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- PDB-5f3k: X-Ray Crystallographic Structure of hTrap1 N-terminal Domain-apo -

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Basic information

Entry
Database: PDB / ID: 5f3k
TitleX-Ray Crystallographic Structure of hTrap1 N-terminal Domain-apo
ComponentsHeat shock protein 75 kDa, mitochondrialHeat shock response
KeywordsCHAPERONE / Trap1 / Hsp90 / apo
Function / homology
Function and homology information


translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space ...translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane
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
Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsSung, N. / Lee, J. / Kim, J. / Chang, C. / Joachimiak, A. / Lee, S. / Tsai, F.T.F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111084 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104980 United States
Welch FoundationQ-1530 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mitochondrial Hsp90 is a ligand-activated molecular chaperone coupling ATP binding to dimer closure through a coiled-coil intermediate.
Authors: Sung, N. / Lee, J. / Kim, J.H. / Chang, C. / Joachimiak, A. / Lee, S. / Tsai, F.T.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Heat shock protein 75 kDa, mitochondrial
B: Heat shock protein 75 kDa, mitochondrial


Theoretical massNumber of molelcules
Total (without water)52,0922
Polymers52,0922
Non-polymers00
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-23 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.250, 65.250, 233.372
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Heat shock protein 75 kDa, mitochondrial / Heat shock response / HSP 75 / TNFR-associated protein 1 / Tumor necrosis factor type 1 receptor-associated protein / TRAP-1


Mass: 26046.145 Da / Num. of mol.: 2 / Fragment: UNP residues 60-294
Source method: isolated from a genetically manipulated source
Details: Mitochondrial localization signal (1-59) / Source: (gene. exp.) Homo sapiens (human) / Gene: TRAP1, HSP75 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): codon plus-RIL / References: UniProt: Q12931
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 micro liter hTRAP1N, 25 mg/ml, in 30 mM TrisHCl pH 8.5, 0.15 M NaCl, and 1 mM TCEP was mixed with an equal volume of reservoir solution consisting of 100 mM HEPES pH 7.5, 100 mM CaCl2 , 23 ...Details: 2 micro liter hTRAP1N, 25 mg/ml, in 30 mM TrisHCl pH 8.5, 0.15 M NaCl, and 1 mM TCEP was mixed with an equal volume of reservoir solution consisting of 100 mM HEPES pH 7.5, 100 mM CaCl2 , 23 percent PEG3350, 4 percent isopropanol, and 0.4 micro liter of 1 M LiCl2.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.82→77.79 Å / Num. obs: 52606 / % possible obs: 99.4 % / Redundancy: 6.7 % / Rsym value: 0.053 / Net I/σ(I): 14
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 7 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.75 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F5R

5f5r


Resolution: 1.82→77.79 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.782 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 2662 5.1 %RANDOM
Rwork0.18166 ---
obs0.18332 49944 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.583 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----1.13 Å2
Refinement stepCycle: 1 / Resolution: 1.82→77.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 0 408 3570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8351.9564314
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56924.069145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69115581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4681522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.022378
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4891.52009
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.85123217
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.14431199
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.6074.51097
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 192 -
Rwork0.244 3634 -
obs--99.66 %
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)
10.4896-0.1368-0.24890.07550.06950.1418-0.00730.0646-0.0632-0.017-0.0317-0.0087-0.0386-0.03480.0390.11320.0131-0.02110.0601-0.04880.077132.9282-24.345137.4608
20.3425-0.34410.19250.3584-0.19980.1119-0.0756-0.0956-0.0190.0460.09320.0158-0.0234-0.0499-0.01750.10120.0477-0.0290.0747-0.0250.05336.2409-14.188879.0201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A82 - 294
2X-RAY DIFFRACTION2B82 - 294

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