9YW2: Complex structure of human p97

Complex structure of human p97 bound to Faf1 and Ufd1 (NTD focused). Determined by electron microscopy at 3.27 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 3.27 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,610
Mol. weight: 228.64 kDa
Released: 22 Apr 2026

Explore 9YW2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YW2 contains 13 α-helices and 23 β-strands across 3 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: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	1
β-strand	38-42	5	1
α-helix	43-49	7
β-strand	56-60	5	1
β-strand	66-74	9	1
β-strand	81-84	4	1
α-helix	86-91	6
β-strand	99-104	6	1
β-strand	110	1	2
β-strand	113-118	6	3
β-strand	119	1	4
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	2
β-strand	151-154	4	3
β-strand	161-168	8	3
β-strand	173-175	3	2
β-strand	181-183	3	3
β-strand	189	1	4
α-helix	191-196	6

Chain H: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	531-556	26
α-helix	558-560	3
α-helix	562-566	5
β-strand	573-579	7	5
α-helix	580	1
β-strand	587-591	5	5
β-strand	595	1	6
α-helix	597-604	8
β-strand	613-616	4	5
β-strand	623	1	5
α-helix	624-626	3
β-strand	632	1	6
β-strand	641-648	8	5

Chain I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	233-234	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A	protein	821	Homo sapiens	P55072 (AlphaFold model)
Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated factor 1	H	protein	880	Homo sapiens	P08515 (AlphaFold model), Q9UNN5 (AlphaFold model)
Ubiquitin recognition factor in ER-associated degradation protein 1	I	protein	326	Homo sapiens	Q92890 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9YW2_1 Transitional endoplasmic reticulum ATPase (chains A)
MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLK
GKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPID
DTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDT
VIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRG
ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAI
IFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF
GRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL
QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIG
GLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFI
SIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRV
INQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKAN
LRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAM
EVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGG
AGPSQGSGGGTGGSVYTEDNDDDLYGVDKLAAALEHHHHHH

Sequence of entity 2 (H), FASTA

>9YW2_2 Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated factor 1 (chains H)
MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYID
GDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKV
DFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFK
KRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDLEVLFQGPLGMASNMDREMI
LADFQACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSEYGGETIPGPAFNPAS
HPASAPTSSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILE
NELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNSLYVLTPDLPPPSSSSHAGALQESL
NQNFMLIITHREVQREYNLNFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSMC
LAESGLSYPCHRLTVGRRSSPAQTREQSEEQITDVHMVSDSDGDDFEDATEFGVDDGEVF
GMASSALRKSPMMPENAENEGDALLQFTAEFSSRYGDCHPVFFIGSLEAAFQEAFYVKAR
DRKLLAIYLHHDESVLTNVFCSQMLCAESIVSYLSQNFITWAWDLTKDSNRARFLTMCNR
HFGSVVAQTIRTQKTDQFPLFLIIMGKRSSNEVLNVIQGNTTVDELMMRLMAAMEIFTAQ
QQEDIKDEDEREARENVKREQDEAYRLSLEADRAKREAHEREMAEQFRLEQIRKEQEEER
EAIRLSLEQALPPEPKEENAEPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPW
DEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE

Sequence of entity 3 (I), FASTA

>9YW2_3 Ubiquitin recognition factor in ER-associated degradation protein 1 (chains I)
MSSHHHHHHSSGLVPRGSHMFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAGPNDRSDVE
KGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQN
LLLEEGGLVQVESVNLQVATYSKFQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAIN
YNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGYKEPERQVQHEESTEGEADHSGYAG
ELGFRAFSGSGNRLDGKKKGVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKV
EEDEAGGRFVAFSGEGQSLRKKGRKP

Primary citation

Faf1 accelerates p97-mediated protein unfolding by promoting ubiquitin engagement. Liao, Z., Arkinson, C., Martin, A. Cell Rep (2026) 45:117393-117393. DOI 10.1016/j.celrep.2026.117393 · 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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