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

Name: PDB 8WQB: Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (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 CCDC89 (conformation 2). Determined by electron microscopy at 3.37 Å resolution. Released 3 Apr 2024.

Method: Electron microscopy
Resolution: 3.37 Å
Organism: Homo sapiens
Chains: 11
Atoms: 26,255
Mol. weight: 388.93 kDa
Ligands: ZN
Released: 3 Apr 2024

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

Secondary structure: helices and β-sheets

8WQB contains 164 α-helices and 70 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: 38 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	106-108	3
α-helix	109-113	5
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	203-206	4
α-helix	208-226	19
α-helix	232-253	22
α-helix	256-258	3
α-helix	259-270	12
α-helix	275-280	6
α-helix	282-287	6
α-helix	291-303	13
α-helix	308-326	19
α-helix	335-356	22
α-helix	362-376	15
α-helix	387-399	13
β-strand	400	1	1
α-helix	408-414	7
α-helix	419-422	4
α-helix	428-443	16
β-strand	448	1	1
α-helix	451-469	19
α-helix	472-496	25
β-strand	508-513	6	2
α-helix	527-530	4
α-helix	534-547	14
β-strand	551-556	6	2
β-strand	561	1	3
β-strand	562	1	4
β-strand	578	1	3
α-helix	579-581	3
α-helix	582-585	4
α-helix	586-589	4
β-strand	593-594	2	5
α-helix	596-599	4
α-helix	607-618	12
β-strand	638-639	2	5
α-helix	662-688	27
α-helix	696-706	11
α-helix	715-727	13
β-strand	732-733	2	6
β-strand	741-742	2	6

Chain B: 34 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	106-108	3
α-helix	109-113	5
α-helix	139-151	13
α-helix	156-172	17
α-helix	178-188	11
α-helix	192-194	3
α-helix	201-203	3
α-helix	204-208	5
α-helix	209-229	21
α-helix	232-253	22
α-helix	256-258	3
α-helix	259-267	9
α-helix	275-288	14
α-helix	291-303	13
α-helix	309-327	19
α-helix	335-357	23
α-helix	362-376	15
α-helix	386-399	14
β-strand	400	1	14
α-helix	408-422	15
α-helix	428-444	17
β-strand	448	1	14
α-helix	451-464	14
α-helix	471-495	25
β-strand	506	1	15
β-strand	509-513	5	16
α-helix	531-546	16
β-strand	551-565	15	16
α-helix	567-569	3
β-strand	574-578	5	16
α-helix	579-590	12
α-helix	596-603	8
α-helix	607-618	12
β-strand	623-625	3	17
β-strand	638-640	3	17
β-strand	652	1	16
α-helix	662-691	30
α-helix	696-706	11
α-helix	715-727	13
β-strand	731-733	3	18
β-strand	741-743	3	18

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	19
β-strand	28-32	5	19
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	19
α-helix	67-82	16
α-helix	90-93	4
α-helix	103-110	8

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	19
β-strand	12-18	7	19
β-strand	23	1	20
α-helix	25-35	11
α-helix	39-41	3
β-strand	43-46	4	19
β-strand	50	1	19
β-strand	56	1	20
β-strand	75-78	4	19
α-helix	90-97	8

Chain E: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	23-24	2	16
β-strand	26	1	15
β-strand	28-35	8	16
β-strand	41-42	2	23
β-strand	47-48	2	23
α-helix	52-53	2
α-helix	54-57	4
β-strand	70-72	3	24
β-strand	73	1	25
β-strand	78-80	3	24
α-helix	81-88	8
β-strand	93	1	26
β-strand	100	1	26
β-strand	103	1	25

Chain F: 34 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
α-helix	18-22	5
α-helix	29-36	8
β-strand	40-42	3	27
β-strand	45-47	3	27
α-helix	49-55	7
α-helix	59-68	10
β-strand	77	1	28
β-strand	89	1	28
α-helix	91-97	7
α-helix	101-109	9
α-helix	124-131	8
α-helix	134-141	8
α-helix	157-163	7
α-helix	167-174	8
α-helix	191-194	4
α-helix	200-208	9
α-helix	222-228	7
α-helix	232-238	7
α-helix	247-261	15
α-helix	269-283	15
α-helix	295-298	4
α-helix	311-315	5
α-helix	321-336	16
α-helix	345-356	12
α-helix	361-376	16
α-helix	382-397	16
α-helix	404-427	24
α-helix	433-455	23
α-helix	461-475	15
α-helix	487-492	6
α-helix	503-506	4
α-helix	512-521	10
α-helix	535-539	5
α-helix	549-562	14
α-helix	583-592	10
α-helix	597-607	11
α-helix	618-626	9

Chain G: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	7
β-strand	21	1	8
β-strand	30	1	9
β-strand	31-32	2	7
α-helix	33-36	4
α-helix	40-46	7
β-strand	60	1	8
α-helix	67-82	16
α-helix	92-94	3
α-helix	103-109	7

Chain H: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	9
β-strand	13-18	6	9
α-helix	24-35	12
β-strand	43-45	3	9
β-strand	46	1	10
β-strand	49	1	10
α-helix	58-60	3
β-strand	74-78	5	9
α-helix	90-97	8

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
Coiled-coil domain-containing protein 89	K	protein	31	Homo sapiens	Q8N998

Sequence of entity 1 (A, B), FASTA

>8WQB_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

>8WQB_2 Elongin-C (chains C, G)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (D, H), FASTA

>8WQB_3 Elongin-B (chains D, H)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 4 (E, I), FASTA

>8WQB_4 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains E, I)
SHMGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAW
GVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 5 (F, J), FASTA

>8WQB_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

>8WQB_6 Coiled-coil domain-containing protein 89 (chains K)
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)
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)

Browse structure collections

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