3L1Z: U-BOX domain of human E4B ubiquitin ligase

Name: PDB 3L1Z: Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme
Published: 2010-05-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme. Determined by X-ray diffraction at 3.17 Å resolution. Released 5 May 2010.

Method: X-ray diffraction
Resolution: 3.17 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,865
Mol. weight: 29.55 kDa
Released: 5 May 2010

Explore 3L1Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3L1Z 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	-3-12	16
β-strand	21-25	5	1
β-strand	32-37	6	1
β-strand	50-55	6	1
α-helix	64-65	2
β-strand	66-69	4	1
β-strand	75	1	2
β-strand	78	1	2
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-110	12
α-helix	121-129	9
α-helix	131-144	14

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1230-1232	3
β-strand	1233	1	3
α-helix	1239	1
β-strand	1240	1	3
α-helix	1241	1
β-strand	1244-1246	3	4
β-strand	1252-1254	3	4
α-helix	1255-1264	10
β-strand	1267	1	5
β-strand	1274	1	5
α-helix	1277-1279	3
β-strand	1281-1282	2	4
α-helix	1284-1296	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D3	A	protein	157	Homo sapiens	P61077 (AlphaFold model)
Ubiquitin conjugation factor E4 B	B	protein	100	Homo sapiens	O95155 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3L1Z_1 Ubiquitin-conjugating enzyme E2 D3 (chains A)
MHHHHHHMNSMALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVF
FLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLL
CDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM

Sequence of entity 2 (B), FASTA

>3L1Z_2 Ubiquitin conjugation factor E4 B (chains B)
GSHKFAEKVEEIVAKNARAEIDYSDAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHL
LNSPTDPFNRQTLTESMLEPVPELKEQIQAWMREKQNSDH

Primary citation

Molecular Basis for the Association of Human E4B U Box Ubiquitin Ligase with E2-Conjugating Enzymes UbcH5c and Ubc4. Benirschke, R.C., Thompson, J.R., Nomine, Y. et al. Structure (2010) 18:955-965. DOI 10.1016/j.str.2010.04.017 · PubMed

Other PDB entries of the same protein (UniProt P61077 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EGG 1.76 Å, Crystal structure of human ubiquitin-conjugating enzyme UBCH5C
1X23 1.85 Å, Crystal structure of ubch5c
4S3O 2.0 Å, PCGF5-RING1B-UbcH5c complex
8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
5IFR 2.2 Å, Structure of the stable UBE2D3-UbDha conjugate
8UQ9 2.3 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker
8UQ8 2.34 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker
3UGB 2.35 Å, UbcH5c~Ubiquitin Conjugate
8AMS 2.4 Å, Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin
8UQB 2.48 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
6T7F 2.58 Å, RCR E3 ligase E2-Ubiquitin transthiolation intermediate
8UQC 2.61 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…

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