6G2X: Transitional endoplasmic reticulum ATPase

Crystal structure of the p97 D2 domain in a helical split-washer conformation. Determined by X-ray diffraction at 2.08 Å resolution. Released 10 Apr 2019.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,298
Mol. weight: 35.75 kDa
Ligands: ADP, EJQ
Released: 10 Apr 2019

Explore 6G2X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6G2X contains 21 α-helices and 8 β-strands across 1 chain. 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: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	470	1	1
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
α-helix	508-511	4
β-strand	513-517	5	1
α-helix	524-534	11
β-strand	538-543	6	1
α-helix	544-547	4
α-helix	557-568	12
β-strand	572-577	6	1
α-helix	579-582	4
α-helix	597-609	13
α-helix	613-615	3
β-strand	617-623	7	1
α-helix	626-628	3
α-helix	631-634	4
β-strand	642-644	3	1
α-helix	646-648	3
α-helix	650-660	11
β-strand	666	1	2
α-helix	672-677	6
α-helix	684-709	26
α-helix	728-730	3
β-strand	731	1	2
α-helix	732	1
α-helix	733-739	7
α-helix	740-742	3
α-helix	749-761	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A	protein	306	Homo sapiens	P55072 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6G2X_1 Transitional endoplasmic reticulum ATPase (chains A)
GPGSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYG
PPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDE
LDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGR
LDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLA
IRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMF
AQTLQQ

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
EJQ	~{N}-(4-fluorophenyl)-2-pyrrolidin-1-yl-ethanamide	C12 H15 F N2 O	2

Water and common crystallization additives (NA, DMS, MPD) are not listed.

Primary citation

Crystal structure of the catalytic D2 domain of the AAA+ ATPase p97 reveals a putative helical split-washer-type mechanism for substrate unfolding. Stach, L., Morgan, R.M., Makhlouf, L. et al. FEBS Lett (2020) 594:933-943. DOI 10.1002/1873-3468.13667 · 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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