7UN6: Complex of UBE2O with NAP1L1

Complex of UBE2O with NAP1L1. Determined by electron microscopy at 3.3 Å resolution. Released 3 Aug 2022.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,042
Mol. weight: 243.91 kDa
Released: 3 Aug 2022

Explore 7UN6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UN6 contains 45 α-helices and 60 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: 21 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	65-71	7	1
β-strand	73-79	7	1
β-strand	123-126	4	1
β-strand	133-134	2	1
β-strand	141-144	4	1
β-strand	152-155	4	2
β-strand	163-177	15	2
β-strand	183-188	6	2
α-helix	189-191	3
β-strand	193	1	2
β-strand	203-205	3	3
β-strand	210-212	3	3
β-strand	213-224	12	4
β-strand	229-233	5	4
α-helix	234-237	4
β-strand	265-269	5	4
α-helix	270-274	5
β-strand	277-280	4	4
α-helix	282-284	3
β-strand	291-306	16	4
β-strand	310	1	3
α-helix	323-325	3
β-strand	327-328	2	4
α-helix	330-333	4
β-strand	337-338	2	3
α-helix	340-342	3
β-strand	352-356	5	2
β-strand	543-559	17	2
β-strand	564-569	6	2
α-helix	570-572	3
β-strand	573-575	3	2
α-helix	584-585	2
β-strand	589-592	4	5
β-strand	603-611	9	5
β-strand	616-624	9	5
β-strand	631-635	5	5
β-strand	640-641	2	5
α-helix	642-644	3
β-strand	645-647	3	5
β-strand	657-658	2	6
β-strand	659-661	3	7
β-strand	678	1	8
β-strand	680-681	2	6
β-strand	684	1	9
β-strand	690	1	9
β-strand	694	1	8
β-strand	702	1	9
α-helix	704-706	3
β-strand	707-709	3	7
β-strand	931-932	2	10
α-helix	946-948	3
α-helix	951-967	17
β-strand	973-978	6	10
β-strand	984-991	8	10
α-helix	992	1
β-strand	999-1007	9	10
β-strand	1018-1021	4	10
α-helix	1061-1070	10
α-helix	1084-1087	4
α-helix	1091-1117	27
α-helix	1124-1145	22
α-helix	1259	1
α-helix	1261-1262	2
α-helix	1263-1282	20

Chain B: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	74-121	48
α-helix	170-177	8
α-helix	179-182	4
α-helix	190-193	4
β-strand	196-203	8	11
α-helix	204-205	2
β-strand	211-218	8	11
β-strand	224	1	12
β-strand	228-236	9	11
α-helix	244-246	3
β-strand	251-256	6	11
α-helix	261	1
β-strand	262	1	12
α-helix	263	1
β-strand	270-278	9	13
β-strand	285-293	9	13
α-helix	297-300	4
α-helix	303-307	5
α-helix	314-329	16
α-helix	330-334	5
α-helix	338-342	5

Chain C: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	74-122	49
α-helix	170-176	7
α-helix	179-182	4
α-helix	190-193	4
β-strand	199-203	5	14
α-helix	204-205	2
β-strand	212-216	5	14
β-strand	224	1	15
β-strand	229-230	2	14
β-strand	233-235	3	16
α-helix	244-246	3
β-strand	252-255	4	16
β-strand	262	1	15
α-helix	263	1
β-strand	270-278	9	17
β-strand	285-293	9	17
α-helix	297-301	5
α-helix	316-329	14
α-helix	330-334	5
α-helix	338-342	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
(E3-independent) E2 ubiquitin-conjugating enzyme	A	protein	1342	Homo sapiens	Q9C0C9 (AlphaFold model)
Nucleosome assembly protein 1-like 1	B, C	protein	416	Homo sapiens	P55209 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7UN6_1 (E3-independent) E2 ubiquitin-conjugating enzyme (chains A)
MASWSHPQFEKGAWSHPQFEKGSWSHPQFEKGPAGSENLYFQGSGIRDRTMADPAAPTPA
APAPAQAPAPAPEAVPAPAAAPVPAPAPASDSASGPSSDSGPEAGSQRLLFSHDLVSGRY
RGSVHFGLVRLIHGEDSDSEGEEEGRGSSGCSEAGGAGHEEGRASPLRRGYVRVQWYPEG
VKQHVKETKLKLEDRSVVPRDVVRHMRSTDSQCGTVIDVNIDCAVKLIGTNCIIYPVNSK
DLQHIWPFMYGDYIAYDCWLGKVYDLKNQIILKLSNGARCSMNTEDGAKLYDVCPHVSDS
GLFFDDSYGFYPGQVLIGPAKIFSSVQWLSGVKPVLSTKSKFRVVVEEVQVVELKVTWIT
KSFCPGGTDSVSPPPSVITQENLGRVKRLGCFDHAQRQLGERCLYVFPAKVEPAKIAWEC
PEKNCAQGEGSMAKKVKRLLKKQVVRIMSCSPDTQCSRDHSMEDPDKKGESKTKSEAESA
SPEETPDGSASPVEMQDEGAEEPHEAGEQLPPFLLKEGRDDRLHSAEQDADDEAADDTDD
TSSVTSSASSTTSSQSGSGTSRKKSIPLSIKNLKRKHKRKKNKITRDFKPGDRVAVEVVT
TMTSADVMWQDGSVECNIRSNDLFPVHHLDNNEFCPGDFVVDKRVQSCPDPAVYGVVQSG
DHIGRTCMVKWFKLRPSGDDVELIGEEEDVSVYDIADHPDFRFRTTDIVIRIGNTEDGAP
HKEDEPSVGQVARVDVSSKVEVVWADNSKTIILPQHLYNIESEIEESDYDSVEGSTSGAS
SDEWEDDSDSWETDNGLVEDEHPKIEEPPIPPLEQPVAPEDKGVVISEEAATAAVQGAVA
MAAPMAGLMEKAGKDGPPKSFRELKEAIKILESLKNMTVEQLLTGSPTSPTVEPEKPTRE
KKFLDDIKKLQENLKKTLDNVAIVEEEKMEAVPDVERKEDKPEGQSPVKAEWPSETPVLC
QQCGGKPGVTFTSAKGEVFSVLEFAPSNHSFKKIEFQPPEAKKFFSTVRKEMALLATSLP
EGIMVKTFEDRMDLFSALIKGPTRTPYEDGLYLFDIQLPNIYPAVPPHFCYLSQCSGRLN
PNLYDNGKVKVSLLGTWIGKGTERWTSKSSLLQVLISIQGLILVNEPYYNEAGFDSDRGL
QEGYENSRCYNEMALIRVVQSMTQLVRRPPEVFEQEIRQHFSTGGWRLVNRIESWLETHA
LLEKAQALPNGVPKASSSPEPPAVAELSDSGQQEPEDGGPAPGEASQGSDSEGGAQGLAS
ASRDHTDQTSETAPDASVPPSVKPKKRRKSYRSFLPEKSGYPDIGFPLFPLSKGFIKSIR
GVLTQFRAALLEAGMPECTEDK

Sequence of entity 2 (B, C), FASTA

>7UN6_2 Nucleosome assembly protein 1-like 1 (chains B, C)
MDYKDHDGDYKDHDIDYKDDDDKAGSADIDNKEQSELDQDLDDVEEVEEEETGEETKLKA
RQLTVQMMQNPQILAALQERLDGLVETPTGYIESLPRVVKRRVNALKNLQVKCAQIEAKF
YEEVHDLERKYAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEEDEISEELKEKAKIEDE
KKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPMSFVLE
FHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKK
KQKHKGRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDAEAILAADFEIGHFLRERII
PRSVLYFTGEAIEDDDDDYDEEGEEADEEGEEEGDEENDPDYDPKKDQNPAECKQQ

Primary citation

Mechanism of client selection by the protein quality-control factor UBE2O. Yip, M.C.J., Sedor, S.F., Shao, S. Nat Struct Mol Biol (2022) 29:774-780. DOI 10.1038/s41594-022-00807-6 · PubMed

Other PDB entries of the same protein (UniProt Q9C0C9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QUG 1.8 Å, Structure of a UBC-Ubiquitin conjugate
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
7UN3 3.5 Å, Complex of UBE2O with NAP1L1 and ubiquitylated uL2

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