8OOI | pdb_00008ooi

Full composite cryo-EM map of p97/VCP in ADP.Pi state

PDB DOI: https://doi.org/10.2210/pdb8OOI/pdb
EM Map EMD-17016: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-05 Released: 2024-01-31
Deposition Author(s): Cheng, T.C., Sakata, E., Schuetz, A.K.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.61 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Characterizing ATP processing by the AAA+ protein p97 at the atomic level.

Shein, M., Hitzenberger, M., Cheng, T.C., Rout, S.R., Leitl, K.D., Sato, Y., Zacharias, M., Sakata, E., Schutz, A.K.

(2024) Nat Chem 16: 363-372

PubMed: 38326645 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41557-024-01440-0
Primary Citation Related Structures:
8OOI

PubMed Abstract:
The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an impactful pharmacological target. The hexameric complex undergoes substantial conformational changes throughout its catalytic cycle. Here we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations. p97 populates a metastable reaction intermediate, the ADP·P _i state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.

Organizational Affiliation

Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany.

Macromolecule Content

Total Structure Weight: 543.32 kDa
Atom Count: 35,256
Modeled Residue Count: 4,404
Deposited Residue Count: 4,836
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transitional endoplasmic reticulum ATPase	A B [auth F] C [auth B] D E [auth C] A, B [auth F], C [auth B], D, E [auth C], F [auth E]	806	Homo sapiens	Mutation(s): 0 Gene Names: VCP EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens) Explore P55072 Go to UniProtKB: P55072
PHAROS: P55072 GTEx: ENSG00000165280
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55072
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain T [auth B] SDF format, chain O [auth F] SDF format, chain MA [auth E] SDF format, chain H [auth A] SDF format, chain GA [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth B] MOL2 format, chain O [auth F] MOL2 format, chain MA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth B] mmCIF format, chain O [auth F] mmCIF format, chain MA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C]	GA [auth C] H [auth A] MA [auth E] O [auth F] T [auth B] GA [auth C], H [auth A], MA [auth E], O [auth F], T [auth B], Z [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain GA [auth C] Focus chain H [auth A] Focus chain MA [auth E] Focus chain O [auth F] Focus chain T [auth B] Focus chain Z [auth D] Interactions & Density Focus chain GA [auth C] Focus chain H [auth A] Focus chain MA [auth E] Focus chain O [auth F] Focus chain T [auth B] Focus chain Z [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain S [auth B] SDF format, chain Y [auth D] SDF format, chain N [auth F] SDF format, chain LA [auth E] SDF format, chain G [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain N [auth F] MOL2 format, chain LA [auth E] MOL2 format, chain G [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain N [auth F] mmCIF format, chain LA [auth E] mmCIF format, chain G [auth A]	FA [auth C] G [auth A] LA [auth E] N [auth F] S [auth B] FA [auth C], G [auth A], LA [auth E], N [auth F], S [auth B], Y [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain FA [auth C] Focus chain G [auth A] Focus chain LA [auth E] Focus chain N [auth F] Focus chain S [auth B] Focus chain Y [auth D] Interactions & Density Focus chain FA [auth C] Focus chain G [auth A] Focus chain LA [auth E] Focus chain N [auth F] Focus chain S [auth B] Focus chain Y [auth D]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth F] SDF format, chain X [auth B] SDF format, chain KA [auth E] SDF format, chain EA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth F] MOL2 format, chain X [auth B] MOL2 format, chain KA [auth E] MOL2 format, chain EA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth F] mmCIF format, chain X [auth B] mmCIF format, chain KA [auth E] mmCIF format, chain EA [auth C]	DA [auth D] EA [auth C] KA [auth E] L [auth A] M [auth F] DA [auth D], EA [auth C], KA [auth E], L [auth A], M [auth F], X [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth D] Focus chain EA [auth C] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth F] Focus chain X [auth B] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth C] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth F] Focus chain X [auth B]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain R [auth F] SDF format, chain PA [auth E] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain CA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain R [auth F] MOL2 format, chain PA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain CA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain R [auth F] mmCIF format, chain PA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain CA [auth D]	CA [auth D] JA [auth C] K [auth A] PA [auth E] R [auth F] CA [auth D], JA [auth C], K [auth A], PA [auth E], R [auth F], W [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain JA [auth C] Focus chain K [auth A] Focus chain PA [auth E] Focus chain R [auth F] Focus chain W [auth B] Interactions & Density Focus chain CA [auth D] Focus chain JA [auth C] Focus chain K [auth A] Focus chain PA [auth E] Focus chain R [auth F] Focus chain W [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain OA [auth E] SDF format, chain P [auth F] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain Q [auth F] SDF format, chain NA [auth E] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth F] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Q [auth F] MOL2 format, chain NA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain OA [auth E] mmCIF format, chain P [auth F] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Q [auth F] mmCIF format, chain NA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] HA [auth C] I [auth A] IA [auth C] AA [auth D], BA [auth D], HA [auth C], I [auth A], IA [auth C], J [auth A], NA [auth E], OA [auth E], P [auth F], Q [auth F], U [auth B], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth F] Focus chain Q [auth F] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth F] Focus chain Q [auth F] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.61 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-31

Deposition Author(s):

Cheng, T.C.

Sakata, E.

Schuetz, A.K.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	394455587
German Research Foundation (DFG)	Germany	201302640
German Research Foundation (DFG)	Germany	390729940
German Research Foundation (DFG)	Germany	--