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- PDB-21fe: Neutron crystal structure of the ADP bound form of the human Hsp9... -

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Basic information

Entry
Database: PDB / ID: 21fe
TitleNeutron crystal structure of the ADP bound form of the human Hsp90 N-terminal domain
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / ATP hydrolysis / Protein folding
Function / homology
Function and homology information


sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / dATP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / dATP binding / sperm plasma membrane / chaperone-mediated autophagy / mitochondrial transport / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / Uptake and function of diphtheria toxin / protein import into mitochondrial matrix / dendritic growth cone / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / protein folding chaperone complex / response to unfolded protein / regulation of protein-containing complex assembly / Attenuation phase / enzyme-substrate adaptor activity / HSF1 activation / neurofibrillary tangle assembly / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / axonal growth cone / telomere maintenance via telomerase / regulation of postsynaptic membrane neurotransmitter receptor levels / nitric oxide metabolic process / positive regulation of lamellipodium assembly / skeletal muscle contraction / positive regulation of defense response to virus by host / Signaling by ERBB2 / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of telomere maintenance via telomerase / cardiac muscle cell apoptotic process / response to salt stress / endocytic vesicle lumen / DNA polymerase binding / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / lysosomal lumen / activation of innate immune response / Anchoring of the basal body to the plasma membrane / ESR-mediated signaling / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / response to cold / protein tyrosine kinase binding / Constitutive Signaling by Overexpressed ERBB2 / nitric-oxide synthase regulator activity / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / cellular response to virus / Signaling by ERBB2 KD Mutants / positive regulation of protein import into nucleus / Regulation of actin dynamics for phagocytic cup formation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to estrogen / VEGFA-VEGFR2 Pathway / Regulation of necroptotic cell death / tau protein binding / neuron migration / histone deacetylase binding / Downregulation of ERBB2 signaling / Chaperone Mediated Autophagy / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / Aggrephagy / positive regulation of protein catabolic process
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHirano, Y. / Kusaka, K. / Ose, T. / Kurihara, K. / Aburai, K. / Saito, J. / Tamada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Protein Sci. / Year: 2026
Title: Unperturbed hydration structure involves ADP recognition in the N-terminal domain of human heat shock protein 90 alpha.
Authors: Hirano, Y. / Kusaka, K. / Ose, T. / Kurihara, K. / Aburai, K. / Saito, J.I. / Tamada, T.
History
DepositionDec 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1083
Polymers25,6571
Non-polymers4522
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-13 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.120, 42.450, 54.910
Angle α, β, γ (deg.)90.000, 116.600, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / ...Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 25656.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: P07900
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% (w/v) PEG 4000, 0.1M HEPES-NaOH pH 7.5, 0.2M MgCl2, 20mM EDTA-Na

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: JPARC MLF / Beamline: BL-03 / Type: J-PARC MLF BEAMLINE BL-03 / Wavelength: 2.28-6.19
DetectorType: iBIX / Detector: DIFFRACTOMETER / Date: May 14, 2024
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.281
26.191
ReflectionResolution: 2.1→21.23 Å / Num. obs: 12610 / % possible obs: 95.9 % / Redundancy: 4 % / Biso Wilson estimate: 17.56 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.078 / Net I/σ(I): 7.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1684 / CC1/2: 0.627 / Rpim(I) all: 0.392 / % possible all: 89.4

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→21.23 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2261 629 4.99 %
Rwork0.1853 11971 -
obs0.1873 12600 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.08 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.01191814
NEUTRON DIFFRACTIONf_angle_d1.1852471
NEUTRON DIFFRACTIONf_chiral_restr0.0601282
NEUTRON DIFFRACTIONf_plane_restr0.0064316
NEUTRON DIFFRACTIONf_dihedral_angle_d16.4979702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.310.30641430.24782830NEUTRON DIFFRACTION91.17
2.31-2.640.24221690.21152965NEUTRON DIFFRACTION95.46
2.65-3.330.26381570.18173041NEUTRON DIFFRACTION97.56
3.33-21.230.17161600.15413135NEUTRON DIFFRACTION97.6

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