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- PDB-5tvu: Crystal structure of mitochondrial Hsp90 (TRAP1) with ATP in abse... -

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Basic information

Entry
Database: PDB / ID: 5tvu
TitleCrystal structure of mitochondrial Hsp90 (TRAP1) with ATP in absence of Mg
ComponentsTNF receptor-associated protein 1
KeywordsCHAPERONE / Hsp90 / ATP / TRAP1 / Structural Genomics / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


: / nucleic acid metabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / mitochondrial inner membrane / calcium ion binding / protein kinase binding / magnesium ion binding / ATP hydrolysis activity ...: / nucleic acid metabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / mitochondrial inner membrane / calcium ion binding / protein kinase binding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding
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
ADENOSINE-5'-TRIPHOSPHATE / Heat shock protein 75 kDa, mitochondrial / TNF receptor-associated protein 1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsElnatan, D. / Betegon, M. / Agard, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2017
Title: Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1.
Authors: Elnatan, D. / Betegon, M. / Liu, Y. / Ramelot, T. / Kennedy, M.A. / Agard, D.A.
History
DepositionNov 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

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Assembly

Deposited unit
A: TNF receptor-associated protein 1
B: TNF receptor-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2864
Polymers149,2712
Non-polymers1,0142
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-69 kcal/mol
Surface area53880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.881, 96.990, 124.961
Angle α, β, γ (deg.)90.00, 134.57, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein TNF receptor-associated protein 1 / Trap1 protein


Mass: 74635.625 Da / Num. of mol.: 2 / Fragment: UNP residues 73-719
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trap1 / Variant: delta1-72 / Plasmid: pET151DTOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A8WFV1, UniProt: F1Q9X9*PLUS
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NaK Tartrate, 20% (v/v) PEG3350, 36 mM hexamine cobalt, 5 mM ATP,5 mM EDTA

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Data collection

DiffractionMean temperature: 91.4 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.3→44.52 Å / Num. obs: 61835 / % possible obs: 93.4 % / Redundancy: 1.8 % / CC1/2: 0.734 / Net I/σ(I): 2.2
Reflection shellResolution: 2.3→2.39 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
iMOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IPE

4ipe


Resolution: 3.5→39.759 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 1012 5.38 %
Rwork0.2248 --
obs0.2272 18823 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→39.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9573 0 62 0 9635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0019834
X-RAY DIFFRACTIONf_angle_d0.44413267
X-RAY DIFFRACTIONf_dihedral_angle_d13.1526020
X-RAY DIFFRACTIONf_chiral_restr0.0371475
X-RAY DIFFRACTIONf_plane_restr0.0031695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.68460.30831480.28942502X-RAY DIFFRACTION98
3.6846-3.91520.33341430.26332517X-RAY DIFFRACTION99
3.9152-4.21720.29661680.24022513X-RAY DIFFRACTION99
4.2172-4.6410.27871470.21442537X-RAY DIFFRACTION99
4.641-5.31120.23931350.20832560X-RAY DIFFRACTION99
5.3112-6.68640.25521310.23342558X-RAY DIFFRACTION99
6.6864-39.76180.22251400.18292624X-RAY DIFFRACTION99
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)
11.2099-0.2912-0.3691.64830.12941.8861-0.02930.1098-0.03880.0291-0.05610.0375-0.04020.07330.09330.421-0.05080.01310.27820.0150.4281226.869422.5986-3.1466
22.82821.2385-0.63470.594-0.43130.52090.5995-0.75790.57540.5043-0.29630.4109-0.4983-0.1546-0.26830.8938-0.06370.28690.7664-0.09640.9287183.630532.032924.6735
31.314-0.1094-0.83841.92780.52834.36870.1306-0.2846-0.29080.2171-0.1327-0.50420.10380.9337-0.00860.5618-0.0647-0.0770.62970.15690.5685242.921119.405120.8149
43.66253.2458-0.34012.8927-0.19791.93650.12130.04780.39870.2938-0.26280.2404-0.12990.19410.14680.63170.0066-0.06930.35360.02930.4598219.506413.714229.5082
55.2714-1.28241.33380.7349-0.41031.5079-0.10960.1353-0.26850.12490.25490.3328-0.1343-0.3888-0.16310.48670.00490.110.40050.06720.595176.4452.87415.2009
61.36760.47981.96620.66891.34143.7573-0.23590.032-0.29220.09310.0878-0.07630.03150.25780.13460.6085-0.2920.05260.56720.05080.6944241.961516.136623.5943
71.7877-0.22380.97434.3183-5.48087.22440.1228-0.26690.43761.51640.22950.6364-0.9595-0.3737-0.37331.20260.09230.14450.35640.05880.3984235.496223.722-4.6101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 85:388 )A85 - 388
2X-RAY DIFFRACTION2( CHAIN A AND RESID 389:717 )A389 - 717
3X-RAY DIFFRACTION3( CHAIN B AND RESID 85:264 )B85 - 264
4X-RAY DIFFRACTION4( CHAIN B AND RESID 265:424 )B265 - 424
5X-RAY DIFFRACTION5( CHAIN B AND RESID 425:717 )B425 - 717
6X-RAY DIFFRACTION6( CHAIN B AND RESID 801:801 )B801
7X-RAY DIFFRACTION7( CHAIN A AND RESID 801:801 )A801

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