8WQI: Local refinement of FEM1B

Local refinement of FEM1B bound with the C-degron of CUX1. Determined by electron microscopy at 3.5 Å resolution. Released 3 Apr 2024.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,074
Mol. weight: 73.5 kDa
Released: 3 Apr 2024

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

Secondary structure: helices and β-sheets

8WQI contains 37 α-helices and 4 β-strands across 2 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 D: 36 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
α-helix	18-23	6
α-helix	29-36	8
α-helix	49-55	7
α-helix	59-65	7
β-strand	79	1	1
β-strand	86	1	1
α-helix	91-98	8
α-helix	101-105	5
α-helix	124-131	8
α-helix	134-142	9
α-helix	157-163	7
α-helix	167-175	9
α-helix	190-197	8
α-helix	200-208	9
α-helix	222-228	7
α-helix	232-238	7
α-helix	239-241	3
α-helix	245-259	15
α-helix	270-283	14
α-helix	293-295	3
α-helix	311-315	5
α-helix	321-336	16
α-helix	344-356	13
α-helix	360-375	16
α-helix	384-398	15
α-helix	400-403	4
α-helix	404-426	23
α-helix	433-455	23
α-helix	461-477	17
α-helix	489-492	4
α-helix	512-519	8
β-strand	528	1	2
β-strand	534	1	2
α-helix	535-540	6
α-helix	550-553	4
α-helix	576-579	4
α-helix	584-591	8
α-helix	597-607	11
α-helix	618-626	9

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	-20--15	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein fem-1 homolog B	D	protein	627	Homo sapiens	Q9UK73 (AlphaFold model)
Protein CASP	G	protein	31	Homo sapiens	Q13948 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>8WQI_1 Protein fem-1 homolog B (chains D)
MEGLAGYVYKAASEGKVLTLAALLLNRSESDIRYLLGYVSQQGGQRSTPLIIAARNGHAK
VVRLLLEHYRVQTQQTGTVRFDGYVIDGATALWCAAGAGHFEVVKLLVSHGANVNHTTVT
NSTPLRAACFDGRLDIVKYLVENNANISIANKYDNTCLMIAAYKGHTDVVRYLLEQRADP
NAKAHCGATALHFAAEAGHIDIVKELIKWRAAIVVNGHGMTPLKVAAESCKADVVELLLS
HADCDRRSRIEALELLGASFANDRENYDIIKTYHYLYLAMLERFQDGDNILEKEVLPPIH
AYGNRTECRNPQELESIRQDRDALHMEGLIVRERILGADNIDVSHPIIYRGAVYADNMEF
EQCIKLWLHALHLRQKGNRNTHKDLLRFAQVFSQMIHLNETVKAPDIECVLRCSVLEIEQ
SMNRVKNISDADVHNAMDNYECNLYTFLYLVCISTKTQCSEEDQCKINKQIYNLIHLDPR
TREGFTLLHLAVNSNTPVDDFHTNDVCSFPNALVTKLLLDCGAEVNAVDNEGNSALHIIV
QYNRPISDFLTLHSIIISLVEAGAHTDMTNKQNKTPLDKSTTGVSEILLKTQMKMSLKCL
AARAVRANDINYQDQIPRTLEEFVGFH

Sequence of entity 2 (G), FASTA

>8WQI_2 Protein CASP (chains G)
GGGSGGGSKFADHLHKFHENDNGAAAGDLWQ

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 Q9UK73 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PW8 2.8 Å, Fem-1 homolog B (FEM1B) in complex with VU0417412
7EL6 2.8 Å, Structure of SMCR8 bound FEM1B
9PQA 2.9 Å, Fem-1 homolog B (FEM1B) in complex with VU0432623
9PQ9 2.93 Å, Fem-1 homolog B (FEM1B) in complex with VU0421763
9PWJ 3.0 Å, Fem-1 homolog B (FEM1B) in complex with VU0081201
9PXP 3.0 Å, Fem-1 homolog B (FEM1B) in complex with VU0416476
9PXO 3.05 Å, Fem-1 homolog B (FEM1B) in complex with VU0023775
9PQE 3.1 Å, Fem-1 homolog B (FEM1B) in complex with VU0412674
6LBF 3.25 Å, Crystal structure of FEM1B
8WQF 3.27 Å, cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1…
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…

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