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- PDB-5hph: Structure of TRAP1 fragment -

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Basic information

Entry
Database: PDB / ID: 5hph
TitleStructure of TRAP1 fragment
ComponentsHeat shock protein 75 kDa, mitochondrialHeat shock response
KeywordsCHAPERONE / Trap1 / Hsp90
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-, 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.429 Å
AuthorsSung, N. / Chang, C. / 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: Acta Crystallogr D Struct Biol / Year: 2016
Title: 2.4 angstrom resolution crystal structure of human TRAP1NM, the Hsp90 paralog in the mitochondrial matrix.
Authors: Sung, N. / Lee, J. / Kim, J.H. / Chang, C. / Tsai, F.T. / Lee, S.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,81215
Polymers113,9052
Non-polymers1,90613
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-101 kcal/mol
Surface area41210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.437, 104.946, 156.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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: 56952.570 Da / Num. of mol.: 2 / Fragment: UNP residues 60-554
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

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Non-polymers , 6 types, 148 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.48 Å3/Da / Density % sol: 64.69 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.25 / Details: 1.8M Ammonium Sulfate, 0.1M MES, 1% dioxane

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.429→49.764 Å / Num. obs: 58241 / % possible obs: 99 % / Redundancy: 6.8 % / Net I/σ(I): 10.6
Reflection shellResolution: 2.43→2.47 Å / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.429→49.764 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.86
RfactorNum. reflection% reflection
Rfree0.2379 1998 3.44 %
Rwork0.1951 --
obs0.1966 58112 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 250.07 Å2 / Biso mean: 80.6986 Å2 / Biso min: 40.19 Å2
Refinement stepCycle: final / Resolution: 2.429→49.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7646 0 108 135 7889
Biso mean--73.67 72.45 -
Num. residues----965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077899
X-RAY DIFFRACTIONf_angle_d1.03510673
X-RAY DIFFRACTIONf_chiral_restr0.0561189
X-RAY DIFFRACTIONf_plane_restr0.0081349
X-RAY DIFFRACTIONf_dihedral_angle_d16.1474786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4286-2.48940.38711260.33393510363687
2.4894-2.55670.37981390.28813931407098
2.5567-2.63190.35081420.26733978412099
2.6319-2.71680.3471420.25973980412299
2.7168-2.81390.2811430.24714029417299
2.8139-2.92660.31061420.233340294171100
2.9266-3.05980.27011420.227239964138100
3.0598-3.22110.30061430.21240254168100
3.2211-3.42280.23921440.211740304174100
3.4228-3.6870.23721440.196940604204100
3.687-4.05790.22211460.172840834229100
4.0579-4.64470.19381450.154340754220100
4.6447-5.85040.18851490.182541664315100
5.8504-49.77450.23441510.18474222437398
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)
11.1175-0.40070.39720.56790.49183.1787-0.1513-0.0676-0.21490.0141-0.0345-0.02320.41930.1374-0.03150.51830.05390.14230.47430.04350.5936-6.42811.8907-3.016
20.36750.7722-0.09962.7338-1.46631.09180.0038-0.0888-0.16880.0248-0.21370.0372-0.10730.04160.00010.49180.01310.0710.63370.02130.51471.473529.5102-2.6903
30.00910.5547-0.62551.8545-2.01991.58070.2322-0.01280.08050.4497-0.0724-0.2047-1.0814-0.14020.02410.95730.07840.07280.6060.06880.59714.756856.8663-14.7258
40.69470.22310.59080.56140.71233.1014-0.05580.0489-0.0191-0.0399-0.26860.2553-0.0334-0.2828-0.01430.47690.04390.04840.505-0.12950.62-18.04246.5667-28.5567
52.13920.90580.41330.55640.07560.2168-0.22640.11990.0845-0.19590.03370.1665-0.1781-0.0274-0.00010.6969-0.01360.03070.5029-0.08310.54623.157821.892-36.3532
62.96380.61491.04930.6380.87731.554-0.08940.0813-0.2812-0.11130.0513-0.29310.14460.487900.52650.1120.03470.60440.08330.562331.180330.276-30.3736
71.99992.00012.00011.99951.99991.99980.34820.98980.98141.7156-0.11840.4083-0.3292-0.2549-0.24781.72540.66990.38830.59380.71930.432343.486736.8649-17.9815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 287 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 288 through 432 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 433 through 551 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 70 through 277 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 278 through 407 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 408 through 551 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 552 through 552 )B0

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