5FTJ

Cryo-EM structure of human p97 bound to UPCDC30245 inhibitor

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

2.3 A Resolution Cryo-Em Structure of Human P97 and Mechanism of Allosteric Inhibition

Banerjee, S., Bartesaghi, A., Merk, A., Rao, P., Bulfer, S.L., Yan, Y., Green, N., Mroczkowski, B., Neitz, R.J., Wipf, P., Falconieri, V., Deshaies, R.J., Milne, J.L.S., Huryn, D., Arkin, M., Subramaniam, S.

(2016) Science 351: 871

  • DOI: 10.1126/science.aad7974
  • Primary Citation of Related Structures:  
    5FTJ, 5FTK, 5FTL, 5FTM, 5FTN

  • PubMed Abstract: 

    • p97 is a hexameric AAA+ adenosine triphosphatase (ATPase) that is an attractive target for cancer drug development. We report cryo-electron microscopy (cryo-EM) structures for adenosine diphosphate (ADP)-bound, full-length, hexameric wild-type p97 in the presence and absence of an allosteric inhibitor at resolutions of 2 ...

    p97 is a hexameric AAA+ adenosine triphosphatase (ATPase) that is an attractive target for cancer drug development. We report cryo-electron microscopy (cryo-EM) structures for adenosine diphosphate (ADP)-bound, full-length, hexameric wild-type p97 in the presence and absence of an allosteric inhibitor at resolutions of 2.3 and 2.4 angstroms, respectively. We also report cryo-EM structures (at resolutions of ~3.3, 3.2, and 3.3 angstroms, respectively) for three distinct, coexisting functional states of p97 with occupancies of zero, one, or two molecules of adenosine 5'-O-(3-thiotriphosphate) (ATPγS) per protomer. A large corkscrew-like change in molecular architecture, coupled with upward displacement of the N-terminal domain, is observed only when ATPγS is bound to both the D1 and D2 domains of the protomer. These cryo-EM structures establish the sequence of nucleotide-driven structural changes in p97 at atomic resolution. They also enable elucidation of the binding mode of an allosteric small-molecule inhibitor to p97 and illustrate how inhibitor binding at the interface between the D1 and D2 domains prevents propagation of the conformational changes necessary for p97 function.

    Organizational Affiliation: 

    Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA. ss1@nih.gov.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE
A, B, C, D, E, F
A, B, C, D, E, F
806Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55072
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OJA
Query on OJA
Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
1-(3-(5-FLUORO-1H-INDOL-2-YL)PHENYL)PIPERIDIN-4-YL)(2-(4-ISOPROPYL-PIPERAZIN1-YL)ETHYL)-CARBAMATE
C28 H38 F N5
LZHXZCVDLATFAR-UHFFFAOYSA-N		 Ligand Interaction
ADP
Query on ADP
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth B],
K [auth B],
M [auth C],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D],
S [auth E],
T [auth E],
V [auth F],
W [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
OJA BindingDB:  5FTJ IC50: min: 20, max: 70 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references, Other
  • Version 1.2: 2016-02-17
    Changes: Atomic model, Derived calculations
  • Version 1.3: 2016-03-09
    Changes: Database references
  • Version 1.4: 2017-08-30
    Changes: Data collection
  • Version 1.5: 2018-10-03
    Changes: Data collection