3KYC: Human SUMO E1 complex with a SUMO1-AMP mimic

Human SUMO E1 complex with a SUMO1-AMP mimic. Determined by X-ray diffraction at 2.45 Å resolution. Released 16 Feb 2010.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,681
Mol. weight: 123.56 kDa
Ligands: ZN, JZU
Released: 16 Feb 2010

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

Secondary structure: helices and β-sheets

3KYC contains 50 α-helices and 42 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: 15 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	13-18	6
α-helix	20-35	16
β-strand	38-42	5	1
α-helix	46-58	13
β-strand	62-66	5	1
β-strand	70	1	2
β-strand	79	1	3
β-strand	82	1	3
β-strand	90	1	2
α-helix	91-101	11
β-strand	107-111	5	1
α-helix	115-117	3
α-helix	120-125	6
β-strand	128-132	5	1
α-helix	136-148	13
β-strand	152-159	8	1
β-strand	160	1	4
β-strand	162-168	7	1
β-strand	171-177	7	5
β-strand	206-212	7	5
α-helix	216-220	5
α-helix	227-232	6
α-helix	233-235	3
α-helix	239-251	13
α-helix	262-278	17
α-helix	291-294	4
β-strand	298	1	4
α-helix	300-319	20
β-strand	321	1	5
α-helix	323-325	3
β-strand	328-332	5	1
β-strand	337-341	5	1

Chain B: 33 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
β-strand	19-23	5	1
α-helix	27-38	12
β-strand	43-48	6	1
β-strand	51	1	6
α-helix	54-58	5
α-helix	65-67	3
β-strand	71	1	6
α-helix	72-83	12
β-strand	88-93	6	1
α-helix	103-107	5
β-strand	111-114	4	1
α-helix	119-131	13
β-strand	136-142	7	1
β-strand	145-151	7	1
α-helix	165-168	4
α-helix	172-176	5
α-helix	182-197	16
α-helix	202-204	3
α-helix	213-215	3
α-helix	236-239	4
α-helix	240-247	8
α-helix	251-256	6
α-helix	257-261	5
α-helix	262-266	5
α-helix	270-273	4
α-helix	277-279	3
α-helix	284-289	6
α-helix	308-310	3
α-helix	315-335	21
α-helix	340-342	3
α-helix	349-365	17
α-helix	373-381	9
α-helix	388-406	19
β-strand	414-418	5	1
β-strand	427-433	7	1
α-helix	436-438	3
β-strand	449-454	6	7
β-strand	460	1	8
α-helix	461-463	3
α-helix	464-472	9
β-strand	479-482	4	7
β-strand	489-491	3	7
α-helix	499-501	3
β-strand	505	1	8
α-helix	506-509	4
β-strand	516-521	6	7
β-strand	526-534	9	7
β-strand	544-546	3	7
α-helix	620-626	7
α-helix	627-629	3
β-strand	636-638	3	9

Chain D: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	21-28	8	9
β-strand	33-39	7	9
α-helix	44-54	11
α-helix	59-61	3
β-strand	63-66	4	9
β-strand	69-70	2	9
β-strand	87-91	5	9
β-strand	96	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-activating enzyme subunit 1	A	protein	346	Homo sapiens	Q9UBE0 (AlphaFold model)
SUMO-activating enzyme subunit 2	B	protein	660	Homo sapiens	Q9UBT2 (AlphaFold model)
Small ubiquitin-related modifier 1	D	protein	97	Homo sapiens	P63165 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3KYC_1 SUMO-activating enzyme subunit 1 (chains A)
MVEKEEAGGGISEEEAAQYDRQIRLWGLEAQKRLRASRVLLVGLKGLGAEIAKNLILAGV
KGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPE
SFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTK
VAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKRTTSDY
FLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSLGISPDLLPEDFVRYCFSEMA
PVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK

Sequence of entity 2 (B), FASTA

>3KYC_2 SUMO-activating enzyme subunit 2 (chains B)
MGSSHHHHHHSSGLVPRGSHMALSRGLPRELAEAVAGGRVLVVGAGGIGCELLKNLVLTG
FSHIDLIDLDTIDVSNLNRQFLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDSIMNPD
YNVEFFRQFILVMNALDNRAARNHVNRMCLAADVPLIESGTAGYLGQVTTIKKGVTECYE
CHPKPTQRTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPT
EAEARARACNEDGDIKRISTKEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPV
PLDWAEVQSQGEETNASDQQNEPQLGLKDQQVLDVKSYARLFSKSIETLRVHLAEKGDGA
ELIWDKDDPSAMDFVTSAANLRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVL
EGLKILSGKIDQCRTIFLNKQPNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVT
VLTLQDKIVKEKFAMVAPDVQIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQAD
DFLQDYTLLINILHSEDLGKDVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTST
AQEQDDVLIVDSDEEDSSNNADVSEEERSRKRKLDEKENLSAKRSRIEQKEELDDVIALD

Sequence of entity 3 (D), FASTA

>3KYC_3 Small ubiquitin-related modifier 1 (chains D)
MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMN
SLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQCGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
JZU	5'-deoxy-5'-(sulfamoylamino)adenosine	C10 H15 N7 O5 S	1

Primary citation

Active site remodelling accompanies thioester bond formation in the SUMO E1. Olsen, S.K., Capili, A.D., Lu, X. et al. Nature (2010) 463:906-912. DOI 10.1038/nature08765 · PubMed

Other PDB entries of the same protein (UniProt Q9UBE0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QN5 1.97 Å, Crystal structure of human SUMO E1 with small unit cell parameters in the P1 21 1 space…
6XOG 1.98 Å, Structure of SUMO1-ML786519 adduct bound to SAE
6XOI 2.0 Å, Structure of SUMO1-ML00752641 adduct bound to SAE
8VY5 2.01 Å, Crystal structure of human SAE1
6XOH 2.23 Å, Structure of SUMO1-ML00789344 adduct bound to SAE
1Y8Q 2.25 Å, Sumo E1 activating enzyme SAE1-SAE2-MG-ATP complex
6CWY 2.46 Å, Crystal structure of SUMO E1 in complex with an allosteric inhibitor
9IF6 2.51 Å, Crystal structure of human SUMO E1 with large unit cell parameters in the P1 21 1 space…
3KYD 2.61 Å, Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic
9DRJ 2.7 Å, Cryo-EM structure of a SUMO E1-E2-SUMO1 complex.
1Y8R 2.75 Å, Sumo E1 activating enzyme SAE1-SAE2-SUMO1-MG-ATP complex
6CWZ 3.1 Å, Crystal structure of apo SUMO E1

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