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- PDB-4z1h: Crystal structure of human Trap1 with SMTIN-P01 -

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Basic information

Entry
Database: PDB / ID: 4z1h
TitleCrystal structure of human Trap1 with SMTIN-P01
ComponentsHeat shock protein 75 kDa, mitochondrial
KeywordsCHAPERONE / Mitochondrial Hsp90
Function / homology
Function and homology information


translational attenuation / negative regulation of cellular respiration / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of reactive oxygen species biosynthetic process / chaperone-mediated protein folding / cell periphery / ATP-dependent protein folding chaperone ...translational attenuation / negative regulation of cellular respiration / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of reactive oxygen species biosynthetic process / chaperone-mediated protein folding / 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-, 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-4KP / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsLee, C. / Park, H.K. / Ryu, J.H. / Kang, B.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Development of a Mitochondria-Targeted Hsp90 Inhibitor Based on the Crystal Structures of Human TRAP1
Authors: Lee, C. / Park, H.K. / Jeong, H. / Lim, J. / Lee, A.J. / Cheon, K.Y. / Kim, C.S. / Thomas, A.P. / Bae, B. / Kim, N.D. / Kim, S.H. / Suh, P.G. / Ryu, J.H. / Kang, B.H.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1822
Polymers57,4221
Non-polymers7601
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22330 Å2
Unit cell
Length a, b, c (Å)69.336, 69.336, 255.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 57422.090 Da / Num. of mol.: 1 / Fragment: UNP residues 60-561
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-4KP / 8-[(6-iodo-1,3-benzodioxol-5-yl)sulfanyl]-9-[6-(triphenyl-lambda~5~-phosphanyl)hexyl]-9H-purin-6-amine


Mass: 759.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H35IN5O2PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 8K, 100mM calcium acetate, 100mM sodium cacodylate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. obs: 14775 / % possible obs: 99.8 % / Redundancy: 4.1 % / Net I/σ(I): 23.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data processing
Cootmodel building
PHENIXphasing
RefinementResolution: 2.9→34.354 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 736 5 %
Rwork0.2355 --
obs0.2382 14710 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→34.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 46 21 3567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053607
X-RAY DIFFRACTIONf_angle_d0.9874863
X-RAY DIFFRACTIONf_dihedral_angle_d16.0141341
X-RAY DIFFRACTIONf_chiral_restr0.035530
X-RAY DIFFRACTIONf_plane_restr0.005614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8948-3.11810.3261420.27032703X-RAY DIFFRACTION100
3.1181-3.43170.32441440.25162735X-RAY DIFFRACTION100
3.4317-3.92760.30651450.22192755X-RAY DIFFRACTION100
3.9276-4.94610.26331480.21322808X-RAY DIFFRACTION100
4.9461-34.35630.26711570.24612973X-RAY DIFFRACTION100
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)
13.9050.31060.79113.99890.9013.6018-0.37860.58510.2418-0.43070.34670.83230.2250.1564-0.02730.8561-0.0969-0.36670.37350.06210.527916.4621.516322.5056
21.3785-0.193-0.36023.16940.69541.1679-0.04510.31130.0277-0.4680.2510.41230.1735-0.1646-0.04670.8672-0.1178-0.33130.33330.03890.490412.602411.378320.8564
32.0995-1.17110.69431.8179-1.26912.12990.0689-0.1936-0.21750.0820.31350.3770.3572-0.09830.25160.6952-0.0329-0.53470.40490.32460.6354-2.617937.649219.5391
42.71-1.16760.6063.4724-1.32282.92710.0965-0.35330.19450.37780.60050.7281-0.4224-1.0401-0.12130.53680.1413-0.27590.64470.5561.022-21.059858.297311.368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 297 )
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 434 )
4X-RAY DIFFRACTION4chain 'A' and (resid 435 through 552 )

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