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

Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused). Determined by electron microscopy at 4.28 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 4.28 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,018
Mol. weight: 138.18 kDa
Ligands: ZN
Released: 22 Apr 2026

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

Secondary structure: helices and β-sheets

11SY contains 25 α-helices and 46 β-strands across 6 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 G: 18 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	109-115	7
β-strand	121	1	1
α-helix	124-126	3
β-strand	144	1	1
α-helix	149-152	4
α-helix	158-159	2
β-strand	162-163	2	2
α-helix	164-172	9
α-helix	210-212	3
β-strand	213-214	2	3
β-strand	220-221	2	2
β-strand	225-228	4	4
α-helix	233-244	12
β-strand	249-259	11	4
β-strand	265-274	10	4
β-strand	278	1	5
β-strand	284-285	2	6
β-strand	287	1	5
α-helix	293-302	10
β-strand	306-314	9	4
β-strand	319	1	7
β-strand	324	1	7
α-helix	338-350	13
β-strand	352-354	3	8
β-strand	362-365	4	8
β-strand	368-374	7	4
β-strand	380-387	8	4
α-helix	389-396	8
β-strand	400-402	3	9
β-strand	403	1	10
β-strand	409-412	4	9
α-helix	413-414	2
β-strand	424-429	6	3
β-strand	435-439	5	3
β-strand	442-444	3	9
β-strand	449-455	7	4
β-strand	456-457	2	11
α-helix	470-472	3
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	547-557	11

Chain H: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	12
β-strand	12-16	5	12
α-helix	23-34	12
α-helix	38-40	3
β-strand	42	1	13
β-strand	67-68	2	12
β-strand	70	1	13

Chain I: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	23-30	8
β-strand	40-41	2	11

Chain J: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	14
β-strand	5-6	2	15
β-strand	12	1	15
β-strand	15-16	2	14
α-helix	23-34	12
β-strand	44-45	2	15
β-strand	48-49	2	15
β-strand	67-68	2	15

Chain K: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	16
β-strand	12-16	5	16
α-helix	23-33	11
α-helix	38-40	3
β-strand	43-45	3	16
β-strand	49	1	16
α-helix	50-51	2
β-strand	66-69	4	16

Chain P: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	259	1	10
β-strand	268-269	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear protein localization protein 4 homolog	G	protein	611	Homo sapiens	Q8TAT6 (AlphaFold model)
Ubiquitin	H, I, J, K	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin recognition factor in ER-associated degradation protein 1	P	protein	313	Homo sapiens	Q92890 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>11SY_1 Nuclear protein localization protein 4 homolog (chains G)
MGGGAESIIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEIT
ASSNKSLNLLKIKHGDLLFLFPSSLAGPSSEMETSVPPGFKVFGAPNVVEDEIDQYLSKQ
DGKIYRSRDPQLCRHGPLGKCVHCVPLEPFDEDYLNHLEPPVKHMSFHAYIRKLTGGADK
GKFVALENISCKIKSGCEGHLPWPNGICTKCQPSAITLNRQKYRHVDNIMFENHTVADRF
LDFWRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVD
EIAAKLGLRKVGWIFTDLVSEDTRKGTVRYSRNKDTYFLSSEECITAGDFQNKHPNMCRL
SPDGHFGSKFVTAVATGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDAPELGYAKESSS
EQYVPDVFYKDVDKFGNEITQLARPLPVEYLIIDITTTFPKDPVYTFSISQNPFPIENRD
VLGETQDFHSLATYLSQNTSSVFLDTISDFHLLLFLVTNEVMPLQDSISLLLEAVRTRNE
ELAQTWKRSEQWATIEQLCSTVGGQLPGLHEYGAVGGSTHTATAAMWACQHCTFMNQPGT
GHCEMCSLPRT

Sequence of entity 2 (H, I, J, K), FASTA

>11SY_2 Ubiquitin (chains H, I, J, K)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (P), FASTA

>11SY_3 Ubiquitin recognition factor in ER-associated degradation protein 1 (chains P)
MFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLN
ITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVA
TYSKFQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAV
SIIECDMNVDFDAPLGYKEPERQVQHEESTEGEADHSGYAGELGFRAFSGSGNRLDGKKK
GVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGRFVAFSGEGQSL
RKKGRKPHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
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
11TA 3.58 Å, Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused)
11VE 3.85 Å, Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (State1)

Browse structure collections

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