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- PDB-4nh9: Correlation between chemotype-dependent binding conformations of ... -

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Basic information

Entry
Database: PDB / ID: 4nh9
TitleCorrelation between chemotype-dependent binding conformations of HSP90 alpha/beta and isoform selectivity
ComponentsEndoplasmin
KeywordsCHAPERONE / a/b structure / endoplasmic reticulum
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 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
Chem-2LC / Endoplasmin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.77 Å
AuthorsZuccola, H.J. / Ernst, J.T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Correlation between chemotype-dependent binding conformations of HSP90 alpha / beta and isoform selectivity-Implications for the structure-based design of HSP90 alpha / beta selective ...Title: Correlation between chemotype-dependent binding conformations of HSP90 alpha / beta and isoform selectivity-Implications for the structure-based design of HSP90 alpha / beta selective inhibitors for treating neurodegenerative diseases.
Authors: Ernst, J.T. / Liu, M. / Zuccola, H. / Neubert, T. / Beaumont, K. / Turnbull, A. / Kallel, A. / Vought, B. / Stamos, D.
History
DepositionNov 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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

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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)31,4852
Polymers31,0861
Non-polymers3991
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.102, 101.194, 63.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#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: 31085.818 Da / Num. of mol.: 1 / Fragment: UNP residues 69-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90B1, GRP94, TRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P14625
#2: Chemical ChemComp-2LC / 2-fluoro-6-[(3S)-tetrahydrofuran-3-ylamino]-4-(3,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indol-1-yl)benzamide


Mass: 399.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26FN3O3

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.6
Details: 25-30% PEG400, 50-200mM MgCl2, 100mM TRIS pH 7.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2010
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→63.5 Å / Num. obs: 7586 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 73.44 Å2
Reflection shellResolution: 2.77→2.799 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.2 / Num. unique all: 64 / % possible all: 100

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Processing

SoftwareName: BUSTER / Version: 2.11.5 / Classification: refinement
RefinementResolution: 2.77→50.6 Å / Cor.coef. Fo:Fc: 0.9004 / Cor.coef. Fo:Fc free: 0.8628 / SU R Cruickshank DPI: 0.915 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.909 / SU Rfree Blow DPI: 0.353 / SU Rfree Cruickshank DPI: 0.359
RfactorNum. reflection% reflectionSelection details
Rfree0.277 751 9.7 %RANDOM
Rwork0.2446 ---
obs0.2476 7739 99.69 %-
Displacement parametersBiso mean: 72.63 Å2
Baniso -1Baniso -2Baniso -3
1-10.8492 Å20 Å20 Å2
2--14.9347 Å20 Å2
3----25.7839 Å2
Refinement stepCycle: LAST / Resolution: 2.77→50.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 29 0 1704
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0131729HARMONIC1
X-RAY DIFFRACTIONt_angle_deg1.462344HARMONIC1
X-RAY DIFFRACTIONt_dihedral_angle_d602SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes242HARMONIC5
X-RAY DIFFRACTIONt_it1729HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.44
X-RAY DIFFRACTIONt_other_torsion19.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion235SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1808SEMIHARMONIC4
LS refinement shellResolution: 2.77→3.1 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2957 219 10.14 %
Rwork0.2634 1940 -
all0.2669 2159 -
obs--99.69 %
Refinement TLS params.Method: refined / Origin x: -13.548 Å / Origin y: -30.7901 Å / Origin z: -4.22 Å
111213212223313233
T-0.245 Å20.0223 Å20.0221 Å2--0.1971 Å20.0524 Å2--0.158 Å2
L1.5725 °2-0.8161 °2-0.1417 °2-3.2767 °2-0.5037 °2--2.3117 °2
S-0.1014 Å °0.0758 Å °-0.4497 Å °0.0563 Å °-0.0867 Å °-0.1931 Å °-0.1682 Å °0.1479 Å °0.1881 Å °

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