4ORH: RNF8

Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer. Determined by X-ray diffraction at 4.8 Å resolution. Released 26 Feb 2014.

Method: X-ray diffraction
Resolution: 4.8 Å
Organism: Homo sapiens
Chains: 11
Atoms: 11,524
Mol. weight: 194.21 kDa
Ligands: ZN
Released: 26 Feb 2014

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

Secondary structure: helices and β-sheets

4ORH contains 83 α-helices and 86 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: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	11-24	14
β-strand	31-35	5	1
β-strand	45-51	7	1
α-helix	52-53	2
β-strand	62-68	7	1
α-helix	77-78	2
β-strand	79-82	4	1
β-strand	84	1	2
β-strand	91	1	3
β-strand	97	1	1
β-strand	98	1	3
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-126	12
α-helix	129-132	4
α-helix	137-138	2
β-strand	142	1	2

Chains B, F and J: 8 helices, 8 β-strands

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

Chain C: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	393-396	4
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	447-449	3	7
α-helix	451-461	11
α-helix	466-482	17

Chains E and I: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-24	14
β-strand	31-35	5	9
β-strand	45-51	7	9
α-helix	52-53	2
β-strand	62-68	7	9
α-helix	77-78	2
β-strand	79-82	4	9
β-strand	84	1	10
β-strand	91	1	11
β-strand	97	1	9
β-strand	98	1	11
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-126	12
α-helix	129-132	4
α-helix	137-138	2
β-strand	142	1	10

Chains G and K: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	346-400	55
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	466-482	17

Chain H: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	343-396	54
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	447-449	3	18
α-helix	451-461	11
α-helix	466-482	17

Chain L: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	343-393	51
β-strand	402	1	28
β-strand	409	1	28
β-strand	413-416	4	29
β-strand	421-423	3	29
α-helix	424-433	10
β-strand	436	1	30
α-helix	442	1
β-strand	443	1	30
α-helix	444	1
β-strand	447-449	3	29
α-helix	451-461	11
α-helix	466-482	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 variant 2	A, E, I	protein	153	Homo sapiens	Q15819 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B, F, J	protein	160	Homo sapiens	P61088 (AlphaFold model)
E3 ubiquitin-protein ligase RNF8	C, G, H, K, L	protein	149	Homo sapiens	O76064 (AlphaFold model)

Sequence of entity 1 (A, E, I), FASTA

>4ORH_1 Ubiquitin-conjugating enzyme E2 variant 2 (chains A, E, I)
GPLGSPEFMAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIG
PPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNS
YSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN

Sequence of entity 2 (B, F, J), FASTA

>4ORH_2 Ubiquitin-conjugating enzyme E2 N (chains B, F, J)
GPLGSPEFMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTF
KLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALL
SAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 3 (C, G, H, K, L), FASTA

>4ORH_3 E3 ubiquitin-protein ligase RNF8 (chains C, G, H, K, L)
GPLGSPEFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDV
LENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNC
INKMVNNLSSEVKERRIVLIRERKAKRLF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	10

Primary citation

Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation. Campbell, S.J., Edwards, R.A., Leung, C.C. et al. J Biol Chem (2012) 287:23900-23910. DOI 10.1074/jbc.M112.359653 · PubMed

Other PDB entries of the same protein (UniProt Q15819 (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
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
8WR5 1.7 Å, The Crystal Structure of Mms2 from Biortus
4NR3 1.8 Å, Crystal Structure of a human Mms2/Ubc13 L121G mutant
1J7D 1.85 Å, Crystal Structure of hMms2-hUbc13
1J74 1.9 Å, Crystal Structure of Mms2
4NRG 1.95 Å, Crystal Structure of a human Mms2/Ubc13 D118G mutant
9N1F 2.1 Å, Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex
7BBD 2.2 Å, Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin…

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