1Z5S: Ubiquitin-conjugating enzyme E2 I

Name: PDB 1Z5S: Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2
Published: 2005-06-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2. Determined by X-ray diffraction at 3.01 Å resolution. Released 7 Jun 2005.

Method: X-ray diffraction
Resolution: 3.01 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,592
Mol. weight: 55.74 kDa
Released: 7 Jun 2005

Explore 1Z5S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Z5S contains 21 α-helices and 13 β-strands across 4 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	25-30	6	1
β-strand	36-46	11	1
β-strand	57-63	7	1
α-helix	72-73	2
β-strand	74-77	4	1
β-strand	86	1	2
β-strand	91	1	1
β-strand	92	1	2
α-helix	93	1
α-helix	95-97	3
α-helix	109-121	13
α-helix	131-139	9
α-helix	141-153	13

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	3
β-strand	33-38	6	3
α-helix	44-53	10
β-strand	64-66	3	3
β-strand	69-70	2	3
α-helix	77-80	4
β-strand	87-90	4	3

Chain C: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	433-439	7
α-helix	447-453	7
α-helix	457-460	4
α-helix	466-477	12
α-helix	485-501	17
α-helix	509-519	11
α-helix	536-545	10
α-helix	556-564	9
α-helix	569-571	3
α-helix	574-586	13

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2632-2637	6	3
α-helix	2642-2650	9
α-helix	2677-2683	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 I	A	protein	158	Homo sapiens	P63279 (AlphaFold model)
Ubiquitin-like protein SMT3C	B	protein	82	Homo sapiens	P63165 (AlphaFold model)
Ran GTPase-activating protein 1	C	protein	172	Homo sapiens	P46060 (AlphaFold model)
Ran-binding protein 2	D	protein	83	Homo sapiens	P49792

Sequence of entity 1 (A), FASTA

>1Z5S_1 Ubiquitin-conjugating enzyme E2 I (chains A)
MSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKL
RMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELL
NEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS

Sequence of entity 2 (B), FASTA

>1Z5S_2 Ubiquitin-like protein SMT3C (chains B)
MGEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNH
TPKELGMEEEDVIEVYQEQTGG

Sequence of entity 3 (C), FASTA

>1Z5S_3 Ran GTPase-activating protein 1 (chains C)
SLNTGEPAPVLSSPPPADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLK
VSSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANL
YGPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV

Sequence of entity 4 (D), FASTA

>1Z5S_4 Ran-binding protein 2 (chains D)
SLDVLIVYELTPTAEQKALATKLKLPPTFFCYKNRPDYVSEEEEDDEDFETAVKKLNGKL
YLDGSEKCRPLEENTADNEKECI

Primary citation

Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex. Reverter, D., Lima, C.D. Nature (2005) 435:687-692. DOI 10.1038/nature03588 · PubMed

Other PDB entries of the same protein (UniProt P63279 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5F6E 1.12 Å, Crystal Structure of human Ubc9 (K48A/K49A/E54A)
5F6Y 1.14 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)
2GRR 1.3 Å, Crystal Structure of human RanGAP1-Ubc9-D127S
5F6V 1.49 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol from…
5F6U 1.55 Å, Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146)
5F6D 1.55 Å, Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6
5F6X 1.56 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole…
5F6W 1.7 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol)
2GRO 1.7 Å, Crystal Structure of human RanGAP1-Ubc9-N85Q
2GRQ 1.7 Å, Crystal Structure of human RanGAP1-Ubc9-D127A
9GLR 1.72 Å, Crystal Structure of Human UBC9 C93E
2GRN 1.8 Å, Crystal Structure of human RanGAP1-Ubc9

Browse structure collections

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