7UN3: PDB entry 7UN3

Complex of UBE2O with NAP1L1 and ubiquitylated uL2. Determined by electron microscopy at 3.5 Å resolution. Released 3 Aug 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,423
Mol. weight: 478.18 kDa
Released: 3 Aug 2022

Explore 7UN3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UN3 contains 44 α-helices and 60 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: 21 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	65-70	6	3
β-strand	73-81	9	3
β-strand	123-125	3	3
α-helix	127-129	3
β-strand	132-134	3	3
α-helix	137-139	3
β-strand	141-144	4	3
β-strand	152-155	4	4
β-strand	163-171	9	4
β-strand	172-177	6	5
β-strand	183-188	6	5
β-strand	193-194	2	5
β-strand	204-205	2	6
β-strand	209-224	16	6
β-strand	229-233	5	6
α-helix	234-237	4
β-strand	265-269	5	6
α-helix	270-274	5
β-strand	277-280	4	6
α-helix	282-285	4
β-strand	291-311	21	6
β-strand	327-328	2	6
α-helix	330-335	6
β-strand	337-338	2	6
β-strand	352-355	4	5
β-strand	544-550	7	5
β-strand	553-559	7	4
β-strand	564-569	6	4
α-helix	570-572	3
β-strand	573-575	3	4
β-strand	589-592	4	7
β-strand	604-611	8	7
β-strand	616-624	9	7
β-strand	631-641	11	7
α-helix	642-644	3
β-strand	645-647	3	7
β-strand	658-661	4	8
β-strand	678-684	7	8
β-strand	690-694	5	8
β-strand	698-702	5	8
α-helix	704-706	3
β-strand	707-709	3	8
β-strand	931-932	2	9
α-helix	951-967	17
β-strand	974-978	5	9
β-strand	984-990	7	9
β-strand	1001-1007	7	9
α-helix	1008-1009	2
β-strand	1018-1021	4	9
α-helix	1042-1044	3
α-helix	1061-1067	7
α-helix	1068-1072	5
α-helix	1077-1079	3
α-helix	1085-1087	3
α-helix	1091-1117	27
α-helix	1124-1130	7
α-helix	1131-1135	5
α-helix	1136-1151	16
α-helix	1263-1282	20

Chain B: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	74-120	47
α-helix	170-176	7
α-helix	179-182	4
α-helix	189-193	5
β-strand	196-203	8	10
α-helix	204-205	2
β-strand	212-218	7	10
β-strand	228-232	5	10
β-strand	233-235	3	11
β-strand	252-255	4	11
β-strand	270-278	9	12
β-strand	285-293	9	12
α-helix	297-301	5
α-helix	320-329	10
α-helix	330-334	5
α-helix	338-342	5

Chain C: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	74-121	48
α-helix	170-176	7
α-helix	179-182	4
α-helix	187-189	3
α-helix	190-193	4
β-strand	196-203	8	13
α-helix	204-205	2
α-helix	209-210	2
β-strand	211-218	8	13
β-strand	224	1	14
β-strand	228-235	8	13
β-strand	252-256	5	13
β-strand	262	1	14
α-helix	263	1
β-strand	270-278	9	15
β-strand	285-293	9	15
α-helix	297-301	5
α-helix	316-329	14
α-helix	330-334	5

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
β-strand	55	1	2
α-helix	57-59	3
β-strand	65-71	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin,60S ribosomal protein L8,(E3-independent) E2 ubiquitin-conjugating enzyme fusion	A, D	protein	1744	Homo sapiens	P62917 (AlphaFold model), P62987 (AlphaFold model), Q9C0C9 (AlphaFold model)
Nucleosome assembly protein 1-like 1	B, C	protein	416	Homo sapiens	P55209 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>7UN3_1 Ubiquitin,60S ribosomal protein L8,(E3-independent) E2 ubiquitin-conjugating enzyme fusion (chains A, D)
MASWSHPQFEKGAWSHPQFEKGSWSHPQFEKGPAGSENLYFQGSGIRMQIFVKTLTGKTI
TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL
RGVGSMGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRG
APLAKVVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNVGNVLPVGTMPEGTIVCC
LEEKPGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRI
DKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKV
GLIAARRTGRLRGTKTVQEKENGGSGLEVLFQGPGGSGGGSGLEVLFQGPGGSGYPYDVP
DYAGYPYDVPDYAGSYPYDVPDYAGSAIRDRTMADPAAPTPAAPAPAQAPAPAPEAVPAP
AAAPVPAPAPASDSASGPSSDSGPEAGSQRLLFSHDLVSGRYRGSVHFGLVRLIHGEDSD
SEGEEEGRGSSGCSEAGGAGHEEGRASPLRRGYVRVQWYPEGVKQHVKETKLKLEDRSVV
PRDVVRHMRSTDSQCGTVIDVNIDCAVKLIGTNCIIYPVNSKDLQHIWPFMYGDYIAYDC
WLGKVYDLKNQIILKLSNGARCSMNTEDGAKLYDVCPHVSDSGLFFDDSYGFYPGQVLIG
PAKIFSSVQWLSGVKPVLSTKSKFRVVVEEVQVVELKVTWITKSFCPGGTDSVSPPPSVI
TQENLGRVKRLGCFDHAQRQLGERCLYVFPAKVEPAKIAWECPEKNCAQGEGSMAKKVKR
LLKKQVVRIMSCSPDTQCSRDHSMEDPDKKGESKTKSEAESASPEETPDGSASPVEMQDE
GAEEPHEAGEQLPPFLLKEGRDDRLHSAEQDADDEAADDTDDTSSVTSSASSTTSSQSGS
GTSRKKSIPLSIKNLKRKHKRKKNKITRDFKPGDRVAVEVVTTMTSADVMWQDGSVECNI
RSNDLFPVHHLDNNEFCPGDFVVDKRVQSCPDPAVYGVVQSGDHIGRTCMVKWFKLRPSG
DDVELIGEEEDVSVYDIADHPDFRFRTTDIVIRIGNTEDGAPHKEDEPSVGQVARVDVSS
KVEVVWADNSKTIILPQHLYNIESEIEESDYDSVEGSTSGASSDEWEDDSDSWETDNGLV
EDEHPKIEEPPIPPLEQPVAPEDKGVVISEEAATAAVQGAVAMAAPMAGLMEKAGKDGPP
KSFRELKEAIKILESLKNMTVEQLLTGSPTSPTVEPEKPTREKKFLDDIKKLQENLKKTL
DNVAIVEEEKMEAVPDVERKEDKPEGQSPVKAEWPSETPVLCQQCGGKPGVTFTSAKGEV
FSVLEFAPSNHSFKKIEFQPPEAKKFFSTVRKEMALLATSLPEGIMVKTFEDRMDLFSAL
IKGPTRTPYEDGLYLFDIQLPNIYPAVPPHFCYLSQCSGRLNPNLYDNGKVKVSLLGTWI
GKGTERWTSKSSLLQVLISIQGLILVNEPYYNEAGFDSDRGLQEGYENSRCYNEMALIRV
VQSMTQLVRRPPEVFEQEIRQHFSTGGWRLVNRIESWLETHALLEKAQALPNGVPKASSS
PEPPAVAELSDSGQQEPEDGGPAPGEASQGSDSEGGAQGLASASRDHTDQTSETAPDASV
PPSVKPKKRRKSYRSFLPEKSGYPDIGFPLFPLSKGFIKSIRGVLTQFRAALLEAGMPEC
TEDK

Sequence of entity 2 (B, C), FASTA

>7UN3_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 P62917 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
8QYX 1.78 Å, Human 60S ribosomal subunit
8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
9PBE 2.19 Å, In situ human 80S ribosome (composite map)
29IX 2.2 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. NT-2 added to purified…

Browse structure collections

About this viewer

MolViewer shows 7UN3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.