9WD1: Human UBA1-UBE2O-Ub -Recruitment state 3

Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 3. Determined by electron microscopy at 3.31 Å resolution. Released 26 Aug 2026.

Method: Electron microscopy
Resolution: 3.31 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,292
Mol. weight: 268.36 kDa
Ligands: AMP
Released: 26 Aug 2026

Explore 9WD1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9WD1 contains 71 α-helices and 64 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: 55 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	74-78	5	1
α-helix	82-93	12
β-strand	98-102	5	1
β-strand	106	1	2
α-helix	107	1
α-helix	109-112	4
α-helix	120-122	3
β-strand	126	1	2
α-helix	127-136	10
β-strand	144-147	4	1
α-helix	153-156	4
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	215-217	3
β-strand	218-220	3	4
β-strand	221-224	4	5
β-strand	231-234	4	5
β-strand	247-251	5	4
α-helix	257-260	4
β-strand	265-266	2	4
β-strand	268-269	2	5
β-strand	274-276	3	5
β-strand	291-295	5	4
β-strand	299-301	3	3
α-helix	306-311	6
β-strand	316	1	1
α-helix	320-322	3
α-helix	325-343	19
α-helix	346-348	3
α-helix	352-368	17
α-helix	380-388	9
α-helix	395-414	20
α-helix	418-420	3
β-strand	424-426	3	1
α-helix	429-431	3
α-helix	441-444	4
α-helix	452-467	16
β-strand	470-474	5	6
α-helix	478-490	13
β-strand	499-503	5	6
β-strand	507	1	7
α-helix	510-512	3
β-strand	527	1	7
α-helix	528-539	12
β-strand	545-548	4	6
α-helix	550-552	3
α-helix	554-558	5
α-helix	562-567	6
β-strand	570-573	4	6
α-helix	578-591	14
β-strand	595-601	7	6
β-strand	602	1	8
β-strand	604-610	7	6
β-strand	615	1	9
α-helix	632-634	3
α-helix	641-652	12
α-helix	653-657	5
α-helix	658-668	11
α-helix	672-679	8
α-helix	684-692	9
α-helix	693-697	5
α-helix	703-728	26
α-helix	733	1
β-strand	734	1	10
α-helix	735	1
β-strand	740	1	10
α-helix	748-750	3
α-helix	759-775	17
α-helix	784-793	10
α-helix	795-796	2
α-helix	823-832	10
α-helix	834-835	2
α-helix	836-838	3
α-helix	844-847	4
α-helix	858-869	12
α-helix	875-877	3
α-helix	880-887	8
β-strand	893	1	8
α-helix	895-914	20
β-strand	924-928	5	6
β-strand	933-937	5	6
α-helix	938-940	3
β-strand	941	1	9
α-helix	942-943	2
β-strand	945-947	3	11
β-strand	950-952	3	11
β-strand	958-961	4	12
β-strand	963	1	13
β-strand	969	1	13
α-helix	970	1
β-strand	971	1	14
α-helix	972-983	12
β-strand	986-992	7	15
β-strand	995-999	5	15
α-helix	1004-1012	9
β-strand	1014	1	14
α-helix	1015-1023	9
β-strand	1033-1036	4	12
β-strand	1037-1041	5	15
β-strand	1047-1048	2	15
β-strand	1053-1056	4	12

Chain B: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	929-932	4	16
α-helix	940-943	4
α-helix	952-968	17
α-helix	969-970	2
β-strand	973-978	6	16
β-strand	984-989	6	16
α-helix	990-992	3
β-strand	1002-1007	6	16
α-helix	1012-1014	3
α-helix	1016-1017	2
β-strand	1018-1021	4	16
β-strand	1033	1	17
β-strand	1038	1	16
β-strand	1039	1	17
α-helix	1042-1044	3
α-helix	1061-1067	7
α-helix	1068-1072	5
α-helix	1085-1087	3
α-helix	1091-1117	27
α-helix	1124-1139	16
α-helix	1142-1150	9
α-helix	1263-1282	20

Chain C: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	18
β-strand	12-16	5	18
β-strand	22	1	19
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	18
β-strand	48-49	2	18
β-strand	55	1	19
β-strand	65-70	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 1	A	protein	1058	Homo sapiens	P22314 (AlphaFold model)
(E3-independent) E2 ubiquitin-conjugating enzyme	B	protein	1292	Homo sapiens	Q9C0C9 (AlphaFold model)
Ubiquitin	C	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9WD1_1 Ubiquitin-like modifier-activating enzyme 1 (chains A)
MSSSPLSKKRRVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAKNGSEADIDEGLYSRQLY
VLGHEAMKRLQTSSVLVSGLRGLGVEIAKNIILGGVKAVTLHDQGTAQWADLSSQFYLRE
EDIGKNRAEVSQPRLAELNSYVPVTAYTGPLVEDFLSGFQVVVLTNTPLEDQLRVGEFCH
NRGIKLVVADTRGLFGQLFCDFGEEMILTDSNGEQPLSAMVSMVTKDNPGVVTCLDEARH
GFESGDFVSFSEVQGMVELNGNQPMEIKVLGPYTFSICDTSNFSDYIRGGIVSQVKVPKK
ISFKSLVASLAEPDFVVTDFAKFSRPAQLHIGFQALHQFCAQHGRPPRPRNEEDAAELVA
LAQAVNARALPAVQQNNLDEDLIRKLAYVAAGDLAPINAFIGGLAAQEVMKACSGKFMPI
MQWLYFDALECLPEDKEVLTEDKCLQRQNRYDGQVAVFGSDLQEKLGKQKYFLVGAGAIG
CELLKNFAMIGLGCGEGGEIIVTDMDTIEKSNLNRQFLFRPWDVTKLKSDTAAAAVRQMN
PHIRVTSHQNRVGPDTERIYDDDFFQNLDGVANALDNVDARMYMDRRCVYYRKPLLESGT
LGTKGNVQVVIPFLTESYSSSQDPPEKSIPICTLKNFPNAIEHTLQWARDEFEGLFKQPA
ENVNQYLTDPKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWADCVTWACHHWHTQYSN
NIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTG
SQDRAAVATFLQSVQVPEFTPKSGVKIHVSDQELQSANASVDDSRLEELKATLPSPDKLP
GFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDIPSADRHKSKLIAGKIIPAIATTTAA
VVGLVCLELYKVVQGHRQLDSYKNGFLNLALPFFGFSEPLAAPRHQYYNQEWTLWDRFEV
QGLQPNGEEMTLKQFLDYFKTEHKLEITMLSQGVSMLYSFFMPAAKLKERLDQPMTEIVS
RVSKRKLGRHVRALVLELCCNDESGEDVEVPYVRYTIR

Sequence of entity 2 (B), FASTA

>9WD1_2 (E3-independent) E2 ubiquitin-conjugating enzyme (chains B)
MADPAAPTPAAPAPAQAPAPAPEAVPAPAAAPVPAPAPASDSASGPSSDSGPEAGSQRLL
FSHDLVSGRYRGSVHFGLVRLIHGEDSDSEGEEEGRGSSGCSEAGGAGHEEGRASPLRRG
YVRVQWYPEGVKQHVKETKLKLEDRSVVPRDVVRHMRSTDSQCGTVIDVNIDCAVKLIGT
NCIIYPVNSKDLQHIWPFMYGDYIAYDCWLGKVYDLKNQIILKLSNGARCSMNTEDGAKL
YDVCPHVSDSGLFFDDSYGFYPGQVLIGPAKIFSSVQWLSGVKPVLSTKSKFRVVVEEVQ
VVELKVTWITKSFCPGGTDSVSPPPSVITQENLGRVKRLGCFDHAQRQLGERCLYVFPAK
VEPAKIAWECPEKNCAQGEGSMAKKVKRLLKKQVVRIMSCSPDTQCSRDHSMEDPDKKGE
SKTKSEAESASPEETPDGSASPVEMQDEGAEEPHEAGEQLPPFLLKEGRDDRLHSAEQDA
DDEAADDTDDTSSVTSSASSTTSSQSGSGTSRKKSIPLSIKNLKRKHKRKKNKITRDFKP
GDRVAVEVVTTMTSADVMWQDGSVECNIRSNDLFPVHHLDNNEFCPGDFVVDKRVQSCPD
PAVYGVVQSGDHIGRTCMVKWFKLRPSGDDVELIGEEEDVSVYDIADHPDFRFRTTDIVI
RIGNTEDGAPHKEDEPSVGQVARVDVSSKVEVVWADNSKTIILPQHLYNIESEIEESDYD
SVEGSTSGASSDEWEDDSDSWETDNGLVEDEHPKIEEPPIPPLEQPVAPEDKGVVISEEA
ATAAVQGAVAMAAPMAGLMEKAGKDGPPKSFRELKEAIKILESLKNMTVEQLLTGSPTSP
TVEPEKPTREKKFLDDIKKLQENLKKTLDNVAIVEEEKMEAVPDVERKEDKPEGQSPVKA
EWPSETPVLCQQCGGKPGVTFTSAKGEVFSVLEFAPSNHSFKKIEFQPPEAKKFFSTVRK
EMALLATSLPEGIMVKTFEDRMDLFSALIKGPTRTPYEDGLYLFDIQLPNIYPAVPPHFC
YLSQCSGRLNPNLYDNGKVCVSLLGTWIGKGTERWTSKSSLLQVLISIQGLILVNEPYYN
EAGFDSDRGLQEGYENSRCYNEMALIRVVQSMTQLVRRPPEVFEQEIRQHFSTGGWRLVN
RIESWLETHALLEKAQALPNGVPKASSSPEPPAVAELSDSGQQEPEDGGPAPGEASQGSD
SEGGAQGLASASRDHTDQTSETAPDASVPPSVKPKKRRKSYRSFLPEKSGYPDIGFPLFP
LSKGFIKSIRGVLTQFRAALLEAGMPECTEDK

Sequence of entity 3 (C), FASTA

>9WD1_3 Ubiquitin (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	1

Primary citation

Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 1. Chen, P.-T., Wu, K.-P. To be published.

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
6DC6 3.14 Å, Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin
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
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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