5AIT: E3 ubiquitin-protein ligase RNF4

A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink). Determined by X-ray diffraction at 3.4 Å resolution. Released 8 Jul 2015.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: RATTUS NORVEGICUS, HOMO SAPIENS, BOS TAURUS
Chains: 7
Atoms: 6,742
Mol. weight: 99.7 kDa
Ligands: ZN
Released: 8 Jul 2015

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

Secondary structure: helices and β-sheets

5AIT contains 40 α-helices and 62 β-strands across 7 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: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	135-136	2	1
β-strand	141-142	2	1
α-helix	143-148	6
β-strand	153-156	4	2
β-strand	161-163	3	2
α-helix	164-171	8
β-strand	176	1	3
β-strand	183	1	3
β-strand	189-192	4	2
β-strand	193	1	4
β-strand	200-201	2	5
β-strand	206-207	2	5
α-helix	208-213	6
β-strand	218-221	4	6
β-strand	225	1	4
β-strand	226-228	3	6
α-helix	229-238	10
β-strand	241	1	7
β-strand	248	1	7
α-helix	251-253	3
β-strand	254-256	3	6

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	8
β-strand	34-40	7	8
α-helix	41-42	2
β-strand	51-57	7	8
α-helix	66-67	2
β-strand	68-71	4	8
β-strand	80	1	9
β-strand	85	1	8
β-strand	86	1	9
α-helix	89-91	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-148	16

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	10
β-strand	12-15	4	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
α-helix	50-51	2
β-strand	55	1	11
β-strand	66-71	6	10

Chain D: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
β-strand	31-35	5	12
β-strand	45-51	7	12
α-helix	52-53	2
β-strand	62-68	7	12
α-helix	77-78	2
β-strand	79-82	4	12
β-strand	84	1	13
β-strand	91	1	14
β-strand	97	1	12
β-strand	98	1	14
α-helix	99	1
α-helix	104-107	4
α-helix	115-127	13
α-helix	129-132	4
α-helix	137-138	2
β-strand	142	1	13

Chain E: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
β-strand	23-27	5	15
β-strand	34-40	7	15
α-helix	41-42	2
β-strand	51-57	7	15
α-helix	66-67	2
β-strand	68-71	4	15
β-strand	80	1	16
β-strand	85	1	15
β-strand	86	1	16
α-helix	89-91	3
α-helix	97-99	3
α-helix	100-113	14
α-helix	123-131	9
α-helix	133-148	16

Chain F: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	12-15	4	17
β-strand	22	1	18
α-helix	23-34	12
β-strand	41-45	5	17
β-strand	48-49	2	17
β-strand	55	1	18
β-strand	66-71	6	17

Chain G: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
β-strand	31-35	5	19
β-strand	45-51	7	19
α-helix	52-53	2
β-strand	62-68	7	19
α-helix	77-78	2
β-strand	79-82	4	19
β-strand	84	1	20
β-strand	91	1	21
β-strand	97	1	19
β-strand	98	1	21
α-helix	99	1
α-helix	104-107	4
α-helix	115-127	13
α-helix	129-132	4
β-strand	142	1	20

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	BOS TAURUS	P0CH28 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 variant 2	D, G	protein	147	HOMO SAPIENS	Q15819 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5AIT_1 E3 UBIQUITIN-PROTEIN LIGASE RNF4 (chains A)
GAMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH
KRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR
KKINHKRYHPIYI

Sequence of entity 2 (B, E), FASTA

>5AIT_2 UBIQUITIN-CONJUGATING ENZYME E2 N (chains B, E)
GAMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFL
PEEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILADKWSPALQIRTVLLSIQALLSAPNPD
DPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 3 (C, F), FASTA

>5AIT_3 POLYUBIQUITIN-C (chains C, F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 4 (D, G), FASTA

>5AIT_4 UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2 (chains D, G)
GAMAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNY
ENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVV
LQELRRLMMSKENMKLPQPPEGQTYNN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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
5AIU 2.21 Å, A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink)

Browse structure collections

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