4LJP: E3 ubiquitin-protein ligase RNF31

Name: PDB 4LJP: Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex
Published: 2013-10-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex. Determined by X-ray diffraction at 2.15 Å resolution. Released 16 Oct 2013.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Homo sapiens, Bos taurus
Chains: 2
Atoms: 2,416
Mol. weight: 33.87 kDa
Ligands: ZN
Released: 16 Oct 2013

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

Secondary structure: helices and β-sheets

4LJP contains 17 α-helices and 16 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: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	858-864	7
α-helix	866-867	2
β-strand	868-870	3	1
β-strand	877-879	3	1
β-strand	887-889	3	2
β-strand	896-898	3	2
β-strand	904	1	2
β-strand	906	1	3
α-helix	907	1
β-strand	923	1	3
α-helix	931-934	4
α-helix	939-948	10
α-helix	961-964	4
β-strand	972-977	6	4
β-strand	980-985	6	4
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1034	12
α-helix	1040-1041	2
α-helix	1046-1060	15
α-helix	1062	1
α-helix	1064	1

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
β-strand	12-16	5	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-71	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF31	A	protein	223	Homo sapiens	Q96EP0 (AlphaFold model)
Polyubiquitin-C	B	protein	76	Bos taurus	P63048 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4LJP_1 E3 ubiquitin-protein ligase RNF31 (chains A)
GPGPEYQAQGLAMYLQENGIDCPKCKFSYALARGGCMHFACTQCRHQFCSGCYNAFYAKN
KCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVMFNTEPPAGARAVPGGGC
RVIEQKEVPNGLRDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETA
TERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRRRK

Sequence of entity 2 (B), FASTA

>4LJP_2 Polyubiquitin-C (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Stieglitz, B., Rana, R.R., Koliopoulos, M.G. et al. Nature (2013) 503:422-426. DOI 10.1038/nature12638 · PubMed

Other PDB entries of the same protein (UniProt Q96EP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KC5 1.54 Å, HOIP-HOIPIN1 complex
4LJO 1.56 Å, Structure of an active ligase (HOIP)/ubiquitin transfer complex
7V8F 1.66 Å, Crystal structure of UBE2L3 bound to HOIP RING1 domain.
4P09 1.7 Å, Crystal structure of HOIP PUB domain
9B0B 1.7 Å, Structure of Optineurin bound to HOIP NZF1 domain
9B12 1.81 Å, Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal…
4OWF 2.0 Å, Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain
4OYK 2.0 Å, Structure of HOIP PUB domain bound to OTULIN PIM
6SC5 2.1 Å, dAb3/HOIP-RBR-Ligand2
6SC8 2.11 Å, dAb3/HOIP-RBR-Ligand4
6KC6 2.12 Å, HOIP-HOIPIN8 complex
6GZY 2.15 Å, HOIP-fragment5 complex

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