9YRC: Transitional endoplasmic reticulum ATPase

p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP. Determined by electron microscopy at 2.97 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 2.97 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae
Chains: 9
Atoms: 28,118
Mol. weight: 653.27 kDa
Ligands: ATP, ADP
Released: 25 Mar 2026

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

Secondary structure: helices and β-sheets

9YRC contains 198 α-helices and 130 β-strands across 9 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: 30 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	210-218	9
α-helix	222-225	4
β-strand	239	1	1
α-helix	251-255	5
α-helix	259-262	4
β-strand	265	1	2
α-helix	271-274	4
α-helix	280-287	8
α-helix	288-292	5
β-strand	299	1	2
α-helix	319-333	15
β-strand	342	1	1
α-helix	374-384	11
β-strand	390	1	3
α-helix	396-401	6
α-helix	408-425	18
α-helix	439-443	5
β-strand	447	1	3
α-helix	449-458	10
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	4
α-helix	524-534	11
β-strand	538-542	5	4
α-helix	545-547	3
β-strand	551	1	5
α-helix	554-568	15
β-strand	572-576	5	4
α-helix	579-581	3
β-strand	584	1	6
α-helix	588-591	4
α-helix	597-610	14
β-strand	617-623	7	4
α-helix	626-628	3
β-strand	629	1	6
α-helix	631-634	4
β-strand	641-644	4	4
α-helix	650-660	11
β-strand	666	1	7
α-helix	672-678	7
α-helix	684-713	30
β-strand	731	1	7
α-helix	733-741	9
α-helix	749-765	17

Chain B: 34 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	203-205	3
α-helix	211-220	10
α-helix	222-225	4
α-helix	227-232	6
α-helix	235-238	4
β-strand	240-244	5	8
α-helix	251-260	10
β-strand	265-269	5	8
α-helix	271-274	4
β-strand	278	1	9
α-helix	281-295	15
β-strand	299-303	5	8
α-helix	306-308	3
β-strand	311	1	10
α-helix	319-332	14
β-strand	341-347	7	8
α-helix	350-352	3
β-strand	353	1	10
α-helix	355-357	3
β-strand	365-368	4	8
α-helix	374-384	11
β-strand	390	1	11
α-helix	396-402	7
α-helix	409-424	16
α-helix	427-429	3
α-helix	439-444	6
β-strand	447	1	11
α-helix	449-458	10
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
α-helix	509-511	3
β-strand	514-517	4	12
α-helix	524-534	11
β-strand	538-542	5	12
α-helix	545-547	3
β-strand	551	1	13
α-helix	554-568	15
β-strand	572-576	5	12
α-helix	579-581	3
β-strand	584	1	14
α-helix	585	1
α-helix	592-608	17
β-strand	617-623	7	12
β-strand	629	1	14
α-helix	631-634	4
β-strand	641-644	4	12
α-helix	650-660	11
β-strand	666	1	15
α-helix	672-678	7
α-helix	684-713	30
β-strand	731	1	15
α-helix	733-742	10
α-helix	749-766	18

Chain C: 30 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	16
α-helix	251-261	11
β-strand	265-269	5	16
α-helix	271-273	3
β-strand	278	1	17
α-helix	282-295	14
β-strand	299-303	5	16
α-helix	306-309	4
β-strand	311	1	18
α-helix	319-333	15
β-strand	342-347	6	16
α-helix	350-352	3
β-strand	353	1	18
α-helix	355-357	3
β-strand	365-368	4	16
α-helix	374-384	11
β-strand	390	1	19
α-helix	396-402	7
α-helix	409-427	19
α-helix	439-443	5
β-strand	447	1	19
α-helix	449-458	10
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	20
α-helix	524-534	11
β-strand	538-542	5	20
β-strand	551	1	21
α-helix	554-568	15
β-strand	572-577	6	20
α-helix	579-581	3
α-helix	596-608	13
β-strand	617-623	7	20
β-strand	641-644	4	20
α-helix	646-648	3
α-helix	650-660	11
β-strand	666	1	22
α-helix	672-678	7
α-helix	684-708	25
β-strand	731	1	22
α-helix	733-739	7
α-helix	749-766	18

Chain D: 30 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	203-205	3
α-helix	211-225	15
α-helix	229-232	4
β-strand	240-244	5	23
α-helix	252-261	10
β-strand	265-270	6	23
α-helix	271-275	5
α-helix	281-295	15
β-strand	299-304	6	23
α-helix	306-309	4
α-helix	319-332	14
β-strand	341-347	7	23
α-helix	350-352	3
α-helix	355-358	4
β-strand	365-368	4	23
α-helix	374-384	11
β-strand	390	1	24
α-helix	396-402	7
α-helix	408-427	20
α-helix	439-443	5
β-strand	447	1	24
α-helix	449-456	8
α-helix	462-464	3
α-helix	476-478	3
α-helix	483-498	16
α-helix	502-505	4
α-helix	509-511	3
β-strand	513-517	5	25
α-helix	524-530	7
β-strand	538-543	6	25
β-strand	551	1	26
α-helix	554-568	15
β-strand	572-577	6	25
α-helix	579-581	3
β-strand	584	1	27
α-helix	585	1
α-helix	596-608	13
β-strand	617-623	7	25
β-strand	629	1	27
β-strand	635	1	28
β-strand	638	1	28
β-strand	641-644	4	25
α-helix	650-660	11
β-strand	666	1	29
α-helix	672-678	7
α-helix	684-713	30
β-strand	731	1	29
α-helix	733-740	8
α-helix	749-766	18

Chain E: 35 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	210-216	7
α-helix	217-221	5
α-helix	222-225	4
α-helix	228-233	6
α-helix	236-238	3
β-strand	240-244	5	30
α-helix	251-260	10
β-strand	268	1	30
α-helix	271-276	6
α-helix	281-295	15
β-strand	300-302	3	30
α-helix	306-309	4
α-helix	320-334	15
β-strand	342-346	5	30
α-helix	355-358	4
β-strand	365-368	4	30
α-helix	371-373	3
α-helix	375-383	9
α-helix	397-401	5
α-helix	410-416	7
α-helix	417-419	3
α-helix	421-424	4
α-helix	440-443	4
α-helix	449-451	3
α-helix	452-458	7
α-helix	483-498	16
α-helix	500-502	3
β-strand	516-517	2	31
α-helix	524-535	12
β-strand	538-543	6	32
α-helix	544-547	4
α-helix	554-569	16
β-strand	572-577	6	32
α-helix	579-581	3
α-helix	594-611	18
β-strand	618-620	3	32
β-strand	623	1	31
α-helix	626-628	3
α-helix	631-634	4
β-strand	643-644	2	31
α-helix	650-660	11
β-strand	666	1	33
α-helix	672-678	7
α-helix	684-713	30
β-strand	731	1	33
α-helix	732	1
α-helix	733-742	10
α-helix	749-765	17

Chain F: 19 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	210-216	7
α-helix	217-221	5
α-helix	222-225	4
α-helix	227-232	6
β-strand	242-243	2	34
α-helix	251-261	11
β-strand	268-270	3	34
α-helix	271-276	6
α-helix	281-294	14
β-strand	300-304	5	34
α-helix	306-308	3
α-helix	313-315	3
α-helix	320-334	15
α-helix	337-339	3
β-strand	342-346	5	34
α-helix	350-352	3
α-helix	355-358	4
β-strand	366	1	34
α-helix	369-371	3
α-helix	374-385	12
α-helix	396-402	7
α-helix	409-427	19
α-helix	439-444	6
α-helix	449-457	9

Chain G: 18 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	109-114	6
β-strand	121	1	35
β-strand	136-137	2	23
α-helix	143	1
β-strand	144	1	35
β-strand	146	1	36
β-strand	148	1	36
β-strand	162-163	2	37
α-helix	164-172	9
α-helix	185-186	2
β-strand	203-204	2	8
α-helix	210-212	3
β-strand	220-221	2	37
β-strand	225-228	4	38
α-helix	231-244	14
β-strand	249-259	11	38
β-strand	265-274	10	38
β-strand	278	1	39
β-strand	281	1	40
β-strand	284	1	40
β-strand	287	1	39
α-helix	293-302	10
β-strand	306-314	9	38
β-strand	317	1	41
β-strand	325	1	41
α-helix	338-350	13
β-strand	352-354	3	42
β-strand	362-365	4	42
β-strand	368-374	7	38
β-strand	380-387	8	38
α-helix	389-396	8
β-strand	400-402	3	43
β-strand	403	1	44
β-strand	409-412	4	43
α-helix	413-415	3
β-strand	425-429	5	45
β-strand	435-439	5	45
β-strand	443-444	2	43
α-helix	446-448	3
β-strand	449-455	7	38
β-strand	456-457	2	46
α-helix	470-473	4
α-helix	485-494	10
α-helix	500-504	5
α-helix	507-514	8
α-helix	526-534	9
α-helix	537-544	8
α-helix	547-554	8

Chain H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	259	1	44

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A, B, C, D, E, F	protein	806	Homo sapiens	P55072 (AlphaFold model)
Nuclear protein localization protein 4 homolog	G	protein	608	Homo sapiens	Q8TAT6 (AlphaFold model)
Ubiquitin recognition factor in ER-associated degradation protein 1	H	protein	307	Homo sapiens	Q92890 (AlphaFold model)
Ubiquitin	I	protein	76	Saccharomyces cerevisiae	P0CH08 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>9YRC_1 Transitional endoplasmic reticulum ATPase (chains A, B, C, D, E, F)
MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLK
GKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPID
DTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDT
VIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRG
ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAI
IFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF
GRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL
QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIG
GLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFI
SIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDQLDSIAKARGGNIGDGGGAADRV
INQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKAN
LRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAM
EVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGG
AGPSQGSGGGTGGSVYTEDNDDDLYG

Sequence of entity 2 (G), FASTA

>9YRC_2 Nuclear protein localization protein 4 homolog (chains G)
MAESIIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASS
NKSLNLLKIKHGDLLFLFPSSLAGPSSEMETSVPPGFKVFGAPNVVEDEIDQYLSKQDGK
IYRSRDPQLCRHGPLGKCVHCVPLEPFDEDYLNHLEPPVKHMSFHAYIRKLTGGADKGKF
VALENISCKIKSGCEGHLPWPNGICTKCQPSAITLNRQKYRHVDNIMFENHTVADRFLDF
WRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVDEIA
AKLGLRKVGWIFTDLVSEDTRKGTVRYSRNKDTYFLSSEECITAGDFQNKHPNMCRLSPD
GHFGSKFVTAVATGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDAPELGYAKESSSEQY
VPDVFYKDVDKFGNEITQLARPLPVEYLIIDITTTFPKDPVYTFSISQNPFPIENRDVLG
ETQDFHSLATYLSQNTSSVFLDTISDFHLLLFLVTNEVMPLQDSISLLLEAVRTRNEELA
QTWKRSEQWATIEQLCSTVGGQLPGLHEYGAVGGSTHTATAAMWACQHCTFMNQPGTGHC
EMCSLPRT

Sequence of entity 3 (H), FASTA

>9YRC_3 Ubiquitin recognition factor in ER-associated degradation protein 1 (chains H)
MFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLN
ITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVA
TYSKFQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAV
SIIECDMNVDFDAPLGYKEPERQVQHEESTEGEADHSGYAGELGFRAFSGSGNRLDGKKK
GVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGRFVAFSGEGQSL
RKKGRKP

Sequence of entity 4 (I), FASTA

>9YRC_4 Ubiquitin (chains I)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	8
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3

Primary citation

The deubiquitinating enzyme Otu1 releases substrates from the conserved initiation complex of the Cdc48/p97 ATPase for proteasomal degradation. Li, H., Guan, H., Rapoport, T.A. Sci Rep (2026) 16. DOI 10.1038/s41598-026-42811-6 · PubMed

Other PDB entries of the same protein (UniProt P55072 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5B6C 1.55 Å, Structural Details of Ufd1 binding to p97
7PUX 1.73 Å, Structure of p97 N-D1(L198W) in complex with Fragment TROLL2
3TIW 1.8 Å, Crystal structure of p97N in complex with the C-terminus of gp78
4KDL 1.81 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL
4KDI 1.86 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL
5EPP 1.88 Å, Structural Insights into the Interaction of p97 N-terminus Domain and VBM Motif in…
3EBB 1.9 Å, PLAP/P97 complex
6G2V 1.9 Å, Crystal structure of the p97 D2 domain in a helical split-washer conformation
6G2Z 1.92 Å, Crystal structure of the p97 D2 domain in a helical split-washer conformation
4KO8 1.98 Å, Structure of p97 N-D1 R155H mutant in complex with ATPgS
3QQ8 2.0 Å, Crystal structure of p97-N in complex with FAF1-UBX
3QWZ 2.0 Å, Crystal structure of FAF1 UBX-p97N-domain complex

Browse structure collections

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