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- PDB-7ull: Human Grp94 N-terminal domain in complex with 42C -

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Basic information

Entry
Database: PDB / ID: 7ull
TitleHuman Grp94 N-terminal domain in complex with 42C
ComponentsEndoplasmin
KeywordsCHAPERONE / Hsp90 Isoform / Grp94 / Isoform-specific properties / Endoplasmin
Function / homology
Function and homology information


actin rod assembly / regulation of phosphoprotein phosphatase activity / ATF6 (ATF6-alpha) activates chaperone genes / endoplasmic reticulum chaperone complex / sequestering of calcium ion / sarcoplasmic reticulum lumen / protein folding in endoplasmic reticulum / Scavenging by Class A Receptors / Trafficking and processing of endosomal TLR / low-density lipoprotein particle receptor binding ...actin rod assembly / regulation of phosphoprotein phosphatase activity / ATF6 (ATF6-alpha) activates chaperone genes / endoplasmic reticulum chaperone complex / sequestering of calcium ion / sarcoplasmic reticulum lumen / protein folding in endoplasmic reticulum / Scavenging by Class A Receptors / Trafficking and processing of endosomal TLR / low-density lipoprotein particle receptor binding / retrograde protein transport, ER to cytosol / cellular response to ATP / sperm plasma membrane / smooth endoplasmic reticulum / cellular response to manganese ion / : / endocytic vesicle lumen / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / ATP-dependent protein folding chaperone / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / unfolded protein binding / protein transport / protein folding / midbody / collagen-containing extracellular matrix / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / response to hypoxia / endoplasmic reticulum lumen / focal adhesion / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / nucleus / 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 ATPases / Histidine kinase/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-, 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
Similarity search - Domain/homology
N,N-dimethyl-7H-purin-6-amine / Endoplasmin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsStachowski, T.R. / Nithianantham, S. / Vanarotti, M. / Fischer, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142772 United States
CitationJournal: Protein Sci. / Year: 2023
Title: Pan-HSP90 ligand binding reveals isoform-specific differences in plasticity and water networks.
Authors: Stachowski, T.R. / Nithianantham, S. / Vanarotti, M. / Lopez, K. / Fischer, M.
History
DepositionApr 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)62,6928
Polymers61,9092
Non-polymers7836
Water64936
1
A: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4825
Polymers30,9551
Non-polymers5284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2103
Polymers30,9551
Non-polymers2552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.921, 89.461, 98.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Endoplasmin / 94 kDa glucose-regulated protein / GRP-94 / Heat shock protein 90 kDa beta member 1 / Tumor ...94 kDa glucose-regulated protein / GRP-94 / Heat shock protein 90 kDa beta member 1 / Tumor rejection antigen 1 / gp96 homolog


Mass: 30954.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Disordered (residues 286-328) GSH (Tag) / Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90B1, GRP94, TRA1 / Plasmid: pET28a / Details (production host): Cleavable 6His-tag / Production host: Escherichia coli (E. coli) / References: UniProt: P14625

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Non-polymers , 5 types, 42 molecules

#2: Chemical ChemComp-42C / N,N-dimethyl-7H-purin-6-amine


Mass: 163.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 46.12 % / Description: Rectangular
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM MgCl2, 0.1 M Bis-Tris propane pH 6.5, and 22% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→44.731 Å / Num. obs: 25379 / % possible obs: 98.84 % / Redundancy: 6.5 % / Biso Wilson estimate: 59.71 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.053 / Rrim(I) all: 0.131 / Net I/σ(I): 8.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.31-2.396.31.30124190.5980.6131.58497.54
8.95-44.7314.90.054840.9960.0230.05594.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NH9

4nh9


Resolution: 2.31→44.731 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2964 1988 7.88 %
Rwork0.2583 23247 -
obs0.2614 25235 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.48 Å2 / Biso mean: 77.1 Å2 / Biso min: 24.89 Å2
Refinement stepCycle: final / Resolution: 2.31→44.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 53 36 3373
Biso mean--61.61 59.76 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023402
X-RAY DIFFRACTIONf_angle_d0.6384602
X-RAY DIFFRACTIONf_chiral_restr0.042546
X-RAY DIFFRACTIONf_plane_restr0.002578
X-RAY DIFFRACTIONf_dihedral_angle_d9.2432030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.31-2.36780.4061340.3948159197
2.3678-2.43180.40141400.3749163799
2.4318-2.50340.38491370.3657161298
2.5034-2.58410.37261370.3505157196
2.5841-2.67650.3511420.329168399
2.6765-2.78360.34361410.30661641100
2.7836-2.91030.33761420.30091660100
2.9103-3.06370.32471430.29291674100
3.0637-3.25560.32221420.27331655100
3.2556-3.50690.28791430.25261669100
3.5069-3.85960.27951450.24111695100
3.8596-4.41770.25421440.2171688100
4.4177-5.56420.30311460.215170298
5.5642-44.7310.26071520.2538176998

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