8Q7R: Cullin-2

Name: PDB 8Q7R: Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide
Published: 2024-02-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide. Determined by electron microscopy at 3.71 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 3.71 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,536
Mol. weight: 300.67 kDa
Ligands: U9O, ZN
Released: 21 Feb 2024

Explore 8Q7R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q7R contains 88 α-helices and 36 β-strands across 7 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: 32 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-25	15
α-helix	32-46	15
α-helix	55-77	23
α-helix	83-104	22
α-helix	106-108	3
α-helix	109-113	5
α-helix	139-152	14
α-helix	157-166	10
α-helix	178-187	10
α-helix	201-203	3
α-helix	204-208	5
α-helix	209-228	20
α-helix	232-250	19
α-helix	259-267	9
α-helix	268-272	5
α-helix	273	1
α-helix	275-287	13
α-helix	293-301	9
α-helix	308-327	20
α-helix	337-357	21
α-helix	362-375	14
α-helix	387-398	12
α-helix	411-423	13
α-helix	428-443	16
α-helix	451-465	15
α-helix	468-470	3
α-helix	471-494	24
β-strand	506-512	7	1
α-helix	521-523	3
α-helix	531-547	17
β-strand	552-555	4	1
β-strand	561-566	6	1
β-strand	573-578	6	1
α-helix	579-590	12
β-strand	593-595	3	2
α-helix	596-601	6
α-helix	607-620	14
β-strand	623-625	3	2
β-strand	637-640	4	2

Chain C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
β-strand	28-30	3	6
β-strand	43-45	3	6
β-strand	46	1	7
β-strand	57	1	7
β-strand	60-61	2	8
β-strand	76-77	2	8
β-strand	86	1	9
β-strand	91	1	8
β-strand	92	1	9
α-helix	95-97	3
α-helix	121-130	10
α-helix	142-153	12
α-helix	160-178	19
α-helix	182-184	3

Chain D: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	10
β-strand	28-32	5	10
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	10
α-helix	67-77	11
α-helix	90-94	5
α-helix	100-110	11

Chain G: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	10
β-strand	12-19	8	10
α-helix	24-34	11
β-strand	45-46	2	10
β-strand	49-50	2	10
α-helix	51-52	2
β-strand	75-76	2	10
α-helix	91-96	6

Chain H: 37 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-13	10
α-helix	16-22	7
α-helix	31-35	5
α-helix	39-41	3
α-helix	44-50	7
α-helix	54-63	10
β-strand	72-76	5	3
β-strand	79-84	6	3
α-helix	86-92	7
α-helix	96-104	9
α-helix	119-126	8
α-helix	129-137	9
α-helix	152-158	7
α-helix	162-170	9
α-helix	185-192	8
α-helix	195-203	9
α-helix	217-224	8
α-helix	227-233	7
α-helix	246-248	3
α-helix	250-258	9
α-helix	262-267	6
α-helix	271-277	7
α-helix	287-289	3
α-helix	315-330	16
α-helix	335-350	16
α-helix	354-371	18
α-helix	379-394	16
α-helix	405-407	3
α-helix	408-427	20
α-helix	432-434	3
α-helix	437-453	17
α-helix	462-473	12
α-helix	485-489	5
α-helix	492-495	4
α-helix	508-517	10
α-helix	531-537	7
α-helix	541-550	10
α-helix	586-597	12
α-helix	607-615	9

Chain R: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	26-34	9	1
β-strand	41-42	2	11
β-strand	47-48	2	11
α-helix	54-57	4
α-helix	82-88	7

Chain U: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-44	3	4
β-strand	49	1	4
β-strand	55	1	5
α-helix	56-59	4
β-strand	66-70	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-2	A	protein	745	Homo sapiens	Q13617 (AlphaFold model)
Protein fem-1 homolog C	H	protein	617	Homo sapiens	Q96JP0 (AlphaFold model)
Ubiquitin	U	protein	685	Homo sapiens	P0CG48 (AlphaFold model)
Nucleotide exchange factor SIL1	F	protein	20	Homo sapiens	Q9H173 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 R2	C	protein	238	Homo sapiens	Q712K3
Elongin-C	D	protein	112	Homo sapiens	Q15369
Elongin-B	G	protein	118	Homo sapiens	Q15370
E3 ubiquitin-protein ligase RBX1	R	protein	108	Homo sapiens	P62877

Sequence of entity 1 (A), FASTA

>8Q7R_1 Cullin-2 (chains A)
MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA

Sequence of entity 2 (H), FASTA

>8Q7R_2 Protein fem-1 homolog C (chains H)
MDLKTAVFNAARDGKLRLLTKLLASKSKEEVSSLISEKTNGATPLLMAARYGHLDMVEFL
LEQCSASIEVGGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLNHGASVNNTTLTNSTPL
RAACFDGHLEIVKYLVEHKADLEVSNRHGHTCLMISCYKGHKEIAQYLLEKGADVNRKSV
KGNTALHDCAESGSLDIMKMLLMYCAKMEKDGYGMTPLLSASVTGHTNIVDFLTHHAQTS
KTERINALELLGATFVDKKRDLLGALKYWKKAMNMRYSDRTNIISKPVPQTLIMAYDYAK
EVNSAEELEGLIADPDEMRMQALLIRERILGPSHPDTSYYIRYRGAVYADSGNFKRCINL
WKYALDMQQSNLDPLSPMTASSLLSFAELFSFMLQDRAKGLLGTTVTFDDLMGILCKSVL
EIERAIKQTQCPADPLQLNKALSIILHLICLLEKVPCTLEQDHFKKQTIYRFLKLHPRGK
NNFSPLHLAVDKNTTCVGRYPVCKFPSLQVTAILIECGADVNVRDSDDNSPLHIAALNNH
PDIMNLLIKSGAHFDATNLHKQTASDLLDEKEIAKNLIQPINHTTLQCLAARVIVNHRIY
YKGHIPEKLETFVSLHR

Sequence of entity 3 (U), FASTA

>8Q7R_3 Ubiquitin (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKA
KIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKT
ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
LRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIE
NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL
TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH
LVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLED
GRTLSDYNIQKESTLHLVLRLRGGV

Sequence of entity 4 (F), FASTA

>8Q7R_4 Nucleotide exchange factor SIL1 (chains F)
CEGYFQELLGSVNPTQGRAR

Sequence of entity 5 (C), FASTA

>8Q7R_5 Ubiquitin-conjugating enzyme E2 R2 (chains C)
MAQQQMTSSQKALMLELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYFKA
HIKFPIDYPYSPPTFRFLTKMWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNV
RTILLSVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKEYAEIIRKQVSATKAEAEKDG
VKVPTTLAEYCIKTKVPSNDNSSDLLYDDLYDDDIDDEDEEEEDADCYDDDDSGNEES

Sequence of entity 6 (D), FASTA

>8Q7R_6 Elongin-C (chains D)
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 7 (G), FASTA

>8Q7R_7 Elongin-B (chains G)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 8 (R), FASTA

>8Q7R_8 E3 ubiquitin-protein ligase RBX1 (chains R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Ligands and cofactors

ID	Name	Formula	Copies
U9O	5-azanyl-1-oxidanyl-pentan-2-one	C5 H11 N O2	1
ZN	Zinc ion	Zn	3

Primary citation

Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting. Li, J., Purser, N., Liwocha, J. et al. Mol Cell (2024) 84:1304. DOI 10.1016/j.molcel.2024.01.022 · PubMed

Other PDB entries of the same protein (UniProt Q13617 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7PLO 2.8 Å, H. sapiens replisome-CUL2/LRR1 complex
9EFQ 2.96 Å, Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2
4WQO 3.2 Å, Structure of VHL-EloB-EloC-Cul2
8JAU 3.22 Å, Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (dimer)
8JAQ 3.26 Å, Structure of CRL2APPBP2 bound with RxxGP degron (tetramer)
8WQF 3.27 Å, cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1…
9UA3 3.28 Å, Cryo-EM structure of neddylated CUL2-RBX1-FEM1C-ELOB-ELOC
8JAL 3.3 Å, Structure of CRL2APPBP2 bound with RxxGP degron (dimer)
8JAR 3.3 Å, Structure of CRL2APPBP2 bound with RxxGPAA degron (dimer)
8WQB 3.37 Å, Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89…
8WQE 3.38 Å, Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1…
8WQA 3.39 Å, Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89…

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