5A4P: Ubiquitin-conjugating enzyme E2 Z

Structure of UBE2Z provides functional insight into specificity in the FAT10 conjugation machinery. Determined by X-ray diffraction at 2.1 Å resolution. Released 18 Nov 2015.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 1,911
Mol. weight: 38.97 kDa
Ligands: MLI
Released: 18 Nov 2015

Explore 5A4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5A4P contains 17 α-helices and 10 β-strands across 1 chain. 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: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	102-113	12
α-helix	115-116	2
β-strand	119-123	5	1
β-strand	130-136	7	1
α-helix	137-138	2
β-strand	147-153	7	1
α-helix	162-163	2
β-strand	164-167	4	1
β-strand	178	1	2
β-strand	181	1	2
β-strand	186	1	1
β-strand	187	1	2
α-helix	190-192	3
α-helix	199-200	2
α-helix	206-216	11
α-helix	221-224	4
α-helix	236-247	12
α-helix	248-255	8
α-helix	256-257	2
α-helix	265-277	13
α-helix	279-287	9
α-helix	290-292	3
α-helix	295	1
β-strand	296	1	3
α-helix	297	1
β-strand	307	1	3
α-helix	310-325	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 Z	A	protein	354	HOMO SAPIENS	Q9H832 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5A4P_1 UBIQUITIN-CONJUGATING ENZYME E2 Z (chains A)
MAESPTEEAATAGAGAAGPGASSVAGVVGVSGSGGGFGPPFLPDVWAAAAAAGGAGGPGS
GLAPLPGLPPSAAAHGAALLSHWDPTLSSDWDGERTAPQCLLRIKRDIMSIYKEPPPGMF
VVPDTVDMTKIHALITGPFDTPYEGGFFLFVFRCPPDYPIHPPRVKLMTTGNNTVRFNPN
FYRNGKVCLSILGTWTGPAWSPAQSISSVLISIQSLMTENPYHNEPGFEQERHPGDSKNY
NECIRHETIRVAVCDMMEGKCPCPEPLRGVMEKSFLEYYDFYEVACKDRLHLQGQTMQDP
FGEKRGHFDYQSLLMRLGLIRQKVLERLHNENAEMDSDSSSSGTETDLHGSLRV

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	5

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

Primary citation

Structure of Ube2Z Provides Functional Insight Into Specificity in the Fat10 Conjugation Machinery. Schelpe, J., Monte, D., Dewitte, F. et al. J Biol Chem (2016) 291:630. DOI 10.1074/JBC.M115.671545 · PubMed

Other PDB entries of the same protein (UniProt Q9H832 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9YKV 2.73 Å, Cryo-EM structure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT10(a) thioester mimetic…
28MO 3.01 Å, Cryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (singly loaded)
28MQ 3.04 Å, Cryo-EM structure of UBA6-FAT10Dha-UBE2Z trapped ternary complex
28MP 3.12 Å, Cryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)
9YLF 3.14 Å, Cryo-EM structure of single-loaded human UBA6-UBE2Z/Ub(a) adenylate complex.
9YLB 3.24 Å, Cryo-EM structure of single-loaded human UBA6-UBE2Z/FAT10(a) adenylate complex.
9YKW 3.86 Å, Cryo-EM structure of double-loaded human UBA6-UBE2Z-Ub(t)/Ub(a) thioester mimetic complex.

Browse structure collections

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