3KYD: SUMO-activating enzyme subunit 1

Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic. Determined by X-ray diffraction at 2.61 Å resolution. Released 16 Feb 2010.

Method: X-ray diffraction
Resolution: 2.61 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,978
Mol. weight: 113.91 kDa
Ligands: ZN, VMX
Released: 16 Feb 2010

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

Secondary structure: helices and β-sheets

3KYD contains 48 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: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	27-34	8
β-strand	38-42	5	1
α-helix	46-58	13
β-strand	62-66	5	1
α-helix	69	1
β-strand	70	1	2
α-helix	71-72	2
β-strand	90	1	2
α-helix	93-95	3
α-helix	96-101	6
β-strand	107-111	5	1
α-helix	115-117	3
α-helix	120-123	4
β-strand	128-131	4	1
α-helix	136-148	13
β-strand	152-159	8	1
β-strand	160	1	3
β-strand	162-168	7	1
β-strand	171-178	8	4
α-helix	179	1
β-strand	181-182	2	5
β-strand	205-212	8	4
α-helix	216-220	5
α-helix	227-233	7
α-helix	239-253	15
α-helix	259-261	3
α-helix	262-277	16
α-helix	278-280	3
α-helix	289-294	6
β-strand	298	1	3
α-helix	300-319	20
β-strand	328-332	5	1
β-strand	337-341	5	1

Chain B: 27 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
β-strand	20-23	4	1
α-helix	27-39	13
β-strand	43-47	5	1
α-helix	50	1
β-strand	51	1	6
α-helix	52	1
β-strand	55	1	7
β-strand	58	1	7
α-helix	65-67	3
β-strand	71	1	6
α-helix	72-81	10
β-strand	88-92	5	1
α-helix	103-106	4
β-strand	111-114	4	1
α-helix	119-132	14
β-strand	136-142	7	1
β-strand	145-151	7	1
α-helix	163-166	4
β-strand	170-171	2	8
α-helix	183-193	11
α-helix	244-247	4
α-helix	255-256	2
α-helix	257-261	5
α-helix	262-266	5
α-helix	277-279	3
α-helix	284-289	6
α-helix	315-334	20
α-helix	349-365	17
α-helix	373-381	9
β-strand	383-384	2	8
α-helix	385-386	2
α-helix	388-406	19
α-helix	410-412	3
β-strand	415-418	4	1
β-strand	427-432	6	1
α-helix	433-437	5
β-strand	449-454	6	9
β-strand	460	1	10
α-helix	461-464	4
α-helix	465-469	5
β-strand	478-482	5	9
β-strand	489-491	3	9
α-helix	499-501	3
β-strand	505	1	10
α-helix	506-509	4
β-strand	516-521	6	9
β-strand	526-534	9	9
β-strand	544-546	3	9

Chain D: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	5
β-strand	33-39	7	5
α-helix	45-55	11
β-strand	62-66	5	5
β-strand	69-70	2	5
α-helix	82-83	2
α-helix	86	1
β-strand	87-92	6	5

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	551	Homo sapiens	Q9UBT2 (AlphaFold model)
Small ubiquitin-related modifier 1	D	protein	115	Homo sapiens	P63165 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3KYD_1 SUMO-activating enzyme subunit 1 (chains A)
MVEKEEAGGGISEEEAAQYDRQIRLWGLEAQKRLRASRVLLVGLKGLGAEIAKNLILAGV
KGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPE
SFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTK
VAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKRTTSDY
FLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSLGISPDLLPEDFVRYCFSEMA
PVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK

Sequence of entity 2 (B), FASTA

>3KYD_2 SUMO-activating enzyme subunit 2 (chains B)
SLMALSRGLPRELAEAVAGGRVLVVGAGGIGCELLKNLVLTGFSHIDLIDLDTIDVSNLN
RQFLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDSIMNPDYNVEFFRQFILVMNALDN
RAARNHVNRMCLAADVPLIESGTAGYLGQVTTIKKGVTECYECHPKPTQRTFPGCTIRNT
PSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPTEAEARARACNEDGDIKRI
STKEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPLDWAEVQSQGEETNASD
QQNEPQLGLKDQQVLDVKSYARLFSKSIETLRVHLAEKGDGAELIWDKDDPSAMDFVTSA
ANLRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFL
NKQPNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAP
DVQIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADDFLQDYTLLINILHSEDL
GKDVEFEVVGD

Sequence of entity 3 (D), FASTA

>3KYD_3 Small ubiquitin-related modifier 1 (chains D)
MGSSHHHHHHSSGLVPRSHMSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMT
THLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQCG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
VMX	5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine	C13 H21 N7 O5 S	1

Water and common crystallization additives (EDO) are not listed.

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
3KYC 2.45 Å, Human SUMO E1 complex with a SUMO1-AMP mimic
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…
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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