4WHV: E3 ubiquitin-protein ligase RNF8

E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B. Determined by X-ray diffraction at 8.3 Å resolution. Released 30 Sept 2015.

Method: X-ray diffraction
Resolution: 8.3 Å
Organism: Homo sapiens
Chains: 12
Atoms: 9,620
Mol. weight: 180.15 kDa
Ligands: ZN
Released: 30 Sept 2015

Explore 4WHV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WHV contains 70 α-helices and 90 β-strands across 12 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.

Chains A, F, G and L: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	22
β-strand	12-16	5	22
β-strand	22	1	23
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	22
β-strand	48-49	2	22
β-strand	55	1	23
α-helix	57-59	3
β-strand	66-70	5	22

Chains B, E, H and K: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	1
β-strand	34-40	7	1
α-helix	41-42	2
β-strand	51-57	7	1
α-helix	66-67	2
β-strand	68-71	4	1
β-strand	77	1	2
β-strand	80	1	2
β-strand	85	1	1
β-strand	86	1	2
α-helix	89-91	3
α-helix	101-113	13
α-helix	125-131	7
α-helix	133-147	15

Chain C: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	346-398	53
β-strand	402	1	3
β-strand	409	1	3
α-helix	410	1
β-strand	413-416	4	4
β-strand	421-423	3	4
α-helix	424-430	7
β-strand	436	1	5
α-helix	442	1
β-strand	443	1	5
α-helix	444	1
β-strand	447-449	3	4
α-helix	451-461	11
α-helix	466-479	14

Chain D: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	343-396	54
β-strand	402	1	6
β-strand	409	1	6
β-strand	413-416	4	7
β-strand	421-423	3	7
α-helix	424-433	10
β-strand	436	1	8
α-helix	442	1
β-strand	443	1	8
α-helix	444	1
β-strand	446	1	9
β-strand	447-449	3	7
α-helix	451-461	11
α-helix	466-479	14

Chain I: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	381-398	18
β-strand	402	1	14
β-strand	409	1	14
α-helix	410	1
β-strand	413-416	4	15
β-strand	421-423	3	15
α-helix	424-430	7
β-strand	436	1	16
α-helix	442	1
β-strand	443	1	16
α-helix	444	1
β-strand	447-449	3	15
α-helix	451-461	11
α-helix	466-479	14

Chain J: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	381-396	16
β-strand	402	1	17
β-strand	409	1	17
β-strand	413-416	4	18
β-strand	421-423	3	18
α-helix	424-433	10
β-strand	436	1	19
α-helix	442	1
β-strand	443	1	19
α-helix	444	1
β-strand	446	1	9
β-strand	447-449	3	18
α-helix	451-461	11
α-helix	466-479	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 N	B, E, H, K	protein	160	Homo sapiens	P61088 (AlphaFold model)
E3 ubiquitin-protein ligase RNF8	C, D, I, J	protein	149	Homo sapiens	O76064 (AlphaFold model)
Polyubiquitin-B	A, F, G, L	protein	83	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (B, E, H, K), FASTA

>4WHV_1 Ubiquitin-conjugating enzyme E2 N (chains B, E, H, K)
GPLGSPEFMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTF
KLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILKDKWSPALQIRTVLLSIQALL
SAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 2 (C, D, I, J), FASTA

>4WHV_2 E3 ubiquitin-protein ligase RNF8 (chains C, D, I, J)
GPLGSPEFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDV
LENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNC
INKMVNNLSSEVKERRIVLIRERKAKRLF

Sequence of entity 3 (A, F, G, L), FASTA

>4WHV_3 Polyubiquitin-B (chains A, F, G, L)
GPGYQDPMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG
RTLSDYNIQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment. Hodge, C.D., Ismail, I.H., Edwards, R.A. et al. J Biol Chem (2016) 291:9396-9410. DOI 10.1074/jbc.M116.715698 · PubMed

Other PDB entries of the same protein (UniProt P61088 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ONL 1.35 Å, Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P
4ONM 1.35 Å, Crystal structure of human Mms2/Ubc13 - NSC697923
5YWR 1.47 Å, Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13)
4ONN 1.5 Å, Crystal structure of human Mms2/Ubc13 - BAY 11-7082
9BIV 1.68 Å, Crystal Structure of Ubc13 with a New Active Site Loop Conformation
9LHJ 1.68 Å, UBE2N/UBE2V2 complexed with a covalent inhibitor
4DHI 1.8 Å, Structure of C. elegans OTUB1 bound to human UBC13
4NR3 1.8 Å, Crystal Structure of a human Mms2/Ubc13 L121G mutant
1J7D 1.85 Å, Crystal Structure of hMms2-hUbc13
4NRG 1.95 Å, Crystal Structure of a human Mms2/Ubc13 D118G mutant
6ULH 1.97 Å, Structure of MavC in complex with its substrate in R3 spacegroup
4TKP 2.08 Å, Complex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor

Browse structure collections

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