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

Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (State1). Determined by electron microscopy at 3.85 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 3.85 Å
Organism: Homo sapiens
Chains: 10
Atoms: 35,382
Mol. weight: 697.13 kDa
Ligands: ZN, ATP, ADP
Released: 22 Apr 2026

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

Secondary structure: helices and β-sheets

11VE contains 281 α-helices and 194 β-strands across 10 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: 48 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	18
β-strand	38	1	19
β-strand	39-41	3	18
α-helix	43-46	4
β-strand	57-60	4	18
α-helix	62-64	3
β-strand	66-69	4	18
β-strand	70	1	19
α-helix	78	1
β-strand	81-84	4	18
α-helix	86-90	5
α-helix	94	1
β-strand	99-104	6	18
β-strand	110	1	20
β-strand	114-118	5	21
α-helix	121-123	3
α-helix	130-134	5
α-helix	137-139	3
β-strand	145-146	2	20
β-strand	151-154	4	21
β-strand	161-168	8	21
β-strand	174-175	2	20
α-helix	176-177	2
α-helix	192-199	8
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
α-helix	236-238	3
β-strand	240-244	5	22
α-helix	251-259	9
β-strand	265-270	6	22
α-helix	271-276	6
α-helix	279-295	17
β-strand	299-304	6	22
α-helix	306-308	3
β-strand	311	1	23
α-helix	320-333	14
β-strand	341-347	7	22
β-strand	353	1	23
α-helix	355-357	3
β-strand	365-368	4	22
α-helix	374-384	11
α-helix	389	1
β-strand	390	1	24
α-helix	391	1
α-helix	396-402	7
α-helix	408-426	19
α-helix	438-443	6
β-strand	447	1	24
α-helix	449-458	10
α-helix	467-468	2
α-helix	476-479	4
α-helix	483-498	16
α-helix	500-506	7
β-strand	513-517	5	25
α-helix	524-535	12
β-strand	538	1	26
β-strand	541-543	3	25
α-helix	544-548	5
α-helix	549-552	4
α-helix	556-568	13
β-strand	572	1	26
β-strand	575-577	3	25
α-helix	579-581	3
α-helix	599-609	11
α-helix	613-615	3
β-strand	617	1	26
β-strand	619-623	5	25
α-helix	626-628	3
α-helix	631-634	4
β-strand	641-644	4	25
α-helix	646-648	3
α-helix	652-661	10
β-strand	666	1	27
α-helix	672-676	5
α-helix	684-714	31
β-strand	731	1	27
α-helix	733-739	7
α-helix	749-759	11

Chain B: 39 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	193-198	6
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	241-243	3	28
α-helix	251-261	11
β-strand	265-270	6	28
α-helix	271-275	5
α-helix	281-295	15
β-strand	299-304	6	28
α-helix	306-309	4
β-strand	311	1	29
α-helix	313-315	3
α-helix	320-334	15
α-helix	335-337	3
β-strand	341-346	6	28
α-helix	350-352	3
β-strand	353	1	29
α-helix	355-358	4
β-strand	365-367	3	28
α-helix	374-385	12
β-strand	390	1	30
α-helix	396-402	7
α-helix	409-426	18
α-helix	436-438	3
α-helix	439-444	6
β-strand	447	1	30
α-helix	449-457	9
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	31
α-helix	524-535	12
β-strand	538-542	5	31
α-helix	544-553	10
α-helix	557-568	12
β-strand	572-576	5	31
α-helix	579-581	3
α-helix	600-609	10
α-helix	613-615	3
β-strand	617-623	7	31
α-helix	626-628	3
β-strand	641-644	4	31
α-helix	653-660	8
β-strand	666	1	32
α-helix	672-676	5
α-helix	684-714	31
β-strand	731	1	32
α-helix	733-741	9
α-helix	749-759	11

Chain C: 45 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
β-strand	25-27	3	33
β-strand	30	1	34
β-strand	38	1	35
β-strand	40	1	36
β-strand	42	1	37
α-helix	43-48	6
β-strand	56-60	5	35
α-helix	62-64	3
β-strand	66-70	5	35
β-strand	76-77	2	37
α-helix	78	1
β-strand	81	1	33
β-strand	83	1	36
β-strand	84	1	34
α-helix	86-89	4
β-strand	99-101	3	33
β-strand	103-104	2	35
β-strand	110-111	2	38
β-strand	114-118	5	39
α-helix	135-138	4
β-strand	145-147	3	38
α-helix	150	1
β-strand	151	1	39
α-helix	152	1
β-strand	163-168	6	39
β-strand	173-176	4	38
β-strand	184	1	39
α-helix	190-198	9
α-helix	203-205	3
α-helix	210-220	11
α-helix	222-225	4
α-helix	227-233	7
β-strand	240-244	5	40
α-helix	251-261	11
β-strand	265-270	6	40
α-helix	271-276	6
α-helix	281-295	15
β-strand	299-304	6	40
α-helix	306-309	4
α-helix	321-333	13
β-strand	342-346	5	40
α-helix	350-352	3
α-helix	355-357	3
β-strand	359	1	41
β-strand	362	1	41
β-strand	365-368	4	40
α-helix	374-384	11
α-helix	396-402	7
α-helix	408-426	19
α-helix	427-429	3
α-helix	438-442	5
α-helix	449-457	9
α-helix	467-468	2
α-helix	476-478	3
α-helix	483-493	11
α-helix	495-498	4
α-helix	500-505	6
β-strand	513-517	5	42
α-helix	524-535	12
β-strand	538	1	42
β-strand	541-543	3	42
α-helix	544-548	5
α-helix	558-568	11
β-strand	572-577	6	42
α-helix	579-582	4
α-helix	599-609	11
α-helix	613-615	3
β-strand	617-623	7	42
α-helix	626-628	3
β-strand	636	1	43
β-strand	638	1	43
β-strand	640-644	5	42
α-helix	645-648	4
α-helix	653-661	9
β-strand	666	1	44
α-helix	672-676	5
α-helix	684-713	30
β-strand	731	1	44
α-helix	733-737	5
α-helix	738-740	3
α-helix	749-757	9

Chain D: 34 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	193	1
α-helix	194-198	5
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	235-238	4
β-strand	240-243	4	4
α-helix	251-259	9
β-strand	265-270	6	4
α-helix	271-275	5
α-helix	281-294	14
β-strand	299-304	6	4
α-helix	306-309	4
α-helix	313-315	3
α-helix	320-334	15
β-strand	341-346	6	4
β-strand	365-367	3	4
α-helix	374-385	12
α-helix	396-402	7
α-helix	408-427	20
α-helix	438-443	6
α-helix	449-458	10
α-helix	467-468	2
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
β-strand	513-517	5	45
α-helix	524-535	12
β-strand	538-543	6	45
α-helix	544-552	9
α-helix	557-568	12
β-strand	572-577	6	45
α-helix	579-584	6
α-helix	599-611	13
β-strand	618-623	6	45
α-helix	626-628	3
α-helix	631-634	4
β-strand	641-644	4	45
α-helix	646-648	3
α-helix	653-661	9
β-strand	666	1	46
α-helix	672-677	6
α-helix	684-714	31
β-strand	731	1	46
α-helix	733-741	9
α-helix	749-759	11

Chain E: 37 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	195-197	3
α-helix	203-205	3
α-helix	210-225	16
α-helix	228-233	6
β-strand	240-244	5	47
α-helix	251-261	11
β-strand	265-270	6	47
α-helix	271-276	6
α-helix	279-296	18
β-strand	299-304	6	47
α-helix	306-309	4
β-strand	311	1	48
α-helix	319-334	16
α-helix	335-337	3
β-strand	342-346	5	47
α-helix	350-352	3
β-strand	353	1	48
α-helix	355-358	4
β-strand	365-368	4	47
α-helix	374-384	11
β-strand	390	1	49
α-helix	396-402	7
α-helix	409-423	15
α-helix	427-429	3
α-helix	439-444	6
β-strand	447	1	49
α-helix	449-458	10
α-helix	476-479	4
α-helix	483-498	16
α-helix	500-505	6
β-strand	513-517	5	50
α-helix	524-535	12
β-strand	538-543	6	50
α-helix	544-552	9
α-helix	556-558	3
α-helix	559-568	10
β-strand	572-577	6	50
α-helix	579-581	3
α-helix	599-610	12
α-helix	613-615	3
β-strand	617-622	6	50
α-helix	631-634	4
β-strand	642-644	3	50
α-helix	646-648	3
α-helix	652-660	9
β-strand	666	1	51
α-helix	672-678	7
α-helix	684-705	22
α-helix	706-710	5
α-helix	711-715	5
β-strand	731	1	51
α-helix	733-741	9
α-helix	749-759	11

Chain F: 44 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	52
β-strand	29-30	2	53
β-strand	38	1	54
β-strand	40	1	53
α-helix	41-42	2
α-helix	43-48	6
β-strand	56-60	5	54
β-strand	66-70	5	54
β-strand	83-84	2	53
α-helix	86-89	4
β-strand	100	1	52
β-strand	103-104	2	54
α-helix	109	1
β-strand	110-111	2	55
β-strand	117-118	2	56
α-helix	121-123	3
α-helix	130-132	3
β-strand	145-146	2	55
β-strand	151-153	3	56
β-strand	162-164	3	56
β-strand	174-176	3	55
α-helix	190-198	9
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
α-helix	236-238	3
β-strand	240-243	4	57
α-helix	251-261	11
β-strand	265-270	6	57
α-helix	271-274	4
α-helix	281-295	15
β-strand	299-304	6	57
α-helix	306-308	3
β-strand	311	1	58
α-helix	319-334	16
α-helix	335-337	3
β-strand	342-346	5	57
α-helix	350-352	3
β-strand	353	1	58
α-helix	355-358	4
β-strand	365-367	3	57
α-helix	374-385	12
α-helix	396-402	7
α-helix	408-426	19
α-helix	427-429	3
α-helix	440-444	5
α-helix	449-457	9
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
β-strand	514-517	4	59
α-helix	524-535	12
β-strand	538	1	60
β-strand	541-543	3	59
α-helix	544-552	9
α-helix	558-568	11
β-strand	572	1	60
β-strand	573-577	5	59
α-helix	579-582	4
α-helix	599-610	12
α-helix	613-615	3
β-strand	618-623	6	59
α-helix	626-628	3
α-helix	631-634	4
β-strand	641-644	4	59
α-helix	646-648	3
α-helix	653-661	9
β-strand	666	1	61
α-helix	672-678	7
α-helix	684-714	31
β-strand	731	1	61
α-helix	733-740	8
α-helix	749-759	11

Chain G: 27 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
β-strand	16-21	6	1
β-strand	25	1	2
α-helix	26-37	12
β-strand	63	1	2
α-helix	64-66	3
β-strand	74-75	2	1
α-helix	109-115	7
β-strand	121	1	3
β-strand	137	1	4
α-helix	139-141	3
α-helix	143	1
β-strand	144	1	3
α-helix	145	1
α-helix	149-154	6
β-strand	162-163	2	5
α-helix	164-171	8
α-helix	184-186	3
α-helix	190-191	2
β-strand	214	1	6
β-strand	220-221	2	5
β-strand	225-228	4	7
α-helix	232-235	4
α-helix	239-244	6
β-strand	249-259	11	7
β-strand	265-274	10	7
β-strand	278-280	3	8
β-strand	284-287	4	8
α-helix	292-303	12
β-strand	306-313	8	7
β-strand	317-319	3	9
β-strand	324-325	2	9
α-helix	338-350	13
α-helix	352-353	2
β-strand	354	1	10
β-strand	362	1	10
β-strand	368-374	7	7
β-strand	380-387	8	7
α-helix	389-396	8
β-strand	400-402	3	11
β-strand	403	1	12
β-strand	409-412	4	11
α-helix	413-414	2
β-strand	425-429	5	6
β-strand	435-439	5	6
β-strand	442-444	3	11
α-helix	445-448	4
β-strand	449-451	3	7
α-helix	453-457	5
α-helix	470-473	4
β-strand	476	1	13
β-strand	481	1	13
α-helix	485-494	10
α-helix	501-504	4
α-helix	507-515	9
α-helix	525-534	10
α-helix	537-544	8
α-helix	547-559	13
α-helix	567-569	3

Chain M: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	531-560	30
α-helix	564-566	3
β-strand	573-579	7	14
β-strand	585-591	7	14
β-strand	595	1	15
α-helix	596-604	9
β-strand	613-617	5	14
β-strand	622-623	2	14
α-helix	624-626	3
β-strand	632	1	15
β-strand	641-642	2	14
β-strand	645-648	4	14

2 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	608	Homo sapiens	Q8TAT6 (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 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>11VE_1 Nuclear protein localization protein 4 homolog (chains G)
MAESIIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASS
NKSLNLLKIKHGDLLFLFPSSLAGPSSEMETSVPPGFKVFGAPNVVEDEIDQYLSKQDGK
IYRSRDPQLCRHGPLGKCVHCVPLEPFDEDYLNHLEPPVKHMSFHAYIRKLTGGADKGKF
VALENISCKIKSGCEGHLPWPNGICTKCQPSAITLNRQKYRHVDNIMFENHTVADRFLDF
WRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVDEIA
AKLGLRKVGWIFTDLVSEDTRKGTVRYSRNKDTYFLSSEECITAGDFQNKHPNMCRLSPD
GHFGSKFVTAVATGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDAPELGYAKESSSEQY
VPDVFYKDVDKFGNEITQLARPLPVEYLIIDITTTFPKDPVYTFSISQNPFPIENRDVLG
ETQDFHSLATYLSQNTSSVFLDTISDFHLLLFLVTNEVMPLQDSISLLLEAVRTRNEELA
QTWKRSEQWATIEQLCSTVGGQLPGLHEYGAVGGSTHTATAAMWACQHCTFMNQPGTGHC
EMCSLPRT

Sequence of entity 2 (M, O), FASTA

>11VE_2 FAS-associated factor 1 (chains M, O)
PLGMAAMEIFTAQQQEDIKDEDEREARENVKREQDEAYRLSLEADRAKREAHEREMAEQF
RLEQIRKEQEEEREAIRLSLEQALPPEPKEENAEPVSKLRIRTPSGEFLERRFLASNKLQ
IVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE

Sequence of entity 3 (P), FASTA

>11VE_3 Ubiquitin recognition factor in ER-associated degradation protein 1 (chains P)
MFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLN
ITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVA
TYSKFQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAV
SIIECDMNVDFDAPLGYKEPERQVQHEESTEGEADHSGYAGELGFRAFSGSGNRLDGKKK
GVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGRFVAFSGEGQSL
RKKGRKPHHHHHH

Sequence of entity 4 (A, B, C, D, E, F), FASTA

>11VE_4 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
ZN	Zinc ion	Zn	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	9

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
11TA 3.58 Å, Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused)
11SY 4.28 Å, Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused)

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