7JYA: E3 ligase

Name: PDB 7JYA: Crystal structure of E3 ligase in complex with peptide
Published: 2020-10-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of E3 ligase in complex with peptide. Determined by X-ray diffraction at 2.46 Å resolution. Released 14 Oct 2020.

Method: X-ray diffraction
Resolution: 2.46 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 6
Atoms: 8,479
Mol. weight: 128.3 kDa
Released: 14 Oct 2020

Explore 7JYA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JYA contains 76 α-helices and 12 β-strands across 3 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: 26 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	1
β-strand	42	1	1
α-helix	44-50	7
α-helix	54-63	10
α-helix	65-67	3
β-strand	72-76	5	2
β-strand	79-84	6	2
α-helix	86-93	8
α-helix	96-104	9
α-helix	119-126	8
α-helix	129-136	8
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	217-224	8
α-helix	227-233	7
α-helix	241-257	17
α-helix	262-276	15
α-helix	285-289	5
α-helix	294-296	3
α-helix	305-308	4
α-helix	311-313	3
α-helix	315-330	16
α-helix	335-350	16
α-helix	354-369	16

Chain B: 26 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	3
β-strand	42	1	3
α-helix	44-50	7
α-helix	54-63	10
α-helix	66-69	4
β-strand	72-76	5	4
β-strand	79-84	6	4
α-helix	86-93	8
α-helix	96-104	9
α-helix	119-126	8
α-helix	129-136	8
α-helix	152-158	7
α-helix	162-170	9
α-helix	185-192	8
α-helix	195-203	9
α-helix	217-224	8
α-helix	227-233	7
α-helix	241-257	17
α-helix	262-276	15
α-helix	280-282	3
α-helix	285-289	5
α-helix	294-296	3
α-helix	305-309	5
α-helix	310-313	4
α-helix	315-330	16
α-helix	335-350	16
α-helix	354-370	17

Chain C: 24 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	16-21	6
α-helix	28-36	9
β-strand	39	1	5
β-strand	42	1	5
α-helix	44-50	7
α-helix	54-63	10
β-strand	72-76	5	6
β-strand	79-84	6	6
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	185-190	6
α-helix	195-203	9
α-helix	206-208	3
α-helix	217-224	8
α-helix	227-233	7
α-helix	241-257	17
α-helix	262-276	15
α-helix	285-289	5
α-helix	294-296	3
α-helix	311-313	3
α-helix	315-329	15
α-helix	335-350	16
α-helix	354-370	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein fem-1 homolog C	A, B, C	protein	371	Homo sapiens	Q96JP0 (AlphaFold model)
Asn-arg-arg-arg-arg-trp-arg-glu-arg-gln-arg	D, E, F	protein	11	Human immunodeficiency virus 1	P04618

Sequence of entity 1 (A, B, C), FASTA

>7JYA_1 Protein fem-1 homolog C (chains A, B, C)
GDLKTAVFNAARDGKLRLLTKLLASKSKEEVSSLISEKTNGATPLLMAARYGHLDMVEFL
LEQCSASIEVGGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLNHGASVNNTTLTNSTPL
RAACFDGHLEIVKYLVEHKADLEVSNRHGHTCLMISCYKGHKEIAQYLLEKGADVNRKSV
KGNTALHDCAESGSLDIMKMLLMYCAKMEKDGYGMTPLLSASVTGHTNIVDFLTHHAQTS
KTERINALELLGATFVDKKRDLLGALKYWKKAMNMRYSDRTNIISKPVPQTLIMAYDYAK
EVNSAEELEGLIADPDEMRMQALLIRERILGPSHPDTSYYIRYRGAVYADSGNFKRCINL
WKYALDMQQSN

Sequence of entity 2 (D, E, F), FASTA

>7JYA_2 ASN-ARG-ARG-ARG-ARG-TRP-ARG-GLU-ARG-GLN-ARG (chains D, E, F)
NRRRRWRERQR

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:

6XKC 2.03 Å, Crystal structure of E3 ligase
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
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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