532 | 7 | 3 |
| α-helix | 533-536 | 4 | |
| α-helix | 549-562 | 14 | |
| β-strand | 569-573 | 5 | 3 |
| β-strand | 579-585 | 7 | 3 |
| β-strand | 590-596 | 7 | 3 |
| α-helix | 597-603 | 7 | |
| α-helix | 604-606 | 3 | |
| β-strand | 614-615 | 2 | 12 |
| α-helix | 616-623 | 8 | |
| α-helix | 627-638 | 12 | |
| β-strand | 648-650 | 3 | 12 |
| α-helix | 657-659 | 3 | |
| β-strand | 665-668 | 4 | 12 |
| β-strand | 683-687 | 5 | 3 |
| α-helix | 692-693 | 2 | |
| α-helix | 697-699 | 3 | |
| α-helix | 701-717 | 17 | |
| α-helix | 734-742 | 9 | |
| α-helix | 750-762 | 13 | |
Chain H: 17 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-44 | 3 | |
| β-strand | 61-63 | 3 | 13 |
| α-helix | 66-78 | 13 | |
| α-helix | 92-97 | 6 | |
| α-helix | 210-213 | 4 | |
| β-strand | 225-226 | 2 | 13 |
| β-strand | 237-239 | 3 | 13 |
| β-strand | 246-247 | 2 | 14 |
| β-strand | 256-257 | 2 | 14 |
| α-helix | 272-282 | 11 | |
| α-helix | 286-292 | 7 | |
| β-strand | 295-296 | 2 | 8 |
| β-strand | 303-306 | 4 | 8 |
| β-strand | 313-314 | 2 | 15 |
| β-strand | 321-322 | 2 | 15 |
| α-helix | 330-333 | 4 | |
| α-helix | 341-345 | 5 | |
| α-helix | 349-352 | 4 | |
| α-helix | 360-380 | 21 | |
| α-helix | 382-397 | 16 | |
| α-helix | 404-406 | 3 | |
| α-helix | 409-425 | 17 | |
| α-helix | 428-432 | 5 | |
| α-helix | 434-436 | 3 | |
| α-helix | 438-462 | 25 | |
| α-helix | 469-485 | 17 | |
Chain I: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-9 | 8 | 9 |
| β-strand | 12-19 | 8 | 9 |
| β-strand | 23 | 1 | 16 |
| α-helix | 24-35 | 12 | |
| β-strand | 42 | 1 | 17 |
| β-strand | 45 | 1 | 18 |
| β-strand | 50 | 1 | 18 |
| β-strand | 56 | 1 | 16 |
| α-helix | 58-60 | 3 | |
| β-strand | 68 | 1 | 19 |
| β-strand | 71 | 1 | 19 |
| α-helix | 72 | 1 | |
| β-strand | 73-74 | 2 | 9 |
| β-strand | 79 | 1 | 17 |
| α-helix | 91-96 | 6 | |
Chain N: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 10 |
| β-strand | 12-16 | 5 | 10 |
| α-helix | 23-33 | 11 | |
| β-strand | 42-44 | 3 | 10 |
| β-strand | 49 | 1 | 10 |
| α-helix | 50 | 1 | |
| β-strand | 66-70 | 5 | 10 |
Chain O: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 9 |
| β-strand | 28-32 | 5 | 9 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-45 | 6 | |
| α-helix | 48-50 | 3 | |
| β-strand | 59-61 | 3 | 9 |
| α-helix | 67-82 | 16 | |
| α-helix | 99-109 | 11 | |
Chain R: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-43 | 13 | 3 |
| β-strand | 49 | 1 | 4 |
| β-strand | 56 | 1 | 4 |
| α-helix | 63-66 | 4 | |
| β-strand | 75-78 | 4 | 5 |
| β-strand | 83-85 | 3 | 5 |
| α-helix | 88-90 | 3 | |
| β-strand | 98 | 1 | 6 |
| β-strand | 105 | 1 | 6 |
| β-strand | 108-111 | 4 | 5 |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cysteine dioxygenase type 1 | A | protein | 200 | Homo sapiens | Q16878 (AlphaFold model) |
| RING-box protein 2 | R | protein | 109 | Homo sapiens | Q9UBF6 (AlphaFold model) |
| Ubiquitin | U | protein | 75 | Homo sapiens | P0CG48 (AlphaFold model) |
| Elongin-C | O | protein | 112 | Homo sapiens | Q15369 (AlphaFold model) |
| NEDD8 | N | protein | 76 | Homo sapiens | Q15843 |
| Cullin-5 | C | protein | 780 | Homo sapiens | Q93034 |
| E3 ubiquitin-protein ligase ARIH2 | H | protein | 493 | Homo sapiens | O95376 |
| Elongin-B | I | protein | 118 | Homo sapiens | Q15370 |
| Leucine-rich repeat-containing protein 58 | B | protein | 371 | Homo sapiens | Q96CX6 |
Sequence of entity 1 (A), FASTA
>9T7V_1 Cysteine dioxygenase type 1 (chains A)
MEQTEVLCPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTR
NLVDQGNGKFNLMILAWGEGHGSSIHDHTNSHSFLKMLQGNLKETLFAWPDKKSNEMVKK
SERVLRENQAAYINDSVGLHRVENISHTEPAVSLHLYSPPFDTSHAFDQRTGHKNKVTMT
FHSKFGIRTPNATSGSLENN
Sequence of entity 2 (R), FASTA
>9T7V_2 RING-box protein 2 (chains R)
EDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDACLRC
QAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK
Sequence of entity 3 (U), FASTA
>9T7V_3 Ubiquitin (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG
Sequence of entity 4 (O), FASTA
>9T7V_4 Elongin-C (chains O)
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Sequence of entity 5 (N), FASTA
>9T7V_5 NEDD8 (chains N)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG
Sequence of entity 6 (C), FASTA
>9T7V_6 Cullin-5 (chains C)
MATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAK
IHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMG
KQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGV
RESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKE
EEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLM
DKVPNGIEPMLKDLEEHIISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKEAFQ
DDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLKTQPESKCPELLANYCDMLLRKTP
LSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWL
REVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSS
EKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQL
AVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDF
TEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAII
QIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA
Sequence of entity 7 (H), FASTA
>9T7V_7 E3 ubiquitin-protein ligase ARIH2 (chains H)
MSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEEYQ
FTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEA
RVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVG
VSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQ
EPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKC
NICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQARE
ALKKYLFYFERWENHNKSLQAAAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKC
RYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIANLSWKVERADSYDRGDLENQMHIAE
QRRRTLLKDFHDT
Sequence of entity 8 (I), FASTA
>9T7V_8 Elongin-B (chains I)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ
Sequence of entity 9 (B), FASTA
>9T7V_9 Leucine-rich repeat-containing protein 58 (chains B)
MEEAGAAVVTAGEAELNWSRLSVSTETLESELEARGEERRGAREALLRLLLPHNRLVSLP
RALGSGFPHLQLLDVSGNALTALGPELLALRGLRTLLAKNNRLGGPSALPKGLAQSPLCR
SLQVLNLSGNCFQEVPASLLELRALQTLSLGGNQLQSIPAEIENLQSLECLYLGGNFIKE
IPPELGNLPSLNYLVLCDNKIQSIPPQLSQLHSLRSLSLHNNLLTYLPREILNLIHLEEL
SLRGNPLVVRFVRDLTYDPPTLLELAARTIKIRNISYTPYDLPGNLLRYLGSASNCPNPK
CGGVYFDCCVRQIKFVDFCGKYRLPLMHYLCSPECSSPCSSASHSSTSQSESDSEDEASV
AARRMQKVLLG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| FE | FE (III) ion | Fe | 1 |
| SY8 | 5-azanylpentan-2-one | C5 H11 N O | 1 |
| ZN | Zinc ion | Zn | 8 |
Primary citation
Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1. Andree, G.A., Stier, L.J., Schmiederer, K. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-72524-3 · PubMed
Other PDB entries of the same protein (UniProt Q16878 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6BPU 1.8 Å, Crystal structure of ferrous form of the F2-Tyr157 human cysteine dioxygenase with both…
- 6CDH 1.82 Å, Crystal structure of ferrous form of the Cl-Tyr157 human cysteine dioxygenase with both…
- 6BPV 1.95 Å, Crystal structure of cysteine-bound ferrous form of the matured F2-Tyr157 human cysteine…
- 6E87 1.95 Å, Crystal structure of ferrous form of the crosslinked human cysteine dioxygenase in the…
- 6BPR 1.96 Å, Crystal structure of cysteine, nitric oxide-bound ferrous form of the uncrosslinked…
- 6CDN 2.06 Å, Crystal structure of cysteine-bound ferrous form of the crosslinked Cl-Tyr157 human…
- 6BPS 2.1 Å, Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 human…
- 6BPX 2.15 Å, Crystal structure of cysteine-bound ferrous form of the matured Cl2-Tyr157 human…
- 6N42 2.2 Å, Crystal structure of cysteine-bound ferrous form of the crosslinked human cysteine…
- 6BGM 2.21 Å, Crystal structure of ferrous form of the crosslinked human cysteine dioxygenase
- 6BGF 2.25 Å, Crystal structure of cysteine-bound ferrous form of the crosslinked human cysteine…
- 6N43 2.29 Å, Crystal structure of cysteine, nitric oxide-bound ferrous form of the crosslinked human…
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