2IO2: Human Senp2

Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1. Determined by X-ray diffraction at 2.9 Å resolution. Released 21 Nov 2006.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,696
Mol. weight: 55.49 kDa
Released: 21 Nov 2006

Explore 2IO2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IO2 contains 27 α-helices and 16 β-strands across 3 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: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	370-374	5
α-helix	377-380	4
β-strand	390-392	3	1
β-strand	395-397	3	1
α-helix	399-403	5
α-helix	409-411	3
α-helix	414-426	13
β-strand	435-437	3	2
α-helix	443-449	7
α-helix	452-457	6
α-helix	463-465	3
β-strand	468-475	8	2
β-strand	478-485	8	2
β-strand	490-494	5	2
α-helix	502-517	16
β-strand	530-533	4	2
α-helix	548-559	12
α-helix	569-571	3
α-helix	572-585	14

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	3
β-strand	36	1	3
β-strand	40	1	4
β-strand	42	1	4
α-helix	45-51	7
α-helix	52-54	3
β-strand	62-64	3	5
β-strand	65-66	2	6
β-strand	69-70	2	6
α-helix	77-80	4
α-helix	82-83	2
β-strand	86-87	2	3
β-strand	90-92	3	5

Chain C: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	434-439	6
α-helix	443-447	5
α-helix	450-452	3
α-helix	453-459	7
α-helix	466-477	12
α-helix	484-502	19
α-helix	509-519	11
α-helix	528-547	20
α-helix	555-562	8
α-helix	566-569	4
α-helix	573-584	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 2	A	protein	232	Homo sapiens	Q9HC62 (AlphaFold model)
Small ubiquitin-related modifier 1	B	protein	82	Homo sapiens	P63165 (AlphaFold model)
Ran GTPase-activating protein 1	C	protein	172	Homo sapiens	P46060 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2IO2_1 Sentrin-specific protease 2 (chains A)
GSHMASDLLELTEDMEKEISNALGHGPQDEILSSAFKLRITRGDIQTLKNYHWLNDEVIN
FYMNLLVERNKKQGYPALHVFSTFFYPKLKSGGYQAVKRWTKGVNLFEQEIILVPIHRKV
HWSLVVIDLRKKCLKYLDSMGQKGHRICEILLQYLQDESKTKRNSDLNLLEWTHHSMKPH
EIPQQLNGSDSGMFTCKYADYISRDKPITFTQHQMPLFRKKMVWEILHQQLL

Sequence of entity 2 (B), FASTA

>2IO2_2 Small ubiquitin-related modifier 1 (chains B)
MGEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNH
TPKELGMEEEDVIEVYQEQTGG

Sequence of entity 3 (C), FASTA

>2IO2_3 Ran GTPase-activating protein 1 (chains C)
SLNTGEPAPVLSSPPPADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLK
VSSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANL
YGPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESSSFARHSLLQTLYKV

Primary citation

Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates. Reverter, D., Lima, C.D. Nat Struct Mol Biol (2006) 13:1060-1068. DOI 10.1038/nsmb1168 · PubMed

Other PDB entries of the same protein (UniProt Q9HC62 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZO5 2.15 Å, Structure of SENP2-Loop1 in complex with preSUMO-2
1TH0 2.2 Å, Structure of human Senp2
2IO0 2.3 Å, Crystal structure of human Senp2 in complex with preSUMO-2
2IO1 2.6 Å, Crystal structure of human Senp2 in complex with preSUMO-3
1TGZ 2.8 Å, Structure of human Senp2 in complex with SUMO-1
5AEK 3.0 Å, Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W
2IO3 3.2 Å, Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2

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