2EKE: SUMO-binding-motif mimic

Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a noncovalent Ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway. Determined by X-ray diffraction at 1.9 Å resolution. Released 29 May 2007.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 4,290
Mol. weight: 60.25 kDa
Released: 29 May 2007

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

Secondary structure: helices and β-sheets

2EKE contains 20 α-helices and 24 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
β-strand	25-30	6	1
β-strand	36-46	11	1
α-helix	47-48	2
β-strand	57-63	7	1
β-strand	74-76	3	1
β-strand	86	1	2
β-strand	91	1	1
β-strand	92	1	2
α-helix	95-97	3
α-helix	109-121	13
α-helix	131-139	9
α-helix	141-154	14

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
β-strand	25-30	6	3
α-helix	31	1
β-strand	36-46	11	3
α-helix	47-48	2
β-strand	57-63	7	3
α-helix	72-73	2
β-strand	74-76	3	3
β-strand	86	1	4
β-strand	91	1	3
β-strand	92	1	4
α-helix	95-97	3
α-helix	109-120	12
α-helix	131-139	9
α-helix	141-154	14

Chain C: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	1013-1020	8
β-strand	1023-1029	7	5
β-strand	1034-1040	7	5
α-helix	1046-1056	11
α-helix	1060-1062	3
β-strand	1063-1067	5	5
β-strand	1070-1071	2	5
α-helix	1072-1073	2
β-strand	1087-1093	7	5

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	1023-1029	7	6
β-strand	1034-1040	7	6
α-helix	1046-1056	11
α-helix	1060-1062	3
β-strand	1063-1067	5	6
β-strand	1070-1071	2	6
β-strand	1087-1093	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-conjugating enzyme UBC9	A, B	protein	157	Saccharomyces cerevisiae	P50623 (AlphaFold model)
Ubiquitin-like protein SMT3	C, D	protein	106	Saccharomyces cerevisiae	Q12306 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2EKE_1 SUMO-conjugating enzyme UBC9 (chains A, B)
MSSLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPI
TVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLL
DSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK

Sequence of entity 2 (C, D), FASTA

>2EKE_2 Ubiquitin-like protein SMT3 (chains C, D)
MGSSHHHHHHSQDPLVPRGSEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAF
AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG

Primary citation

Structure of a SUMO-binding-motif Mimic Bound to Smt3p-Ubc9p: Conservation of a Non-covalent Ubiquitin-like Protein-E2 Complex as a Platform for Selective Interactions within a SUMO Pathway. Duda, D.M., van Waardenburg, R.C.A.M., Borg, L.A. et al. J Mol Biol (2007) 369:619-630. DOI 10.1016/j.jmb.2007.04.007 · PubMed

Other PDB entries of the same protein (UniProt P50623 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2GJD 1.75 Å, Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic…
3ONG 2.3 Å, Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways
5JNE 2.85 Å, E2-SUMO-Siz1 E3-SUMO-PCNA complex
7P47 3.31 Å, Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic
6Q83 4.53 Å, Crystal structure of the biportin Pdr6 in complex with UBC9

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