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- PDB-6cyi: Grp94 N-domain bound to NEOCA -

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Basic information

Entry
Database: PDB / ID: 6cyi
TitleGrp94 N-domain bound to NEOCA
ComponentsEndoplasmin
KeywordsChaperone/Inhibitor / HSP90 / GRP94 / Endoplasmic Reticulum / Chaperone / Inhibitor / 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 / unfolded protein binding / melanosome ...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 / unfolded protein binding / melanosome / protein folding / response to heat / DNA damage response / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / cytosol
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 ATPase, C-terminal domain / Heat Shock Protein 90 ...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 ATPase, C-terminal domain / Heat Shock Protein 90 / 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
5'-N-(2-HYDROXYL)ETHYL CARBOXYAMIDO ADENOSINE / TRIETHYLENE GLYCOL / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75658250614 Å
AuthorsHuck, J.D. / Aw, W.J. / Gewirth, D.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA186866 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA095130 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: NECA derivatives exploit the paralog-specific properties of the site 3 side pocket of Grp94, the endoplasmic reticulum Hsp90.
Authors: Huck, J.D. / Que, N.L.S. / Immormino, R.M. / Shrestha, L. / Taldone, T. / Chiosis, G. / Gewirth, D.T.
History
DepositionApr 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8755
Polymers31,0561
Non-polymers8194
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint15 kcal/mol
Surface area11290 Å2
Unit cell
Length a, b, c (Å)89.055, 100.209, 63.433
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

21A-589-

HOH

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Components

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


Mass: 31055.791 Da / Num. of mol.: 1
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) / Strain (production host): BL21 Star (DE3) / References: UniProt: P41148
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-N5O / 5'-N-(2-HYDROXYL)ETHYL CARBOXYAMIDO ADENOSINE / (2S,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-N-(2-HYDROXYETHYL)TETRAHYDROFURAN-2-CARBOXAMIDE


Mass: 324.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl pH 8.5, PEG 400, MgCl2. Incubate with NEOCA prior to setup

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 24581 / % possible obs: 85.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 33.5837530063 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.054 / Rrim(I) all: 0.124 / Net I/σ(I): 22
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 0.984 / Num. unique obs: 563 / CC1/2: 0.838 / Rpim(I) all: 0.279 / Rrim(I) all: 0.634 / % possible all: 39.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U0Y

1u0y
PDB Unreleased entry


Resolution: 1.75658250614→45.9218937823 Å / SU ML: 0.215857151433 / Cross valid method: FREE R-VALUE / σ(F): 1.38528994748 / Phase error: 35.7200972327
RfactorNum. reflection% reflection
Rfree0.24575538073 1981 8.11918521251 %
Rwork0.203848868938 --
obs0.207210830111 24399 85.0583928883 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.3557141588 Å2
Refinement stepCycle: LAST / Resolution: 1.75658250614→45.9218937823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 53 92 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006294167035911830
X-RAY DIFFRACTIONf_angle_d0.931653352782475
X-RAY DIFFRACTIONf_chiral_restr0.03982892944296
X-RAY DIFFRACTIONf_plane_restr0.00362894746008307
X-RAY DIFFRACTIONf_dihedral_angle_d13.0874269485642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7566-1.80050.357464795727660.375891201508745X-RAY DIFFRACTION39.9704287827
1.8005-1.84920.406517969623880.3243495349671011X-RAY DIFFRACTION54.4868616758
1.8492-1.90360.35054249881110.3336536576541271X-RAY DIFFRACTION68.5856079404
1.9036-1.96510.3324238324761380.3147514734951547X-RAY DIFFRACTION82.9232283465
1.9651-2.03530.3022212552381470.2837444663171671X-RAY DIFFRACTION89.6007885658
2.0353-2.11680.3052958652961500.2574952620441739X-RAY DIFFRACTION93.5611688955
2.1168-2.21310.288054972341550.2548871215071740X-RAY DIFFRACTION94.0446650124
2.2131-2.32980.302994249391540.2361902550581765X-RAY DIFFRACTION93.7927663734
2.3298-2.47570.2665638822521610.2270005064811808X-RAY DIFFRACTION95.8617332035
2.4757-2.66690.2966002350381600.2208801081871796X-RAY DIFFRACTION96.449704142
2.6669-2.93520.2815927296391600.2314484426311792X-RAY DIFFRACTION94.8493683188
2.9352-3.35980.2798997417891640.213245573941842X-RAY DIFFRACTION96.8146718147
3.3598-4.23260.2100265726581610.1801781344381824X-RAY DIFFRACTION94.6590367191
4.2326-45.93760.1932608938431660.1628205208321867X-RAY DIFFRACTION93.6434822662

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