3UIP: SUMO-conjugating enzyme UBC9

Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II. Determined by X-ray diffraction at 2.29 Å resolution. Released 28 Dec 2011.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,954
Mol. weight: 53.8 kDa
Released: 28 Dec 2011

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

Secondary structure: helices and β-sheets

3UIP contains 26 α-helices and 15 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	25-30	6	1
α-helix	31	1
β-strand	36-46	11	1
α-helix	47-48	2
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
β-strand	94	1	3
α-helix	95-97	3
α-helix	109-121	13
α-helix	131-139	9
α-helix	141-154	14

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	21-28	8	4
β-strand	33-39	7	4
α-helix	45-55	11
α-helix	59-61	3
β-strand	62-66	5	4
β-strand	69-70	2	4
α-helix	71-72	2
α-helix	77-80	4
β-strand	87-92	6	4
β-strand	96	1	3

Chain C: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	433-439	7
α-helix	443-448	6
α-helix	453-460	8
α-helix	466-477	12
α-helix	484-502	19
α-helix	509-519	11
α-helix	536-545	10
α-helix	553-555	3
α-helix	556-564	9
α-helix	568-572	5
α-helix	574-585	12

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2632-2637	6	4
α-helix	2642-2650	9
α-helix	2657-2661	5
α-helix	2677-2682	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-conjugating enzyme UBC9	A	protein	158	Homo sapiens	P63279 (AlphaFold model)
Small ubiquitin-related modifier 1	B	protein	80	Homo sapiens	P63165 (AlphaFold model)
Ran GTPase-activating protein 1	C	protein	171	Homo sapiens	P46060 (AlphaFold model)
E3 SUMO-protein ligase RanBP2	D	protein	67	Homo sapiens	P49792

Sequence of entity 1 (A), FASTA

>3UIP_1 SUMO-conjugating enzyme UBC9 (chains A)
MSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKL
RMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELL
NEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS

Sequence of entity 2 (B), FASTA

>3UIP_2 Small ubiquitin-related modifier 1 (chains B)
EGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTP
KELGMEEEDVIEVYQEQTGG

Sequence of entity 3 (C), FASTA

>3UIP_3 Ran GTPase-activating protein 1 (chains C)
SLTGEPAPVLSSPPPADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKV
SSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLY
GPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV

Sequence of entity 4 (D), FASTA

>3UIP_4 E3 SUMO-protein ligase RanBP2 (chains D)
SLDVLIVYELTPTVEEKAKADTLKLPPTFFCYKNRPDYVSEEEEDDEDFETAVKKLNGKL
YLDGSEK

Primary citation

Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2. Gareau, J.R., Reverter, D., Lima, C.D. J Biol Chem (2012) 287:4740-4751. DOI 10.1074/jbc.M111.321141 · 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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