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- PDB-7u8v: hTRAP1 with inhibitors -

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Basic information

Entry
Database: PDB / ID: 7u8v
TitlehTRAP1 with inhibitors
ComponentsHeat shock protein 75 kDa, mitochondrial
KeywordsCHAPERONE / hTRAP1 / inhibitor
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 ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-UJS / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.448 Å
AuthorsDeng, J. / Matts, R. / Peng, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Elucidation of novel TRAP1-Selective inhibitors that regulate mitochondrial processes.
Authors: Merfeld, T. / Peng, S. / Keegan, B.M. / Crowley, V.M. / Brackett, C.M. / Gutierrez, A. / McCann, N.R. / Reynolds, T.S. / Rhodes, M.C. / Byrd, K.M. / Deng, J. / Matts, R.L. / Blagg, B.S.J.
History
DepositionMar 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9623
Polymers55,2011
Non-polymers7612
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.276, 68.744, 182.608
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 75 kDa, mitochondrial / HSP 75 / TNFR-associated protein 1 / Tumor necrosis factor type 1 receptor-associated protein / TRAP-1


Mass: 55200.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAP1, HSP75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12931
#2: Chemical ChemComp-UJS / (4-hydroxy-1,3-phenylene)bis[(2H-isoindol-2-yl)methanone]


Mass: 380.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium malonate PH6.0, 12%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.448→50 Å / Num. obs: 95177 / % possible obs: 99.4 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 31.84
Reflection shellResolution: 1.448→1.5 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.379 / Num. unique obs: 9055 / CC1/2: 0.835 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HPH

5hph


Resolution: 1.448→35.331 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 2000 2.1 %
Rwork0.1809 93078 -
obs0.1814 95078 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.59 Å2 / Biso mean: 31.365 Å2 / Biso min: 13.56 Å2
Refinement stepCycle: final / Resolution: 1.448→35.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3669 0 58 539 4266
Biso mean--24.46 40.85 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053814
X-RAY DIFFRACTIONf_angle_d0.8375143
X-RAY DIFFRACTIONf_chiral_restr0.076559
X-RAY DIFFRACTIONf_plane_restr0.005648
X-RAY DIFFRACTIONf_dihedral_angle_d18.6111417
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.448-1.48410.28741300.2686602891
1.4841-1.52430.251420.2256627100
1.5243-1.56910.19311420.20936583100
1.5691-1.61980.24961420.19956624100
1.6198-1.67770.22851420.19516640100
1.6777-1.74480.21671420.195656799
1.7448-1.82420.20021430.19326657100
1.8242-1.92040.17861430.19356703100
1.9204-2.04070.19691420.18276591100
2.0407-2.19830.21461440.18136700100
2.1983-2.41940.20621440.18346717100
2.4194-2.76940.2171460.18456747100
2.7694-3.48870.19331450.1766817100
3.4887-35.30.18861530.16497077100
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)
11.10850.0453-0.13943.1693-0.26362.1033-0.0762-0.07530.03240.21510.13320.18-0.1319-0.0889-0.0330.15950.03110.01070.1345-0.00450.13921.049332.4107-32.2914
20.80880.8624-0.93861.29-0.94381.56080.0486-0.00520.03880.0171-0.02710.0177-0.0983-0.0516-0.01410.0970.0283-0.01020.14560.00090.1327-16.4746-4.7102-18.5442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 71 through 277 )A71 - 277
2X-RAY DIFFRACTION2chain 'A' and (resid 278 through 552 )A278 - 552

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