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- PDB-6d28: Crystal Structure of the N-domain of the ER Hsp90 chaperone GRP94... -

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Basic information

Entry
Database: PDB / ID: 6d28
TitleCrystal Structure of the N-domain of the ER Hsp90 chaperone GRP94 in complex with the specific ligand NECA
ComponentsEndoplasmin
KeywordsCHAPERONE / Hsp90 / Grp94 / NECA / inhibitor
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
1-METHOXY-2-(2-METHOXYETHOXY)ETHANE / N-ETHYL-5'-CARBOXAMIDO ADENOSINE / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSoldano, K.L. / Jivan, A. / Nicchitta, C.V. / Gewirth, D.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA095130 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA186866 United States
CitationJournal: J. Biol. Chem. / Year: 2003
Title: Structure of the N-terminal domain of GRP94. Basis for ligand specificity and regulation.
Authors: Soldano, K.L. / Jivan, A. / Nicchitta, C.V. / Gewirth, D.T.
History
DepositionApr 13, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMay 16, 2018ID: 1QY5
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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)31,4983
Polymers31,0561
Non-polymers4422
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint3 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.200, 99.180, 63.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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

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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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41148
#2: Chemical ChemComp-NEC / N-ETHYL-5'-CARBOXAMIDO ADENOSINE


Mass: 308.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-M2M / 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 400, Magnesium chloride, Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
Details: The data was collected using the APS-1 CCD area detector at APS beamline 19-BM
Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2001 / Details: SAGITALLY FOCUSED Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 28627 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 27.25 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 20
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4.45 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→49.59 Å / SU ML: 0.1839 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 19.7617
RfactorNum. reflection% reflection
Rfree0.2134 2000 7.23 %
Rwork0.1821 --
obs0.1843 27658 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 31 221 1974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01231779
X-RAY DIFFRACTIONf_angle_d1.15232411
X-RAY DIFFRACTIONf_chiral_restr0.0802288
X-RAY DIFFRACTIONf_plane_restr0.0063302
X-RAY DIFFRACTIONf_dihedral_angle_d4.5951048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.23981270.21361634X-RAY DIFFRACTION86.62
1.79-1.840.23781350.20011725X-RAY DIFFRACTION91.54
1.84-1.890.27691330.18581707X-RAY DIFFRACTION91.72
1.89-1.960.19761390.17851788X-RAY DIFFRACTION94.55
1.96-2.030.24111410.17821810X-RAY DIFFRACTION95.73
2.03-2.110.20981410.16781817X-RAY DIFFRACTION97.66
2.11-2.20.1991460.16861852X-RAY DIFFRACTION98.76
2.2-2.320.20531440.16821862X-RAY DIFFRACTION98.87
2.32-2.460.19151460.16381863X-RAY DIFFRACTION97.86
2.46-2.650.19861440.17581854X-RAY DIFFRACTION98.38
2.65-2.920.20911470.18761892X-RAY DIFFRACTION98.98
2.92-3.340.23751500.18561912X-RAY DIFFRACTION99.47
3.34-4.210.19121500.17391926X-RAY DIFFRACTION99.14
4.21-49.610.22351570.19612016X-RAY DIFFRACTION99.95
Refinement TLS params.Method: refined / Origin x: 13.8010401811 Å / Origin y: -19.3419045879 Å / Origin z: 58.7826464602 Å
111213212223313233
T0.179362559256 Å20.0139243266511 Å2-0.00239935034871 Å2-0.162538002731 Å2-0.00720153531683 Å2--0.157277249605 Å2
L1.25537941016 °2-0.213921785474 °2-0.313004600718 °2-1.49029477186 °20.454370952706 °2--1.58309619413 °2
S-0.10736580595 Å °0.0611870741827 Å °0.0752788668714 Å °0.00130399650258 Å °0.00829080315344 Å °0.138104848051 Å °0.253083111855 Å °-0.0139258525688 Å °-0.00414328941408 Å °
Refinement TLS groupSelection details: all

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