5YWR: RING E3 ligase ZNRF1

Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13). Determined by X-ray diffraction at 1.47 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 1.47 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,353
Mol. weight: 27.57 kDa
Ligands: ZN
Released: 6 Jun 2018

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

Secondary structure: helices and β-sheets

5YWR contains 12 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: 8 helices, 7 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	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	124-131	8
α-helix	133-147	15

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	143-144	2	3
β-strand	151-152	2	3
α-helix	154-156	3
α-helix	157-164	8
α-helix	168-170	3
β-strand	173-176	4	4
β-strand	183	1	5
β-strand	190	1	5
β-strand	196-199	4	4
β-strand	205-207	3	4
α-helix	208-215	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 N	A	protein	152	Homo sapiens	P61088 (AlphaFold model)
E3 ubiquitin-protein ligase ZNRF1	B	protein	89	Homo sapiens	Q8ND25 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YWR_1 Ubiquitin-conjugating enzyme E2 N (chains A)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 2 (B), FASTA

>5YWR_2 E3 ubiquitin-protein ligase ZNRF1 (chains B)
SHSGFKCPICSKSVASDEMEMHFIMCLSKPRLSYNDDVLTKDAGECVICLEELLQGDTIA
RLPCLCIYHKSCIDSWFEVNRSCPEHPAD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Water and common crystallization additives (FMT, PGE) are not listed.

Primary citation

Structural insights into the nanomolar affinity of RING E3 ligase ZNRF1 for Ube2N and its functional implications. Behera, A.P., Naskar, P., Agarwal, S. et al. Biochem J (2018) 475:1569-1582. DOI 10.1042/BCJ20170909 · 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
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
6P5B 2.1 Å, Crystal Structure of MavC in Complex with Ub-UbE2N

Browse structure collections

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