8WQA: CUL2-RBX1-ELOB-ELOC-FEM1B

Name: PDB 8WQA: Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1)
Published: 2024-04-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1). Determined by electron microscopy at 3.39 Å resolution. Released 3 Apr 2024.

Method: Electron microscopy
Resolution: 3.39 Å
Organism: Homo sapiens
Chains: 12
Atoms: 26,479
Mol. weight: 392.16 kDa
Ligands: ZN
Released: 3 Apr 2024

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

Secondary structure: helices and β-sheets

8WQA contains 179 α-helices and 81 β-strands across 12 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: 39 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	10-25	16
α-helix	32-46	15
α-helix	54-78	25
α-helix	83-104	22
α-helix	106-108	3
α-helix	109-113	5
α-helix	136-138	3
α-helix	139-147	9
α-helix	148-152	5
α-helix	156-171	16
α-helix	178-190	13
α-helix	191-194	4
α-helix	201-203	3
α-helix	204-208	5
α-helix	209-227	19
α-helix	232-251	20
α-helix	256-258	3
α-helix	259-267	9
α-helix	268-272	5
α-helix	275-287	13
α-helix	291-301	11
α-helix	308-327	20
α-helix	335-356	22
α-helix	362-376	15
α-helix	387-399	13
β-strand	400	1	26
α-helix	408-422	15
α-helix	428-444	17
β-strand	448	1	26
α-helix	451-469	19
α-helix	472-493	22
β-strand	506-507	2	20
β-strand	510-513	4	21
α-helix	531-546	16
β-strand	551-555	5	21
β-strand	561-565	5	20
α-helix	567-569	3
β-strand	574-576	3	27
β-strand	577-578	2	20
α-helix	579-581	3
α-helix	582-590	9
β-strand	593-594	2	28
α-helix	596-603	8
α-helix	607-618	12
β-strand	623-625	3	28
β-strand	638-640	3	28
β-strand	650-652	3	27
α-helix	656-658	3
α-helix	662-691	30
β-strand	694-695	2	29
α-helix	696-707	12
α-helix	715-727	13
β-strand	731-733	3	29
β-strand	740-743	4	29

Chain B: 39 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	17-24	8
α-helix	29-35	7
β-strand	40-42	3	30
β-strand	45-47	3	30
α-helix	49-55	7
α-helix	59-67	9
α-helix	91-97	7
α-helix	101-110	10
α-helix	124-131	8
α-helix	134-141	8
α-helix	157-163	7
α-helix	167-175	9
α-helix	190-196	7
α-helix	200-208	9
α-helix	222-228	7
α-helix	232-235	4
α-helix	238-241	4
α-helix	247-261	15
α-helix	270-283	14
α-helix	295-297	3
α-helix	300-302	3
α-helix	311-316	6
α-helix	321-336	16
α-helix	341-343	3
α-helix	344-356	13
α-helix	360-376	17
α-helix	382-397	16
α-helix	401-403	3
α-helix	404-425	22
α-helix	433-456	24
α-helix	461-477	17
α-helix	487-492	6
α-helix	503-505	3
α-helix	512-520	9
α-helix	535-539	5
α-helix	549-561	13
α-helix	576-579	4
α-helix	583-592	10
α-helix	597-608	12
α-helix	618-625	8

Chain C: 38 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	10-25	16
α-helix	32-45	14
α-helix	54-77	24
α-helix	83-104	22
α-helix	106-107	2
α-helix	108-113	6
α-helix	139-147	9
α-helix	148-152	5
α-helix	156-172	17
α-helix	178-190	13
α-helix	191-194	4
α-helix	201-203	3
α-helix	204-208	5
α-helix	209-227	19
α-helix	232-251	20
α-helix	256-259	4
α-helix	262-270	9
α-helix	275-288	14
α-helix	291-301	11
α-helix	308-327	20
α-helix	335-356	22
α-helix	362-376	15
α-helix	387-399	13
β-strand	400	1	1
α-helix	408-422	15
α-helix	428-444	17
β-strand	448	1	1
α-helix	451-469	19
α-helix	472-493	22
β-strand	506-507	2	2
β-strand	510-513	4	3
α-helix	531-547	17
β-strand	551-555	5	3
β-strand	561-565	5	2
β-strand	574-578	5	2
α-helix	579-581	3
α-helix	582-590	9
β-strand	593-594	2	4
α-helix	597-599	3
α-helix	600-603	4
α-helix	607-618	12
β-strand	623-625	3	4
β-strand	638-640	3	4
β-strand	650-652	3	2
α-helix	655-658	4
α-helix	660-661	2
α-helix	662-691	30
β-strand	693-695	3	5
α-helix	696-706	11
α-helix	715-727	13
β-strand	731-733	3	5
β-strand	740-743	4	5

Chain D: 37 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	17-23	7
α-helix	29-35	7
β-strand	41-42	2	6
β-strand	45-46	2	6
α-helix	49-56	8
α-helix	59-64	6
α-helix	65-69	5
β-strand	77-80	4	7
β-strand	85-89	5	7
α-helix	91-98	8
α-helix	101-109	9
α-helix	124-130	7
α-helix	134-141	8
α-helix	157-163	7
α-helix	168-174	7
α-helix	190-197	8
α-helix	200-208	9
α-helix	222-228	7
α-helix	234-240	7
α-helix	246-251	6
α-helix	255-261	7
α-helix	270-283	14
α-helix	296-299	4
α-helix	311-316	6
α-helix	321-336	16
α-helix	341-343	3
α-helix	344-355	12
α-helix	361-377	17
α-helix	382-397	16
α-helix	404-426	23
α-helix	433-456	24
α-helix	461-476	16
α-helix	487-491	5
α-helix	502-505	4
α-helix	512-520	9
α-helix	535-539	5
α-helix	549-561	13
α-helix	583-591	9
α-helix	597-607	11
α-helix	618-626	9

Chain E: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	8
β-strand	20-22	3	9
β-strand	28	1	9
β-strand	29-30	2	10
β-strand	31-32	2	8
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	9
α-helix	67-83	17
α-helix	90-93	4
α-helix	103-109	7

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	10
β-strand	13-18	6	10
β-strand	23	1	11
α-helix	24-35	12
β-strand	45	1	10
β-strand	50	1	10
β-strand	56	1	11
α-helix	57-60	4
α-helix	72	1
β-strand	73-76	4	10
α-helix	90-99	10

Chain G: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	16
β-strand	20-22	3	17
β-strand	28	1	17
β-strand	31-32	2	16
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	17
α-helix	67-82	16
α-helix	90-93	4
α-helix	103-109	7

Chain H: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	18
β-strand	13-18	6	18
β-strand	23	1	19
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-45	4	18
β-strand	50	1	18
β-strand	56	1	19
α-helix	57-60	4
α-helix	72	1
β-strand	73-79	7	18
α-helix	94-99	6

4 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
Cullin-2	A, C	protein	750	Homo sapiens	Q13617 (AlphaFold model)
Protein fem-1 homolog B	B, D	protein	627	Homo sapiens	Q9UK73 (AlphaFold model)
Elongin-C	E, G	protein	96	Homo sapiens	Q15369 (AlphaFold model)
Elongin-B	F, H	protein	118	Homo sapiens	Q15370 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1, N-terminally processed	I, J	protein	96	Homo sapiens	P62877
Coiled-coil domain-containing protein 89	K, L	protein	31	Homo sapiens	Q8N998

Sequence of entity 1 (A, C), FASTA

>8WQA_1 Cullin-2 (chains A, C)
SASWSHPQFEKGGGSGGGSGTSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFS
DIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADY
MDCLYRYLNTQFIKKNGGGPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGED
PNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQY
MEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMA
NMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLIN
TVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRL
TSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHR
MYTDMSVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEK
SVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVS
YKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITT
SMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSI
SMIKKCIEVLIDKQYIERSQASADEYSYVA

Sequence of entity 2 (B, D), FASTA

>8WQA_2 Protein fem-1 homolog B (chains B, D)
MEGLAGYVYKAASEGKVLTLAALLLNRSESDIRYLLGYVSQQGGQRSTPLIIAARNGHAK
VVRLLLEHYRVQTQQTGTVRFDGYVIDGATALWCAAGAGHFEVVKLLVSHGANVNHTTVT
NSTPLRAACFDGRLDIVKYLVENNANISIANKYDNTCLMIAAYKGHTDVVRYLLEQRADP
NAKAHCGATALHFAAEAGHIDIVKELIKWRAAIVVNGHGMTPLKVAAESCKADVVELLLS
HADCDRRSRIEALELLGASFANDRENYDIIKTYHYLYLAMLERFQDGDNILEKEVLPPIH
AYGNRTECRNPQELESIRQDRDALHMEGLIVRERILGADNIDVSHPIIYRGAVYADNMEF
EQCIKLWLHALHLRQKGNRNTHKDLLRFAQVFSQMIHLNETVKAPDIECVLRCSVLEIEQ
SMNRVKNISDADVHNAMDNYECNLYTFLYLVCISTKTQCSEEDQCKINKQIYNLIHLDPR
TREGFTLLHLAVNSNTPVDDFHTNDVCSFPNALVTKLLLDCGAEVNAVDNEGNSALHIIV
QYNRPISDFLTLHSIIISLVEAGAHTDMTNKQNKTPLDKSTTGVSEILLKTQMKMSLKCL
AARAVRANDINYQDQIPRTLEEFVGFH

Sequence of entity 3 (E, G), FASTA

>8WQA_3 Elongin-C (chains E, G)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 4 (F, H), FASTA

>8WQA_4 Elongin-B (chains F, H)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 5 (I, J), FASTA

>8WQA_5 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains I, J)
SHMGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAW
GVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 6 (K, L), FASTA

>8WQA_6 Coiled-coil domain-containing protein 89 (chains K, L)
GGGSGGGSKKHSLDLLSKERELNGKLRHLSP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Mechanism of Psi-Pro/C-degron recognition by the CRL2 FEM1B ubiquitin ligase. Chen, X., Raiff, A., Li, S. et al. Nat Commun (2024) 15:3558-3558. DOI 10.1038/s41467-024-47890-5 · 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…
8JAV 3.44 Å, Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (tetramer)

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