6DC6: Human ubiquitin activating enzyme E1

Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin. Determined by X-ray diffraction at 3.14 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 3.14 Å
Organism: Homo sapiens
Chains: 4
Atoms: 16,888
Mol. weight: 245.27 kDa
Ligands: MG, POP
Released: 10 Oct 2018

Explore 6DC6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DC6 contains 121 α-helices and 117 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: 58 helices, 50 β-strands

Element	Residues	Length	Sheet
α-helix	56-71	16
β-strand	74-78	5	1
α-helix	82-94	13
β-strand	98-102	5	1
β-strand	106	1	2
α-helix	109-111	3
β-strand	126	1	2
α-helix	127-130	4
α-helix	132-135	4
β-strand	144-145	2	1
α-helix	156-158	3
β-strand	161-165	5	1
α-helix	169-182	14
β-strand	185-192	8	1
β-strand	195-201	7	1
β-strand	206-208	3	3
α-helix	214-217	4
β-strand	218-220	3	4
β-strand	221-224	4	5
β-strand	229-234	6	5
α-helix	235	1
β-strand	247-251	5	4
β-strand	254	1	6
β-strand	260	1	4
α-helix	262-264	3
β-strand	265-266	2	4
β-strand	268-269	2	5
β-strand	274-279	6	5
β-strand	288	1	6
β-strand	291-295	5	4
α-helix	296-298	3
β-strand	299-301	3	3
α-helix	306-311	6
β-strand	315-316	2	1
α-helix	320-322	3
α-helix	325-342	18
α-helix	346-348	3
α-helix	353-367	15
α-helix	380-388	9
α-helix	395-412	18
α-helix	418-420	3
β-strand	423-427	5	1
α-helix	429-431	3
α-helix	452-455	4
α-helix	460-467	8
β-strand	470-474	5	7
α-helix	478-490	13
β-strand	499-503	5	7
α-helix	506	1
β-strand	507	1	8
α-helix	508	1
α-helix	510-514	5
β-strand	527	1	8
α-helix	528-539	12
β-strand	545-548	4	7
α-helix	555-557	3
α-helix	562-566	5
β-strand	570-573	4	7
α-helix	578-590	13
β-strand	595-601	7	7
β-strand	604-610	7	7
β-strand	615	1	9
α-helix	618-620	3
α-helix	624-626	3
α-helix	632-635	4
α-helix	641-652	12
α-helix	653-657	5
α-helix	658-668	11
α-helix	672-678	7
α-helix	684-692	9
α-helix	693-697	5
α-helix	703-715	13
α-helix	716-720	5
α-helix	721-728	8
β-strand	734	1	10
β-strand	740	1	10
α-helix	759-776	18
α-helix	784-791	8
α-helix	822-832	11
α-helix	834-835	2
α-helix	858-872	15
α-helix	875-877	3
α-helix	880-887	8
α-helix	890-892	3
α-helix	895-912	18
β-strand	924-928	5	7
β-strand	933-937	5	7
α-helix	938-940	3
β-strand	941	1	9
α-helix	942-943	2
β-strand	944-947	4	11
β-strand	950-953	4	11
β-strand	957-961	5	12
β-strand	963	1	13
β-strand	969	1	13
α-helix	970	1
β-strand	971	1	14
α-helix	972-981	10
β-strand	986-992	7	15
β-strand	995-999	5	15
α-helix	1004-1011	8
β-strand	1014	1	14
α-helix	1015-1022	8
α-helix	1026-1028	3
β-strand	1035-1036	2	12
β-strand	1037-1041	5	15
β-strand	1047-1049	3	15
β-strand	1052-1056	5	12

Chain B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	16
β-strand	12-16	5	16
β-strand	22	1	17
α-helix	23-31	9
α-helix	38-40	3
β-strand	42-45	4	16
β-strand	48-49	2	16
β-strand	55	1	17
β-strand	66-70	5	16
β-strand	75	1	7

Chain C: 59 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	56-71	16
β-strand	74-78	5	18
α-helix	83-94	12
β-strand	98-102	5	18
β-strand	106	1	19
β-strand	126	1	19
α-helix	127-130	4
α-helix	132-135	4
β-strand	144-145	2	18
α-helix	153-156	4
β-strand	161-165	5	18
α-helix	169-182	14
β-strand	185-192	8	18
β-strand	195-201	7	18
β-strand	206-208	3	20
α-helix	214-217	4
β-strand	218-220	3	21
β-strand	221-224	4	22
β-strand	231-234	4	22
β-strand	247-251	5	21
α-helix	259-261	3
α-helix	262-264	3
β-strand	265-266	2	21
β-strand	268-269	2	22
β-strand	274-276	3	22
β-strand	291-295	5	21
α-helix	296-298	3
β-strand	299-301	3	20
α-helix	306-311	6
β-strand	315-317	3	18
α-helix	325-342	18
α-helix	346-348	3
α-helix	352-367	16
α-helix	380-388	9
α-helix	395-412	18
α-helix	418-420	3
β-strand	423-427	5	18
α-helix	429-431	3
α-helix	433	1
α-helix	434-436	3
α-helix	440-443	4
α-helix	452-455	4
α-helix	460-467	8
β-strand	470-474	5	23
α-helix	478-490	13
β-strand	494	1	24
β-strand	499-503	5	23
α-helix	506	1
β-strand	507	1	25
α-helix	508-509	2
α-helix	510-514	5
β-strand	527	1	25
α-helix	528-539	12
β-strand	543	1	24
β-strand	545-548	4	23
α-helix	555-557	3
α-helix	562-566	5
β-strand	570-573	4	23
α-helix	578-590	13
β-strand	595-601	7	23
β-strand	602	1	26
β-strand	604-610	7	23
β-strand	615	1	27
α-helix	618-620	3
α-helix	624-626	3
α-helix	632-635	4
α-helix	641-652	12
α-helix	653-657	5
α-helix	658-668	11
α-helix	672-676	5
α-helix	682-692	11
α-helix	693-697	5
α-helix	703-715	13
α-helix	716-720	5
α-helix	721-728	8
β-strand	734	1	28
β-strand	740	1	28
α-helix	759-776	18
α-helix	779-781	3
α-helix	784-791	8
α-helix	817-832	16
α-helix	834-835	2
α-helix	858-872	15
α-helix	875-877	3
α-helix	880-887	8
α-helix	890-892	3
β-strand	893	1	26
α-helix	895-914	20
β-strand	924-928	5	23
β-strand	933-937	5	23
α-helix	938-940	3
β-strand	941	1	27
α-helix	942-943	2
β-strand	944-946	3	29
β-strand	951-953	3	29
β-strand	958-961	4	30
β-strand	963	1	31
β-strand	969	1	31
β-strand	971	1	32
α-helix	972-981	10
β-strand	986-992	7	33
β-strand	995-999	5	33
α-helix	1004-1011	8
β-strand	1014	1	32
α-helix	1015-1022	8
α-helix	1026-1028	3
β-strand	1033-1036	4	30
β-strand	1037-1041	5	33
β-strand	1047-1048	2	33
β-strand	1053-1056	4	30

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	34
β-strand	12-16	5	34
β-strand	22	1	35
α-helix	23-31	9
α-helix	38-40	3
β-strand	42-45	4	34
β-strand	48-49	2	34
β-strand	55	1	35
β-strand	65-70	6	34
β-strand	75	1	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 1	A, C	protein	1015	Homo sapiens	P22314 (AlphaFold model)
Ubiquitin	B, D	protein	80	Homo sapiens	P62979 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6DC6_1 Ubiquitin-like modifier-activating enzyme 1 (chains A, C)
GAMGSDIDEGLYSRQLYVLGHEAMKRLQTSSVLVSGLRGLGVEIAKNIILGGVKAVTLHD
QGTAQWADLSSQFYLREEDIGKNRAEVSQPRLAELNSYVPVTAYTGPLVEDFLSGFQVVV
LTNTPLEDQLRVGEFCHNRGIKLVVADTRGLFGQLFCDFGEEMILTDSNGEQPLSAMVSM
VTKDNPGVVTCLDEARHGFESGDFVSFSEVQGMVELNGNQPMEIKVLGPYTFSICDTSNF
SDYIRGGIVSQVKVPKKISFKSLVASLAEPDFVVTDFAKFSRPAQLHIGFQALHQFCAQH
GRPPRPRNEEDAAELVALAQAVNARALPAVQQNNLDEDLIRKLAYVAAGDLAPINAFIGG
LAAQEVMKACSGKFMPIMQWLYFDALECLPEDKEVLTEDKCLQRQNRYDGQVAVFGSDLQ
EKLGKQKYFLVGAGAIGCELLKNFAMIGLGCGEGGEIIVTDMDTIEKSNLNRQFLFRPWD
VTKLKSDTAAAAVRQMNPHIRVTSHQNRVGPDTERIYDDDFFQNLDGVANALDNVDARMY
MDRRCVYYRKPLLESGTLGTKGNVQVVIPFLTESYSSSQDPPEKSIPIATLKNFPNAIEH
TLQWARDEFEGLFKQPAENVNQYLTDPKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTW
ADCVTWACHHWHTQYSNNIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNPLHLD
YVMAAANLFAQTYGLTGSQDRAAVATFLQSVQVPEFTPKSGVKIHVSDQELQSANASVDD
SRLEELKATLPSPDKLPGFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDIPSADRHKS
KLIAGKIIPAIATTTAAVVGLVCLELYKVVQGHRQLDSYKNGFLNLALPFFGFSEPLAAP
RHQYYNQEWTLWDRFEVQGLQPNGEEMTLKQFLDYFKTEHKLEITMLSQGVSMLYSFFMP
AAKLKERLDQPMTEIVSRVSKRKLGRHVRALVLELCCNDESGEDVEVPYVRYTIR

Sequence of entity 2 (B, D), FASTA

>6DC6_2 Ubiquitin (chains B, D)
GAMAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
POP	Pyrophosphate 2-	H2 O7 P2	2

Primary citation

Crystal structure of a human ubiquitin E1-ubiquitin complex reveals conserved functional elements essential for activity. Lv, Z., Williams, K.M., Yuan, L. et al. J Biol Chem (2018) 293:18337-18352. DOI 10.1074/jbc.RA118.003975 · PubMed

Other PDB entries of the same protein (UniProt P22314 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4P22 2.75 Å, Crystal Structure of N-terminal Fragments of E1
7PYV 3.27 Å, Crystal structure of human UBA6 in complex with the ubiquitin-like modifier FAT10
9MC5 3.29 Å, Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 3
9WD1 3.31 Å, Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 3
9MC4 3.32 Å, Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 4
9MC6 3.32 Å, Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 2
9WD0 3.33 Å, Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 2
9MC7 3.34 Å, Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 4
9MC9 3.37 Å, Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 1
9MCB 3.42 Å, Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 1

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