5AIU: A complex of RNF4-RING domain, Ubc13-Ub

A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink). Determined by X-ray diffraction at 2.21 Å resolution. Released 8 Jul 2015.

Method: X-ray diffraction
Resolution: 2.21 Å
Organisms: RATTUS NORVEGICUS, HOMO SAPIENS
Chains: 5
Atoms: 4,591
Mol. weight: 67.05 kDa
Ligands: ZN
Released: 8 Jul 2015

Explore 5AIU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AIU contains 26 α-helices and 46 β-strands across 5 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: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	135	1	1
β-strand	142	1	1
α-helix	143-148	6
α-helix	151-152	2
β-strand	153-156	4	2
β-strand	161-163	3	2
α-helix	164-173	10
β-strand	176	1	3
β-strand	183	1	3
β-strand	189-191	3	2
β-strand	200	1	4
β-strand	207	1	4
α-helix	208-213	6
α-helix	216-217	2
β-strand	218-220	3	5
β-strand	226-228	3	5
α-helix	229-238	10
β-strand	241	1	6
β-strand	248	1	6
β-strand	255-256	2	5

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

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-28	6	7
β-strand	31-40	10	7
α-helix	41-42	2
β-strand	51-57	7	7
α-helix	66-67	2
β-strand	68-71	4	7
β-strand	80	1	8
β-strand	85	1	7
β-strand	86	1	8
β-strand	88	1	9
α-helix	89-91	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-148	16

Chains C and F: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	10
β-strand	12-16	5	10
β-strand	22	1	11
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	10
β-strand	48-49	2	10
β-strand	55	1	11
β-strand	66-71	6	10
β-strand	75	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF4	A	protein	133	RATTUS NORVEGICUS	O88846 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B, E	protein	154	HOMO SAPIENS	P61088 (AlphaFold model)
Polyubiquitin-C	C, F	protein	76	HOMO SAPIENS	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5AIU_1 E3 UBIQUITIN-PROTEIN LIGASE RNF4 (chains A)
GAMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH
KRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR
KKINHKRYHPIYI

Sequence of entity 2 (B, E), FASTA

>5AIU_2 UBIQUITIN-CONJUGATING ENZYME E2 N (chains B, E)
GAMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFL
PEEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILADKWSPALQIRTVLLSIQALLSAPNPD
DPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 3 (C, F), FASTA

>5AIU_3 POLYUBIQUITIN-C (chains C, F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structural Basis for the Ring Catalyzed Synthesis of K63 Linked Ubiquitin Chains. Branigan, E., Plechanovova, A., Jaffray, E. et al. Nat Struct Mol Biol (2015) 22:597. DOI 10.1038/NSMB.3052 · PubMed

Other PDB entries of the same protein (UniProt O88846 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NG2 1.8 Å, Crystal structure of the RNF4 ring domain dimer
4AP4 2.21 Å, Rnf4 - ubch5a - ubiquitin heterotrimeric complex
5AIT 3.4 Å, A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink)

Browse structure collections

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