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 13DX | pdb_000013dx

Structure of HSP90b bound to de-novo designed binder H4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 13DX

This is version 1.0 of the entry. See complete history. 

Literature

Structural analysis of de novo-designed binders targeting the closed state of HSP90.

Srivastava, D., Singh, S., Boyd, K., Artemyev, N.O.

(2026) Structure 

  • DOI: https://doi.org/10.1016/j.str.2026.09.007
  • Primary Citation Related Structures: 
    13DW, 13DX

  • PubMed Abstract: 

    Heat shock protein 90 (HSP90) assists the folding and maturation of numerous signaling proteins and is an important therapeutic target. Most HSP90 inhibitors target the ATP-binding pocket and disrupt ATP-induced closure, whereas inhibitors targeting the closed state have not been developed. Here, we report de novo-designed protein binders that selectively recognize closed HSP90. Two binders, H2 and H4, have similar folds and affinities for HSP90 but distinct binding kinetics. Cryo-EM structures of HSP90 complexes with H2 and H4 revealed high accuracy of the BindCraft predictions. H2 and H4 compete with p23 at one, but not both, symmetrical p23-binding sites. In HEK293T cells, H2 induced a reduced heat shock response compared with the ATP-site inhibitor 17-DMAG while reducing levels of CDK4, providing functional evidence for HSP90 inhibition. These binders provide tools for probing HSP90 function and potential leads for developing closed-state HSP90 inhibitors.


  • Organizational Affiliation: 
    • Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.

Macromolecule Content 

  • Total Structure Weight: 197.83 kDa 
  • Atom Count: 11,356 
  • Modeled Residue Count: 1,390 
  • Deposited Residue Count: 1,704 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-beta
A, B
756Homo sapiensMutation(s): 0 
Gene Names: HSP90AB1, HSP90B, HSPC2, HSPCB
UniProt & NIH Common Fund Data Resources
Find proteins for P08238 (Homo sapiens)
Explore P08238 
Go to UniProtKB:  P08238
PHAROS:  P08238
GTEx:  ENSG00000096384 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08238
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
De-novo designed binder H4192synthetic constructMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-28
    Type: Initial release