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- PDB-4gqt: N-terminal domain of C. elegans Hsp90 -

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Basic information

Entry
Database: PDB / ID: 4gqt
TitleN-terminal domain of C. elegans Hsp90
ComponentsHeat shock protein 90
KeywordsCHAPERONE / structural genomics / APC102132 / Hsp90 / ADP / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein phosphatase 5 binding / eNOS activation / HSF1 activation / : / Drug-mediated inhibition of ERBB2 signaling / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Attenuation phase / Downregulation of ERBB2 signaling / Aryl hydrocarbon receptor signalling ...protein phosphatase 5 binding / eNOS activation / HSF1 activation / : / Drug-mediated inhibition of ERBB2 signaling / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Attenuation phase / Downregulation of ERBB2 signaling / Aryl hydrocarbon receptor signalling / ESR-mediated signaling / Extra-nuclear estrogen signaling / dauer larval development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / Neutrophil degranulation / nematode larval development / protein serine/threonine phosphatase complex / HSP90-CDC37 chaperone complex / regulation of chemotaxis / nuclear glucocorticoid receptor binding / protein folding chaperone complex / protein maturation by protein folding / positive regulation of phosphoprotein phosphatase activity / chaperone-mediated protein folding / protein export from nucleus / protein dephosphorylation / determination of adult lifespan / ATP-dependent protein folding chaperone / chemotaxis / disordered domain specific binding / unfolded protein binding / protein folding / cellular response to heat / response to heat / defense response to Gram-negative bacterium / protein stabilization / membrane raft / cell cycle / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 ...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
ADENOSINE-5'-DIPHOSPHATE / Heat shock protein 90
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOsipiuk, J. / Chhor, G. / Gu, M. / Van Oosten-Hawle, P. / Morimoto, R.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: N-terminal domain of C. elegans Hsp90
Authors: Osipiuk, J. / Chhor, G. / Gu, M. / Van Oosten-Hawle, P. / Morimoto, R.I. / Joachimiak, A.
History
DepositionAug 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 90
B: Heat shock protein 90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,35614
Polymers50,8482
Non-polymers1,50812
Water3,153175
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-296 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.652, 86.658, 128.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heat shock protein 90 / Abnormal dauer formation protein 21


Mass: 25423.760 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C47E8.5, daf-21 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q18688
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.08 M zinc acetate, 19% PEG-3350, 0.01 M ADP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 5, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→43.3 Å / Num. all: 24707 / Num. obs: 24707 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.104 / Χ2: 1.222 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.15-2.196.90.8352.1812061.06597.1
2.19-2.2370.72212041.10296.1
2.23-2.277.10.61411831.06697.6
2.27-2.326.90.56711911.10297.9
2.32-2.3770.50512021.02397
2.37-2.4270.44412011.05198.2
2.42-2.486.90.36412281.02797.5
2.48-2.557.10.32212151.04799.2
2.55-2.6270.28712221.00498.9
2.62-2.7170.22512151.03398.7
2.71-2.817.10.20412501.05599
2.81-2.927.10.16112181.07199.3
2.92-3.057.20.12912421.10999.2
3.05-3.217.10.112361.16399.4
3.21-3.417.20.07912491.24899.3
3.41-3.687.10.06612591.39599.5
3.68-4.0570.05812571.53499.3
4.05-4.6370.04712691.53499.3
4.63-5.836.70.04612991.38999.1
5.83-506.40.05813612.38597

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JJC

2jjc


Resolution: 2.15→43.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.23 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.267 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1251 5.1 %RANDOM
Rwork0.1944 ---
all0.1973 24670 --
obs0.1973 24670 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.91 Å2 / Biso mean: 35.2362 Å2 / Biso min: 18.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.75 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 64 175 3521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023453
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.9844676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65825.669157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16715644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2761513
X-RAY DIFFRACTIONr_chiral_restr0.1140.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022539
LS refinement shellResolution: 2.146→2.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 90 -
Rwork0.241 1496 -
all-1586 -
obs-1586 93.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.38160.74320.15420.6105-0.24621.4840.0306-0.0024-0.0518-0.03340.0693-0.02050.0213-0.0795-0.09990.06080.02420.02040.05830.01630.028919.440715.893414.8505
20.4736-0.20950.17251.0843-0.1840.59620.018-0.0145-0.0697-0.00660.0288-0.027-0.06030.034-0.04680.0475-0.02750.0330.0355-0.01170.045214.515316.186649.2512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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