1Y8R: Ubiquitin-like 1 activating enzyme E1A

Sumo E1 activating enzyme SAE1-SAE2-SUMO1-MG-ATP complex. Determined by X-ray diffraction at 2.75 Å resolution. Released 25 Jan 2005.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 6
Atoms: 14,695
Mol. weight: 243.06 kDa
Ligands: MG, ZN, ATP
Released: 25 Jan 2005

Explore 1Y8R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Y8R contains 92 α-helices and 86 β-strands across 6 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: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	20-26	7
α-helix	28-35	8
β-strand	38-42	5	1
α-helix	46-58	13
β-strand	62-66	5	1
β-strand	70	1	2
β-strand	90	1	2
α-helix	93-95	3
α-helix	96-101	6
β-strand	107-111	5	1
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	171-177	7	4
β-strand	206-212	7	4
α-helix	216-220	5
α-helix	227-230	4
α-helix	239-252	14
α-helix	259-261	3
α-helix	262-280	19
α-helix	284-286	3
α-helix	289-293	5
β-strand	298	1	3
α-helix	300-319	20
β-strand	321	1	4
β-strand	328-332	5	1
β-strand	337-341	5	1

Chain B: 27 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-17	8
β-strand	19-23	5	1
α-helix	27-39	13
β-strand	43-48	6	1
β-strand	51	1	5
α-helix	54-58	5
α-helix	65-67	3
β-strand	71	1	5
α-helix	72-82	11
β-strand	88-93	6	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	172-176	5
α-helix	182-194	13
α-helix	208-209	2
β-strand	211	1	6
β-strand	216	1	6
α-helix	241-246	6
α-helix	251-256	6
α-helix	257-261	5
α-helix	262-267	6
α-helix	284-287	4
α-helix	308-310	3
α-helix	315-333	19
α-helix	349-365	17
α-helix	368-370	3
α-helix	373-380	8
α-helix	388-406	19
α-helix	410-412	3
β-strand	414-418	5	1
β-strand	427-433	7	1
α-helix	434-437	4
β-strand	449-454	6	7
β-strand	460	1	8
α-helix	461-463	3
α-helix	464-472	9
β-strand	481-482	2	7
β-strand	488-489	2	7
β-strand	505	1	8
α-helix	506-509	4
β-strand	516-521	6	7
α-helix	522-524	3
β-strand	526-533	8	7
β-strand	544-546	3	7

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	9
β-strand	22-27	6	9
β-strand	33-38	6	9
α-helix	45-55	11
α-helix	59-61	3
β-strand	62-66	5	9
β-strand	69-70	2	9
α-helix	77-80	4
α-helix	86	1
β-strand	87-92	6	9
β-strand	96	1	1

Chain D: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	13-18	6
α-helix	20-35	16
β-strand	38-42	5	10
α-helix	46-58	13
β-strand	62-66	5	10
β-strand	70	1	11
α-helix	83	1
β-strand	90	1	11
α-helix	93-101	9
β-strand	107-111	5	10
α-helix	115-117	3
α-helix	120-124	5
β-strand	128-132	5	10
α-helix	136-148	13
β-strand	152-159	8	10
β-strand	160	1	12
β-strand	162-168	7	10
β-strand	171-175	5	13
β-strand	208-212	5	13
α-helix	216-220	5
α-helix	229-235	7
α-helix	239-252	14
α-helix	256-258	3
α-helix	259-261	3
α-helix	262-279	18
α-helix	284-286	3
α-helix	289-293	5
β-strand	298	1	12
α-helix	300-319	20
β-strand	321	1	13
β-strand	328-332	5	10
β-strand	337-341	5	10

Chain E: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
β-strand	19-23	5	10
α-helix	27-39	13
β-strand	43-48	6	10
β-strand	51	1	14
α-helix	54-56	3
α-helix	65-67	3
β-strand	71	1	14
α-helix	72-80	9
β-strand	88-93	6	10
α-helix	103-106	4
β-strand	111-114	4	10
α-helix	119-132	14
β-strand	136-142	7	10
β-strand	143	1	15
β-strand	145-151	7	10
α-helix	159-161	3
α-helix	167-169	3
α-helix	172-176	5
α-helix	182-197	16
β-strand	212	1	16
β-strand	215	1	16
α-helix	240-247	8
α-helix	251-256	6
α-helix	257-261	5
α-helix	262-267	6
α-helix	272-274	3
α-helix	284-287	4
α-helix	308-310	3
α-helix	315-333	19
β-strand	335	1	17
β-strand	337	1	17
α-helix	349-364	16
α-helix	368-372	5
α-helix	373-381	9
β-strand	386	1	15
α-helix	388-405	18
β-strand	415-418	4	10
β-strand	427-432	6	10
β-strand	449-454	6	18
β-strand	460	1	19
α-helix	461-463	3
α-helix	464-470	7
α-helix	471-472	2
β-strand	479-482	4	18
β-strand	488-491	4	18
β-strand	505	1	19
α-helix	506-509	4
β-strand	516-521	6	18
β-strand	526-534	9	18
β-strand	544-546	3	18

Chain F: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	20
β-strand	33-38	6	20
α-helix	45-53	9
β-strand	62-66	5	20
β-strand	69-70	2	20
β-strand	87-92	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like 1 activating enzyme E1A	A, D	protein	346	Homo sapiens	Q9UBE0 (AlphaFold model)
Ubiquitin-like 2 activating enzyme E1B	B, E	protein	640	Homo sapiens	Q9UBT2 (AlphaFold model)
Ubiquitin-like protein SMT3C	C, F	protein	97	Homo sapiens	P63165 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>1Y8R_1 Ubiquitin-like 1 activating enzyme E1A (chains A, D)
MVEKEEAGGGISEEEAAQYDRQIRLWGLEAQKRLRASRVLLVGLKGLGAEIAKNLILAGV
KGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPE
SFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTK
VAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKRTTSDY
FLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSLGISPDLLPEDFVRYCFSEMA
PVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK

Sequence of entity 2 (B, E), FASTA

>1Y8R_2 Ubiquitin-like 2 activating enzyme E1B (chains B, E)
MALSRGLPRELAEAVAGGRVLVVGAGGIGCELLKNLVLTGFSHIDLIDLDTIDVSNLNRQ
FLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDSIMNPDYNVEFFRQFILVMNALDNRA
ARNHVNRMCLAADVPLIESGTAGYLGQVTTIKKGVTECYECHPKPTQRTFPGATIRNTPS
EPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPTEAEARARASNEDGDIKRIST
KEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPLDWAEVQSQGEETNASDQQ
NEPQLGLKDQQVLDVKSYARLFSKSIETLRVHLAEKGDGAELIWDKDDPSAMDFVTSAAN
LRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNK
QPNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDV
QIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADDFLQDYTLLINILHSEDLGK
DVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTSTAQEQDDVLIVDSDEEDSSNN
ADVSEEERSRKRKLDEKENLSAKRSRIEQKEELDDVIALD

Sequence of entity 3 (C, F), FASTA

>1Y8R_3 Ubiquitin-like protein SMT3C (chains C, F)
MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMN
SLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1. Lois, L.M., Lima, C.D. EMBO J (2005) 24:439-451. DOI 10.1038/sj.emboj.7600552 · 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…
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.
6CWZ 3.1 Å, Crystal structure of apo SUMO E1

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