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

Name: PDB 8WQF: cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1 (conformation 2)
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 CUX1 (conformation 2). Determined by electron microscopy at 3.27 Å resolution. Released 3 Apr 2024.

Method: Electron microscopy
Resolution: 3.27 Å
Organism: Homo sapiens
Chains: 11
Atoms: 23,404
Mol. weight: 388.85 kDa
Ligands: ZN
Released: 3 Apr 2024

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

Secondary structure: helices and β-sheets

8WQF contains 150 α-helices and 66 β-strands across 11 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: 42 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
α-helix	32-47	16
α-helix	54-78	25
α-helix	83-94	12
α-helix	96-104	9
α-helix	106-108	3
α-helix	109-114	6
α-helix	139-147	9
α-helix	148-152	5
α-helix	156-159	4
α-helix	162-171	10
α-helix	178-190	13
α-helix	201-203	3
α-helix	204-208	5
α-helix	209-227	19
α-helix	232-249	18
α-helix	256-258	3
α-helix	259-270	12
α-helix	275-278	4
α-helix	282-286	5
α-helix	291-301	11
α-helix	305-307	3
α-helix	308-326	19
α-helix	332-334	3
α-helix	335-356	22
α-helix	362-376	15
α-helix	378-380	3
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	451-465	15
α-helix	472-496	25
α-helix	500-501	2
β-strand	507-513	7	2
α-helix	527-530	4
α-helix	531-547	17
β-strand	551-556	6	2
β-strand	561-564	4	2
β-strand	575-578	4	2
α-helix	579-585	7
β-strand	593-594	2	3
α-helix	596-602	7
α-helix	607-619	13
β-strand	623-625	3	3
β-strand	638-640	3	3
β-strand	652	1	2
α-helix	660-661	2
α-helix	662-691	30
β-strand	694-695	2	4
α-helix	696-706	11
α-helix	715-727	13
β-strand	732-733	2	4
β-strand	740-742	3	4

Chain B: 37 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	10-25	16
α-helix	32-47	16
α-helix	54-78	25
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	156-171	16
α-helix	178-190	13
α-helix	191-194	4
α-helix	201-203	3
α-helix	204-208	5
α-helix	209-229	21
α-helix	232-251	20
α-helix	256-258	3
α-helix	259-270	12
α-helix	275-287	13
α-helix	291-303	13
α-helix	305-307	3
α-helix	308-326	19
α-helix	335-356	22
α-helix	362-376	15
α-helix	387-399	13
β-strand	400	1	13
α-helix	408-422	15
α-helix	428-444	17
β-strand	448	1	13
α-helix	451-465	15
α-helix	473-481	9
α-helix	483-495	13
β-strand	510-513	4	14
α-helix	531-547	17
β-strand	551-565	15	14
α-helix	567-569	3
β-strand	574-578	5	14
α-helix	579-588	10
β-strand	594	1	15
α-helix	596-602	7
α-helix	607-620	14
β-strand	623-625	3	15
β-strand	638-640	3	15
β-strand	652	1	14
α-helix	662-690	29
α-helix	696-707	12
α-helix	715-727	13
β-strand	731-733	3	16
β-strand	741-743	3	16

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	17
β-strand	28-32	5	17
α-helix	33-36	4
α-helix	40-45	6
α-helix	49-53	5
β-strand	60-61	2	17
α-helix	67-82	16
α-helix	90-93	4
α-helix	103-109	7

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	17
β-strand	12-18	7	17
β-strand	23	1	18
α-helix	24-35	12
α-helix	46-48	3
β-strand	56	1	18
α-helix	72	1
β-strand	73-76	4	17
α-helix	91-96	6

Chain E: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	23-35	13	14
β-strand	42	1	21
β-strand	47	1	21
α-helix	52-53	2
β-strand	70-72	3	22
β-strand	73	1	23
β-strand	78-80	3	22
α-helix	81-88	8
β-strand	93	1	24
β-strand	100	1	24
β-strand	103	1	23

Chain F: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	361-376	16
α-helix	382-397	16
α-helix	405-426	22
α-helix	430-456	27
α-helix	461-477	17
α-helix	487-491	5
α-helix	503-506	4
α-helix	512-520	9
α-helix	536-539	4
α-helix	553-561	9
α-helix	583-592	10
α-helix	597-607	11
α-helix	618-621	4
α-helix	623-626	4

Chain G: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	5
β-strand	21	1	6
β-strand	30	1	7
β-strand	31-32	2	5
α-helix	33-36	4
α-helix	40-46	7
β-strand	60	1	6
α-helix	67-82	16
α-helix	91-94	4
α-helix	103-109	7

Chain H: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	7
β-strand	13-18	6	7
α-helix	24-35	12
β-strand	43	1	8
β-strand	46	1	7
β-strand	49	1	7
α-helix	58-60	3
β-strand	68	1	9
β-strand	71	1	9
β-strand	74-76	3	7
β-strand	78	1	8
α-helix	91-99	9

3 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, B	protein	750	Homo sapiens	Q13617 (AlphaFold model)
Elongin-C	C, G	protein	96	Homo sapiens	Q15369 (AlphaFold model)
Elongin-B	D, H	protein	118	Homo sapiens	Q15370 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1, N-terminally processed	E, I	protein	96	Homo sapiens	P62877 (AlphaFold model)
Protein fem-1 homolog B	F, J	protein	627	Homo sapiens	Q9UK73
Protein CASP	K	protein	31	Homo sapiens	Q13948

Sequence of entity 1 (A, B), FASTA

>8WQF_1 Cullin-2 (chains A, B)
SASWSHPQFEKGGGSGGGSGTSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFS
DIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADY
MDCLYRYLNTQFIKKNGGGPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGED
PNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQY
MEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMA
NMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLIN
TVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRL
TSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHR
MYTDMSVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEK
SVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVS
YKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITT
SMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSI
SMIKKCIEVLIDKQYIERSQASADEYSYVA

Sequence of entity 2 (C, G), FASTA

>8WQF_2 Elongin-C (chains C, G)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (D, H), FASTA

>8WQF_3 Elongin-B (chains D, H)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 4 (E, I), FASTA

>8WQF_4 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains E, I)
SHMGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAW
GVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 5 (F, J), FASTA

>8WQF_5 Protein fem-1 homolog B (chains F, J)
MEGLAGYVYKAASEGKVLTLAALLLNRSESDIRYLLGYVSQQGGQRSTPLIIAARNGHAK
VVRLLLEHYRVQTQQTGTVRFDGYVIDGATALWCAAGAGHFEVVKLLVSHGANVNHTTVT
NSTPLRAACFDGRLDIVKYLVENNANISIANKYDNTCLMIAAYKGHTDVVRYLLEQRADP
NAKAHCGATALHFAAEAGHIDIVKELIKWRAAIVVNGHGMTPLKVAAESCKADVVELLLS
HADCDRRSRIEALELLGASFANDRENYDIIKTYHYLYLAMLERFQDGDNILEKEVLPPIH
AYGNRTECRNPQELESIRQDRDALHMEGLIVRERILGADNIDVSHPIIYRGAVYADNMEF
EQCIKLWLHALHLRQKGNRNTHKDLLRFAQVFSQMIHLNETVKAPDIECVLRCSVLEIEQ
SMNRVKNISDADVHNAMDNYECNLYTFLYLVCISTKTQCSEEDQCKINKQIYNLIHLDPR
TREGFTLLHLAVNSNTPVDDFHTNDVCSFPNALVTKLLLDCGAEVNAVDNEGNSALHIIV
QYNRPISDFLTLHSIIISLVEAGAHTDMTNKQNKTPLDKSTTGVSEILLKTQMKMSLKCL
AARAVRANDINYQDQIPRTLEEFVGFH

Sequence of entity 6 (K), FASTA

>8WQF_6 Protein CASP (chains K)
GGGSGGGSKFADHLHKFHENDNGAAAGDLWQ

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)
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…
8JAV 3.44 Å, Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (tetramer)

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