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- PDB-5wmt: Structure of GRP94 N-terminal Domain bound to resorcinylic inhibi... -

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Basic information

Entry
Database: PDB / ID: 5wmt
TitleStructure of GRP94 N-terminal Domain bound to resorcinylic inhibitor BnIm.
ComponentsEndoplasmin
KeywordsChaperone/Inhibitor / Chaperone / Inhibitor / Complex / 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. / Histidine kinase-like ATPase, C-terminal domain / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / 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. / Histidine kinase-like ATPase, C-terminal domain / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / 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 superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9QY / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.748 Å
AuthorsQue, N.S. / Gewirth, D.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01 CA095130 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA186866 United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structure Based Design of a Grp94-Selective Inhibitor: Exploiting a Key Residue in Grp94 To Optimize Paralog-Selective Binding.
Authors: Que, N.L.S. / Crowley, V.M. / Duerfeldt, A.S. / Zhao, J. / Kent, C.N. / Blagg, B.S.J. / Gewirth, D.T.
History
DepositionJul 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,58325
Polymers106,0564
Non-polymers2,52721
Water1,08160
1
A: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1496
Polymers26,5141
Non-polymers6355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1116
Polymers26,5141
Non-polymers5975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1737
Polymers26,5141
Non-polymers6596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1496
Polymers26,5141
Non-polymers6355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-22 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.412, 94.730, 179.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: residues 287-327 are replaced with GGGG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: HSP90B1, GRP94, TRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41148
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-9QY / methyl 2-[2-(1-benzyl-1H-imidazol-2-yl)ethyl]-3-chloro-4,6-dihydroxybenzoate / resorcinylic inhibitor BnIm


Mass: 386.829 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H19ClN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.78 Å3/Da / Density % sol: 67.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 2000, Lithium sulfate, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→34.544 Å / Num. obs: 49257 / % possible obs: 98.1 % / Redundancy: 4.8 % / Rsym value: 0.059 / Net I/σ(I): 34.8

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Processing

Software
NameVersionClassification
PHENIX(1.12rc0_2784: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u0z

1u0z


Resolution: 2.748→34.544 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 2118 5.05 %
Rwork0.2072 --
obs0.2088 41977 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.748→34.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6668 0 170 60 6898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026929
X-RAY DIFFRACTIONf_angle_d0.5149328
X-RAY DIFFRACTIONf_dihedral_angle_d4.4444144
X-RAY DIFFRACTIONf_chiral_restr0.0411076
X-RAY DIFFRACTIONf_plane_restr0.0021163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7481-2.8120.36081290.28092454X-RAY DIFFRACTION93
2.812-2.88230.32991510.27972550X-RAY DIFFRACTION97
2.8823-2.96010.36561280.26392604X-RAY DIFFRACTION97
2.9601-3.04720.37861200.27972624X-RAY DIFFRACTION98
3.0472-3.14550.32441460.26592595X-RAY DIFFRACTION98
3.1455-3.25780.30871520.25292655X-RAY DIFFRACTION99
3.2578-3.38820.26871400.23582649X-RAY DIFFRACTION100
3.3882-3.54220.26161370.22572659X-RAY DIFFRACTION100
3.5422-3.72880.21541340.21572688X-RAY DIFFRACTION100
3.7288-3.96210.22831420.19912704X-RAY DIFFRACTION100
3.9621-4.26750.24621410.18812691X-RAY DIFFRACTION100
4.2675-4.6960.20591340.15852719X-RAY DIFFRACTION100
4.696-5.37330.21361520.1742710X-RAY DIFFRACTION100
5.3733-6.76150.20931500.2242779X-RAY DIFFRACTION100
6.7615-34.54630.20151620.19782778X-RAY DIFFRACTION97

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