4AYC: RNF8 RING domain structure

RNF8 RING domain structure. Determined by X-ray diffraction at 1.9 Å resolution. Released 26 Sept 2012.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,360
Mol. weight: 34.26 kDa
Ligands: CPQ, ZN
Released: 26 Sept 2012

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

Secondary structure: helices and β-sheets

4AYC contains 14 α-helices and 14 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 A: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	350-400	51
β-strand	402	1	1
β-strand	409	1	1
α-helix	410	1
β-strand	413-416	4	2
β-strand	421-423	3	2
α-helix	424-430	7
β-strand	436	1	3
α-helix	442	1
β-strand	443	1	3
α-helix	444	1
β-strand	447-449	3	2
α-helix	451-461	11
α-helix	466-480	15

Chain B: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	361-395	35
α-helix	396-400	5
β-strand	402	1	4
β-strand	409	1	4
β-strand	413-416	4	5
β-strand	421-423	3	5
α-helix	424-433	10
β-strand	436	1	6
α-helix	442	1
β-strand	443	1	6
α-helix	444	1
β-strand	447-449	3	5
α-helix	451-461	11
α-helix	466-478	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF8	A	protein	138	HOMO SAPIENS	O76064 (AlphaFold model)
E3 ubiquitin-protein ligase RNF8	B	protein	138	HOMO SAPIENS	O76064 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4AYC_1 E3 UBIQUITIN-PROTEIN LIGASE RNF8 (chains A)
LGSMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICS
EYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSE
VKERRIVLIRERKAKRLF

Sequence of entity 2 (B), FASTA

>4AYC_2 E3 UBIQUITIN-PROTEIN LIGASE RNF8 (chains B)
LGSMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICS
EYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSE
VKERRIVLIRERKAKRLF

Ligands and cofactors

ID	Name	Formula	Copies
CPQ	N,n-BIS(3-D-gluconamidopropyl)deoxycholamide	C42 H75 N3 O15	1
ZN	Zinc ion	Zn	4

Water and common crystallization additives (SO4, GOL, CL) are not listed.

Primary citation

Rnf168 Ubiquitinates K13-15 on H2A/H2Ax to Drive DNA Damage Signaling. Mattiroli, F., Vissers, J.H.A., Van Dijk, W.J. et al. Cell (2012) 150:1182. DOI 10.1016/J.CELL.2012.08.005 · PubMed

Other PDB entries of the same protein (UniProt O76064 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PIE 1.35 Å, Crystal structure of the FHA domain of RNF8 in complex with its optimal phosphopeptide
4ORH 4.8 Å, Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer
4WHV 8.3 Å, E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and…
2CSW Solution structure of the FHA domain of human ubiquitin ligase protein RNF8

Browse structure collections

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