6XKC: E3 ligase

Name: PDB 6XKC: Crystal structure of E3 ligase
Published: 2020-10-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of E3 ligase. Determined by X-ray diffraction at 2.03 Å resolution. Released 14 Oct 2020.

Method: X-ray diffraction
Resolution: 2.03 Å
Organism: Homo sapiens
Chains: 6
Atoms: 13,062
Mol. weight: 159.75 kDa
Released: 14 Oct 2020

Explore 6XKC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XKC contains 106 α-helices and 24 β-strands across 6 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: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	16-22	7
α-helix	28-35	8
β-strand	39	1	1
β-strand	42	1	1
α-helix	44-50	7
α-helix	54-63	10
α-helix	66-69	4
β-strand	72-76	5	2
β-strand	79-84	6	2
α-helix	86-92	7
α-helix	96-104	9
α-helix	119-126	8
α-helix	129-137	9
α-helix	152-159	8
α-helix	162-170	9
α-helix	185-192	8
α-helix	195-203	9
α-helix	206-208	3
α-helix	217-223	7
α-helix	227-238	12
α-helix	239-242	4

Chains B and E: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	16-23	8
α-helix	28-36	9
β-strand	39	1	3
β-strand	42	1	3
α-helix	44-50	7
α-helix	54-63	10
β-strand	72-76	5	4
β-strand	79-84	6	4
α-helix	86-93	8
α-helix	96-104	9
α-helix	119-125	7
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	206-208	3
α-helix	217-223	7
α-helix	227-238	12
α-helix	239-242	4

Chain C: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	16-23	8
α-helix	28-34	7
β-strand	39	1	5
β-strand	42	1	5
α-helix	44-50	7
α-helix	54-63	10
α-helix	66-69	4
β-strand	72-75	4	6
β-strand	80-84	5	6
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	206-208	3
α-helix	217-223	7
α-helix	227-237	11
α-helix	239-242	4

Chain D: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	16-22	7
α-helix	28-34	7
β-strand	39	1	7
β-strand	42	1	7
α-helix	44-50	7
α-helix	54-61	8
α-helix	66-69	4
β-strand	72-76	5	8
β-strand	79-84	6	8
α-helix	86-92	7
α-helix	96-104	9
α-helix	119-126	8
α-helix	129-137	9
α-helix	152-159	8
α-helix	162-170	9
α-helix	185-192	8
α-helix	195-203	9
α-helix	206-208	3
α-helix	217-223	7
α-helix	227-237	11
α-helix	239-242	4

Chain F: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	16-23	8
α-helix	28-36	9
β-strand	39	1	11
β-strand	42	1	11
α-helix	44-50	7
α-helix	54-63	10
α-helix	66-68	3
β-strand	72-76	5	12
β-strand	79-84	6	12
α-helix	86-93	8
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	186-192	7
α-helix	195-203	9
α-helix	206-208	3
α-helix	217-223	7
α-helix	227-237	11
α-helix	239-242	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein fem-1 homolog C	A, B, C, D, E, F	protein	246	Homo sapiens	Q96JP0 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>6XKC_1 Protein fem-1 homolog C (chains A, B, C, D, E, F)
GSMDLKTAVFNAARDGKLRLLTKLLASKSKEEVSSLISEKTNGATPLLMAARYGHLDMVE
FLLEQCSASIEVGGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLNHGASVNNTTLTNST
PLRAACFDGHLEIVKYLVEHKADLEVSNRHGHTCLMISCYKGHKEIAQYLLEKGADVNRK
SVKGNTALHDCAESGSLDIMKMLLMYCAKMEKDGYGMTPLLSASVTGHTNIVDFLTHHAQ
TSKTER

Primary citation

Molecular basis for ubiquitin ligase CRL2 FEM1C -mediated recognition of C-degron. Yan, X., Wang, X., Li, Y. et al. Nat Chem Biol (2021) 17:263-271. DOI 10.1038/s41589-020-00703-4 · PubMed

Other PDB entries of the same protein (UniProt Q96JP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6LF0 2.11 Å, Structure of FEM1C
6LE6 2.33 Å, Structure of LNLPTQGRAR bound FEM1C
6LDP 2.35 Å, Structure of CDK5R1-bound FEM1C
6LEN 2.38 Å, Structure of NS11 bound FEM1C
6LEY 2.39 Å, Structure of Sil1G bound FEM1C
7JYA 2.46 Å, Crystal structure of E3 ligase in complex with peptide
6LBG 2.51 Å, Structure of OR51B2 bound FEM1C
6LBN 2.9 Å, Structure of SIL1-bound FEM1C
9UA3 3.28 Å, Cryo-EM structure of neddylated CUL2-RBX1-FEM1C-ELOB-ELOC
8Q7R 3.71 Å, Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34:…
8PQL 3.76 Å, K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34:…

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