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- PDB-3o2f: Structure of the N-domain of GRP94 bound to the HSP90 inhibitor PU-H54 -

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Basic information

Entry
Database: PDB / ID: 3o2f
TitleStructure of the N-domain of GRP94 bound to the HSP90 inhibitor PU-H54
ComponentsEndoplasmin
Keywordschaperone/inhibitor / Hsp90 Heat-shock Proteins / chaperone-inhibitor complex
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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-P54 / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeidler, P.M. / Gewirth, D.T.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Paralog-selective Hsp90 inhibitors define tumor-specific regulation of HER2.
Authors: Patel, P.D. / Yan, P. / Seidler, P.M. / Patel, H.J. / Sun, W. / Yang, C. / Que, N.S. / Taldone, T. / Finotti, P. / Stephani, R.A. / Gewirth, D.T. / Chiosis, G.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmin
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0359
Polymers53,0282
Non-polymers1,0077
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-6 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.960, 65.686, 85.453
Angle α, β, γ (deg.)90.00, 98.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26514.012 Da / Num. of mol.: 2 / Fragment: UNP Residues 69-286, 328-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: GRP94, HSP90B1, TRA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P41148
#2: Chemical ChemComp-P54 / 8-[(2,4-dimethylphenyl)sulfanyl]-3-pent-4-yn-1-yl-3H-purin-6-amine


Mass: 337.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19N5S
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2-fold molar excess PU-H54, 14-17% isopropanol, 300-375 mM MgCl2, 0.1-1% glycerol, 100 mM HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 45178 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 18.1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.84 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.287 / SU ML: 0.145 / SU R Cruickshank DPI: 0.1691 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflection
Rfree0.269 2251 5 %
Rwork0.234 --
obs0.236 45178 99.7 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 62.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.26 Å2
2---0.32 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 70 216 3703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223545
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9734797
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2785442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01325.548146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96315607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1681512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022581
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6051.52216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05423545
X-RAY DIFFRACTIONr_scbond_it2.00731329
X-RAY DIFFRACTIONr_scangle_it3.0134.51252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.382 166 -
Rwork0.303 3122 -
obs--99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.73256.2983-9.707614.444-9.282721.0616-0.2371-0.0847-0.4276-0.0454-0.1572-1.01450.3341.4250.39420.1446-0.0704-0.01910.67510.03660.52831.76623.5710.948
21.45750.25161.55993.8366-0.19323.2943-0.0711-0.0886-0.02710.10130.03140.3142-0.06810.00330.03980.0884-0.01660.12910.2882-0.00970.2223.22716.6846.149
319.5273-14.5129.251519.9617-0.26029.42440.64561.9620.5791-2.07140.1019-1.2535-0.78062.22-0.74750.3443-0.25480.19771.1089-0.19161.092525.3321.013-1.333
42.25890.66231.80254.34370.11192.8260.14170.023-0.1748-0.1878-0.01170.01070.24080.2945-0.12990.07490.01750.07550.2686-0.00450.18877.94810.1113.085
52.1568-0.0562.78247.48880.14735.00070.0202-0.9229-0.1151.1221-0.11970.90350.1281-0.90920.09950.2889-0.06380.31060.61980.04310.3921-3.52913.44719.663
61.4480.34690.90331.0401-0.07654.6174-0.11550.22480.11870.65840.0402-0.3921-0.3079-0.06520.07530.619-0.031-0.21990.0705-0.00010.298319.10827.66529.822
74.7564-0.21992.91267.36262.03543.6390.24961.0361-0.2186-0.05880.0122-1.3075-0.41980.702-0.26190.63150.0105-0.22780.3097-0.03990.33829.43131.05831.918
82.44850.18283.41045.170.13927.7541-0.15020.3962-0.07610.5740.1615-0.8504-0.37540.5435-0.01130.5614-0.0162-0.26380.106-0.02720.241425.86234.90533.698
95.83390.08832.603110.2836-1.16238.731-0.2251-0.478-0.16430.9176-0.1410.95320.2671-1.50110.3660.67230.10130.08260.4555-0.01840.35476.35431.18534.334
1019.64762.94170.39061.21011.99185.3553-0.3492-0.15532.0134-0.47710.17770.3711-0.8157-0.17370.17141.93520.16440.08481.22490.01741.16361.47735.09444.777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A76 - 90
2X-RAY DIFFRACTION2A91 - 168
3X-RAY DIFFRACTION3A169 - 187
4X-RAY DIFFRACTION4A188 - 252
5X-RAY DIFFRACTION5A253 - 337
6X-RAY DIFFRACTION6B76 - 143
7X-RAY DIFFRACTION7B144 - 182
8X-RAY DIFFRACTION8B183 - 252
9X-RAY DIFFRACTION9B253 - 285
10X-RAY DIFFRACTION10B286 - 337

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