11TA: Substrate engaged p97-Ufd1-NPL4-Faf1 complex

Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused). Determined by electron microscopy at 3.58 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 3.58 Å
Organism: Homo sapiens
Chains: 12
Atoms: 37,891
Mol. weight: 714.45 kDa
Ligands: ADP, ATP, ZN
Released: 22 Apr 2026

Explore 11TA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

11TA contains 285 α-helices and 204 β-strands across 12 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: 41 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
β-strand	25-30	6	22
β-strand	56-60	5	22
β-strand	66-70	5	22
β-strand	81-84	4	22
α-helix	86-90	5
α-helix	91-93	3
β-strand	99-103	5	22
β-strand	114-118	5	23
α-helix	120-122	3
α-helix	130-132	3
α-helix	136-139	4
β-strand	146	1	24
β-strand	151-153	3	23
β-strand	162-168	7	23
β-strand	174	1	24
α-helix	191-193	3
α-helix	198-200	3
α-helix	203-205	3
α-helix	211-216	6
α-helix	217-221	5
α-helix	222-225	4
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	25
α-helix	251-261	11
β-strand	265-269	5	25
α-helix	272-275	4
α-helix	279-295	17
β-strand	299-304	6	25
α-helix	306-308	3
β-strand	311	1	26
α-helix	320-332	13
β-strand	342-347	6	25
α-helix	350-352	3
β-strand	353	1	26
α-helix	355-358	4
β-strand	365-368	4	25
α-helix	374-384	11
β-strand	390	1	27
α-helix	396-402	7
α-helix	408-425	18
β-strand	447	1	27
α-helix	449-458	10
β-strand	470	1	28
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	28
α-helix	524-534	11
β-strand	538-543	6	28
α-helix	544-548	5
α-helix	557-568	12
β-strand	572-577	6	28
α-helix	579-582	4
α-helix	599-609	11
α-helix	613-615	3
β-strand	617-623	7	28
α-helix	631-634	4
β-strand	636	1	29
β-strand	638	1	29
β-strand	642-644	3	28
α-helix	652-660	9
β-strand	666	1	30
α-helix	685-712	28
β-strand	731	1	30
α-helix	733-739	7
α-helix	740-742	3
α-helix	749-759	11

Chain B: 39 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	191-194	4
α-helix	195-198	4
α-helix	203-205	3
α-helix	210-216	7
α-helix	217-221	5
α-helix	222-225	4
α-helix	227-232	6
β-strand	242-244	3	31
α-helix	251-262	12
β-strand	265-269	5	31
α-helix	271-275	5
α-helix	284-296	13
β-strand	299-303	5	31
α-helix	306-309	4
β-strand	311	1	32
α-helix	325-333	9
β-strand	341-347	7	31
α-helix	350-352	3
β-strand	353	1	32
α-helix	355-358	4
β-strand	366-368	3	31
α-helix	374-384	11
β-strand	390	1	33
α-helix	396-401	6
α-helix	408-426	19
α-helix	427-429	3
α-helix	436-438	3
α-helix	439-443	5
β-strand	447	1	33
α-helix	449-458	10
α-helix	470-472	3
α-helix	476-479	4
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	502-505	4
β-strand	513-517	5	34
α-helix	524-534	11
β-strand	538-543	6	34
α-helix	544-551	8
α-helix	559-567	9
β-strand	572-577	6	34
α-helix	579-582	4
α-helix	599-610	12
β-strand	618-623	6	34
β-strand	636	1	35
β-strand	638	1	35
β-strand	642-644	3	34
α-helix	645-648	4
α-helix	653-660	8
β-strand	666	1	36
α-helix	673-676	4
α-helix	684-713	30
β-strand	731	1	36
α-helix	733-741	9
α-helix	749-756	8
α-helix	757-759	3

Chain C: 47 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	37
β-strand	38-41	4	37
α-helix	43-48	6
β-strand	56-60	5	37
α-helix	62-64	3
β-strand	66-73	8	37
β-strand	81-84	4	37
α-helix	86-91	6
β-strand	99-104	6	37
α-helix	108-109	2
β-strand	110	1	38
α-helix	111	1
β-strand	113-118	6	39
β-strand	119	1	40
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	145-147	3	38
β-strand	151-156	6	39
β-strand	159-169	11	39
β-strand	173-175	3	38
β-strand	181-183	3	39
α-helix	187-188	2
β-strand	189	1	40
α-helix	190	1
α-helix	191-196	6
α-helix	203-205	3
α-helix	210-225	16
α-helix	229-232	4
β-strand	241-244	4	41
α-helix	251-260	10
β-strand	265-270	6	42
α-helix	271-273	3
β-strand	278	1	13
α-helix	281-282	2
α-helix	283-287	5
α-helix	288-294	7
β-strand	299-304	6	42
α-helix	306-308	3
α-helix	320-333	14
β-strand	341-345	5	42
α-helix	355-357	3
β-strand	359	1	43
β-strand	362	1	43
β-strand	365-368	4	41
α-helix	374-384	11
β-strand	390	1	44
α-helix	396-402	7
α-helix	408-425	18
α-helix	439-444	6
β-strand	447	1	44
α-helix	449-458	10
α-helix	476-479	4
α-helix	483-498	16
α-helix	500-505	6
α-helix	509-511	3
β-strand	513-517	5	45
α-helix	524-534	11
β-strand	538-543	6	45
α-helix	544-548	5
α-helix	558-568	11
β-strand	572-577	6	45
α-helix	579-581	3
α-helix	599-609	11
α-helix	613-615	3
β-strand	617-623	7	45
α-helix	626-628	3
β-strand	641-644	4	45
α-helix	646-648	3
α-helix	653-661	9
β-strand	666	1	46
α-helix	672-676	5
α-helix	684-714	31
β-strand	731	1	46
α-helix	732	1
α-helix	733-742	10
α-helix	749-755	7
α-helix	756-759	4

Chain D: 35 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	190-195	6
α-helix	210-225	16
α-helix	227-233	7
α-helix	235-238	4
β-strand	241-244	4	47
α-helix	251-261	11
β-strand	265-270	6	47
α-helix	271-272	2
α-helix	273-277	5
α-helix	282-295	14
β-strand	299-304	6	47
α-helix	306-309	4
β-strand	311	1	48
α-helix	320-333	14
β-strand	343-347	5	47
β-strand	353	1	48
α-helix	355-358	4
β-strand	365-368	4	47
α-helix	375-385	11
β-strand	390	1	49
α-helix	396-402	7
α-helix	408-427	20
α-helix	438-442	5
β-strand	447	1	49
α-helix	449-458	10
α-helix	467-468	2
α-helix	476-478	3
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-506	7
β-strand	513-517	5	50
α-helix	524-535	12
β-strand	538-543	6	50
α-helix	544-548	5
α-helix	558-568	11
β-strand	572-577	6	50
α-helix	579-582	4
α-helix	599-609	11
β-strand	617-623	7	50
α-helix	631-634	4
β-strand	642-644	3	50
α-helix	646-648	3
α-helix	653-662	10
α-helix	684-715	32
α-helix	733-739	7
α-helix	740-742	3
α-helix	749-754	6
α-helix	757-761	5

Chain E: 35 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	191-195	5
α-helix	203-205	3
α-helix	210-216	7
α-helix	217-221	5
α-helix	222-225	4
α-helix	227-233	7
β-strand	241-244	4	51
α-helix	251-260	10
β-strand	265-269	5	51
α-helix	271-276	6
α-helix	279-295	17
β-strand	299-303	5	51
α-helix	306-308	3
β-strand	311	1	52
α-helix	320-333	14
β-strand	341-347	7	51
α-helix	350-352	3
β-strand	353	1	52
α-helix	355-357	3
β-strand	366-368	3	51
α-helix	374-384	11
β-strand	390	1	53
α-helix	396-402	7
α-helix	408-424	17
α-helix	427-430	4
α-helix	439-443	5
β-strand	447	1	53
α-helix	449-458	10
β-strand	470	1	54
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
β-strand	513-517	5	54
α-helix	524-534	11
β-strand	538-541	4	54
α-helix	544-550	7
α-helix	558-568	11
β-strand	572-576	5	54
α-helix	580-583	4
α-helix	599-609	11
β-strand	617-622	6	54
α-helix	631-633	3
β-strand	636	1	55
β-strand	638	1	55
β-strand	642-644	3	54
α-helix	645-648	4
α-helix	653-661	9
β-strand	666	1	56
α-helix	672-678	7
α-helix	684-715	32
β-strand	731	1	56
α-helix	733-735	3
α-helix	738-741	4
α-helix	749-757	9

Chain F: 50 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	57
β-strand	38-41	4	57
α-helix	43-48	6
β-strand	56-60	5	57
β-strand	66-73	8	57
β-strand	81-83	3	57
α-helix	86-91	6
β-strand	99-104	6	57
α-helix	108-109	2
β-strand	110	1	58
α-helix	111	1
β-strand	114-118	5	21
β-strand	119	1	59
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	58
β-strand	151-154	4	21
β-strand	161-168	8	21
β-strand	173-176	4	58
α-helix	181	1
β-strand	182-183	2	21
α-helix	187-188	2
β-strand	189	1	59
α-helix	190	1
α-helix	191-193	3
α-helix	195-198	4
α-helix	210-216	7
α-helix	217-221	5
α-helix	222-225	4
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	60
α-helix	251-261	11
β-strand	265-270	6	60
α-helix	271-276	6
α-helix	278	1
α-helix	281-295	15
β-strand	299-304	6	60
α-helix	306-309	4
β-strand	311	1	61
α-helix	320-333	14
β-strand	341-346	6	60
α-helix	350-352	3
β-strand	353	1	61
α-helix	355-358	4
β-strand	365-368	4	60
α-helix	374-384	11
β-strand	390	1	62
α-helix	396-402	7
α-helix	409-425	17
α-helix	426-429	4
α-helix	436-438	3
α-helix	439-444	6
β-strand	447	1	62
α-helix	449-458	10
α-helix	467-468	2
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-505	6
β-strand	513-514	2	63
β-strand	515-517	3	64
α-helix	524-534	11
β-strand	538-543	6	63
α-helix	544-551	8
α-helix	559-568	10
β-strand	572-577	6	63
α-helix	579-581	3
α-helix	599-608	10
α-helix	613-615	3
β-strand	617-620	4	63
β-strand	623	1	64
β-strand	642-644	3	64
α-helix	646-648	3
α-helix	653-661	9
β-strand	666	1	65
α-helix	673-676	4
α-helix	684-715	32
β-strand	731	1	65
α-helix	733-741	9
α-helix	749-759	11

Chain G: 24 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	1
β-strand	14-21	8	1
β-strand	25	1	2
α-helix	26-37	12
β-strand	44-47	4	1
β-strand	55	1	1
β-strand	63	1	2
β-strand	74-79	6	1
α-helix	109-114	6
β-strand	121	1	3
α-helix	143	1
β-strand	144	1	3
α-helix	145	1
α-helix	151-154	4
β-strand	162-163	2	4
α-helix	164-172	9
α-helix	190-191	2
α-helix	198-199	2
α-helix	210-212	3
β-strand	213-214	2	5
β-strand	220-221	2	4
β-strand	225-228	4	6
α-helix	233-244	12
β-strand	249-259	11	6
β-strand	265-274	10	6
β-strand	278-280	3	7
β-strand	284-287	4	7
α-helix	293-302	10
β-strand	306-314	9	6
β-strand	317-319	3	8
β-strand	324-325	2	8
α-helix	338-350	13
α-helix	352-353	2
β-strand	354	1	9
β-strand	362	1	9
β-strand	368-374	7	6
β-strand	380-387	8	6
α-helix	389-396	8
β-strand	400-402	3	10
β-strand	403	1	11
β-strand	409-412	4	10
β-strand	424-429	6	5
β-strand	435-439	5	5
β-strand	443-444	2	10
α-helix	445-447	3
β-strand	449-455	7	6
β-strand	456-457	2	12
α-helix	470-473	4
α-helix	477-479	3
α-helix	485-493	9
α-helix	500-504	5
α-helix	507-514	8
α-helix	522-524	3
α-helix	526-534	9
α-helix	537-544	8
α-helix	547-557	11

Chain I: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	13
α-helix	24-30	7
β-strand	40-41	2	12

4 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
Nuclear protein localization protein 4 homolog	G	protein	611	Homo sapiens	Q8TAT6 (AlphaFold model)
Ubiquitin	I, K	protein	76	Homo sapiens	P62987 (AlphaFold model)
FAS-associated factor 1	M, O	protein	173	Homo sapiens	Q9UNN5 (AlphaFold model)
Ubiquitin recognition factor in ER-associated degradation protein 1	P	protein	313	Homo sapiens	Q92890 (AlphaFold model)
Transitional endoplasmic reticulum ATPase	A, B, C, D, E, F	protein	821	Homo sapiens	P55072

Sequence of entity 1 (G), FASTA

>11TA_1 Nuclear protein localization protein 4 homolog (chains G)
MGGGAESIIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEIT
ASSNKSLNLLKIKHGDLLFLFPSSLAGPSSEMETSVPPGFKVFGAPNVVEDEIDQYLSKQ
DGKIYRSRDPQLCRHGPLGKCVHCVPLEPFDEDYLNHLEPPVKHMSFHAYIRKLTGGADK
GKFVALENISCKIKSGCEGHLPWPNGICTKCQPSAITLNRQKYRHVDNIMFENHTVADRF
LDFWRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVD
EIAAKLGLRKVGWIFTDLVSEDTRKGTVRYSRNKDTYFLSSEECITAGDFQNKHPNMCRL
SPDGHFGSKFVTAVATGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDAPELGYAKESSS
EQYVPDVFYKDVDKFGNEITQLARPLPVEYLIIDITTTFPKDPVYTFSISQNPFPIENRD
VLGETQDFHSLATYLSQNTSSVFLDTISDFHLLLFLVTNEVMPLQDSISLLLEAVRTRNE
ELAQTWKRSEQWATIEQLCSTVGGQLPGLHEYGAVGGSTHTATAAMWACQHCTFMNQPGT
GHCEMCSLPRT

Sequence of entity 2 (I, K), FASTA

>11TA_2 Ubiquitin (chains I, K)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (M, O), FASTA

>11TA_3 FAS-associated factor 1 (chains M, O)
PLGMAAMEIFTAQQQEDIKDEDEREARENVKREQDEAYRLSLEADRAKREAHEREMAEQF
RLEQIRKEQEEEREAIRLSLEQALPPEPKEENAEPVSKLRIRTPSGEFLERRFLASNKLQ
IVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE

Sequence of entity 4 (P), FASTA

>11TA_4 Ubiquitin recognition factor in ER-associated degradation protein 1 (chains P)
MFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLN
ITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVA
TYSKFQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAV
SIIECDMNVDFDAPLGYKEPERQVQHEESTEGEADHSGYAGELGFRAFSGSGNRLDGKKK
GVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGRFVAFSGEGQSL
RKKGRKPHHHHHH

Sequence of entity 5 (A, B, C, D, E, F), FASTA

>11TA_5 Transitional endoplasmic reticulum ATPase (chains A, B, C, D, E, F)
MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLK
GKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPID
DTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDT
VIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRG
ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAI
IFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF
GRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL
QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIG
GLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFI
SIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRV
INQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKAN
LRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAM
EVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGG
AGPSQGSGGGTGGSVYTEDNDDDLYGVDKLAAALEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	9
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3
ZN	Zinc ion	Zn	2

Primary citation

Faf1 accelerates p97-mediated protein unfolding by promoting ubiquitin engagement. Liao, Z., Arkinson, C., Martin, A. bioRxiv (2025). DOI 10.1101/2025.10.27.684972 · PubMed

Other PDB entries of the same protein (UniProt Q8TAT6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7WWQ 2.72 Å, Crystal structure of human Ufd1-Npl4 complex
9YRC 2.97 Å, p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
7WWP 2.99 Å, Crystal structure of human Npl4
11VE 3.85 Å, Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (State1)
11SY 4.28 Å, Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused)

Browse structure collections

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