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- PDB-8tf0: Crystal structure of Grp94 N-terminal domain bound to the purine ... -

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Basic information

Entry
Database: PDB / ID: 8tf0
TitleCrystal structure of Grp94 N-terminal domain bound to the purine inhibitor PU-H36
ComponentsEndoplasmin
KeywordsCHAPERONE / Inhibitor / GRP94
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding ...Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding / melanosome / protein folding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding
Similarity search - Function
Endoplasmic reticulum targeting sequence. / 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 ...Endoplasmic reticulum targeting sequence. / 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
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsQue, N.L.S. / Gewirth, D.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA186866 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA095130 United States
CitationJournal: Proteins / Year: 2025
Title: Selective Inhibition of hsp90 Paralogs: Uncovering the Role of Helix 1 in Grp94-Selective Ligand Binding.
Authors: Que, N.L.S. / Seidler, P.M. / Aw, W.J. / Chiosis, G. / Gewirth, D.T.
History
DepositionJul 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Endoplasmin
A: Endoplasmin
C: Endoplasmin
D: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,40137
Polymers106,0564
Non-polymers3,34533
Water1,09961
1
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,51111
Polymers26,5141
Non-polymers99710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,43511
Polymers26,5141
Non-polymers92110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0584
Polymers26,5141
Non-polymers5443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,39811
Polymers26,5141
Non-polymers88410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.282, 104.392, 172.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules BACD

#1: Protein
Endoplasmin / 94 kDa glucose-regulated protein / GRP-94 / Heat shock protein 90 kDa beta member 1


Mass: 26514.012 Da / Num. of mol.: 4 / Mutation: Mutated residues 287-327 into GGGG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: HSP90B1, GRP94, TRA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 STAR (DE3) / References: UniProt: P41148

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Non-polymers , 6 types, 94 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ZUY / 9-(pent-4-yn-1-yl)-8-[(2,4,6-trimethylphenyl)sulfanyl]-9H-purin-6-amine


Mass: 351.469 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H21N5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.87 %
Description: Crystals were dehydrated to improve diffraction.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Lithium sulfate, Magnesium sulfate, Manganese sulfate, Tris.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 43634 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 78.71 Å2 / Rsym value: 0.107 / Net I/σ(I): 22.77
Reflection shellResolution: 2.79→2.89 Å / Num. unique obs: 4164 / Rsym value: 0.841 / % possible all: 96.61

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→36.89 Å / SU ML: 0.4681 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1583
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2603 2192 5.04 %
Rwork0.2278 41301 -
obs0.2294 43493 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.2 Å2
Refinement stepCycle: LAST / Resolution: 2.79→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 201 61 6854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00176883
X-RAY DIFFRACTIONf_angle_d0.48219349
X-RAY DIFFRACTIONf_chiral_restr0.03821092
X-RAY DIFFRACTIONf_plane_restr0.00211159
X-RAY DIFFRACTIONf_dihedral_angle_d10.1925939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.860.4571220.4032402X-RAY DIFFRACTION94.53
2.86-2.920.51551290.38612583X-RAY DIFFRACTION99.78
2.92-2.990.37491420.3352538X-RAY DIFFRACTION99.7
2.99-3.080.36661360.32262540X-RAY DIFFRACTION99.07
3.08-3.170.341370.29332562X-RAY DIFFRACTION99.96
3.17-3.270.34681320.30392557X-RAY DIFFRACTION100
3.27-3.390.30071170.25232601X-RAY DIFFRACTION99.96
3.39-3.520.31761410.2342530X-RAY DIFFRACTION99.7
3.52-3.680.28021450.22882554X-RAY DIFFRACTION99.41
3.68-3.870.25871490.22142600X-RAY DIFFRACTION99.85
3.87-4.120.24491160.20832581X-RAY DIFFRACTION99.81
4.12-4.430.2291380.18752608X-RAY DIFFRACTION99.85
4.43-4.880.22761380.18382614X-RAY DIFFRACTION100
4.88-5.580.23981400.2132617X-RAY DIFFRACTION99.93
5.58-7.030.25951600.252638X-RAY DIFFRACTION100
7.03-36.890.20261500.19842776X-RAY DIFFRACTION99.86

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