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- PDB-1yt2: Crystal Structure of the Unliganded Form of GRP94, the ER Hsp90: ... -

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Entry
Database: PDB / ID: 1yt2
TitleCrystal Structure of the Unliganded Form of GRP94, the ER Hsp90: Basis for Nucleotide-Induced Conformational Change, GRP94N APO CRYSTAL
ComponentsEndoplasmin
KeywordsCHAPERONE / GRP94 / gp96 / Hsp90 / Bergerat / Endoplasmic reticulum / HtpG
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 / 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 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
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsDollins, D.E. / Immormino, R.M. / Gewirth, D.T.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure of Unliganded GRP94, the Endoplasmic Reticulum Hsp90: BASIS FOR NUCLEOTIDE-INDUCED CONFORMATIONAL CHANGE
Authors: Dollins, D.E. / Immormino, R.M. / Gewirth, D.T.
History
DepositionFeb 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
Remark 600HETEROGEN ONLY FRAGMENTS OF PEG400 (PG4) WERE IDENTIFIED AND IN MANY CASES SEVERAL ATOMS WERE ...HETEROGEN ONLY FRAGMENTS OF PEG400 (PG4) WERE IDENTIFIED AND IN MANY CASES SEVERAL ATOMS WERE MISSING DUE TO LACK OF ELECTRON DENSITY.
Remark 42MolProbity Structure Validation PROGRAMS : MolProbity (KiNG, REDUCE, and PROBE) AUTHORS : I.W. ...MolProbity Structure Validation PROGRAMS : MolProbity (KiNG, REDUCE, and PROBE) AUTHORS : I.W.Davis,J.M.Word URL : http://kinemage.biochem.duke.edu/molprobity/ AUTHORS : J.S.Richardson,W.B.Arendall,D.C.Richardson REFERENCE : New tools and data for improving : structures, using all-atom contacts : Methods in Enzymology. 2003;374:385-412. MolProbity output scores: All-atom clashscore : 27.10 (11.71 B<40) Bad rotamers : 1.6% 3/187 (target 0-1%) Ramachandran outliers : 0.0% 0/221 (target 0.2%) Ramachandran favored : 93.2% 206/221 (target 98.0%)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8335
Polymers31,0561
Non-polymers7774
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.321, 100.257, 64.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-23-

PG4

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Components

#1: Protein Endoplasmin / 94 kDa glucose-regulated protein / GRP94


Mass: 31055.791 Da / Num. of mol.: 1 / Fragment: N-terminal Domain of GRP94 Residues (69-337)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: TRA1 / Plasmid: PGEX-NB-GRP94 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41148
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG400, MgCl, Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 12, 2004 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 4742 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.107 / Net I/σ(I): 13
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.46 / Num. unique all: 467 / Rsym value: 0.51 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→36.9 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 188481.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.293 439 9.8 %RANDOM
Rwork0.252 ---
obs0.252 4478 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 87.5631 Å2 / ksol: 0.381153 e/Å3
Displacement parametersBiso mean: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1--14.85 Å20 Å20 Å2
2---18.18 Å20 Å2
3---33.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.99 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 3.25→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 40 16 1788
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it1.482
X-RAY DIFFRACTIONc_scangle_it2.592.5
LS refinement shellResolution: 3.25→3.45 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 55 8.9 %
Rwork0.352 564 -
obs--79.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PEG400.PARAMPEG400.TOP

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