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

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Basic information

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


Citric acid cycle (TCA cycle) / 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'-DIPHOSPHATE / 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: 2.5 Å
AuthorsElnatan, D. / Betegon, M. / Agard, D.A. / Northeast Structural Genomics Consortium (NESG)
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 / Derived calculations
Category: pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)150,4418
Polymers149,2712
Non-polymers1,1706
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
ΔGint-94 kcal/mol
Surface area53360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.490, 97.181, 125.904
Angle α, β, γ (deg.)90.00, 134.64, 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
Components on special symmetry positions
IDModelComponents
11B-990-

HOH

21B-994-

HOH

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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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
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: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.14→42.67 Å / Num. obs: 98531 / % possible obs: 99.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 11
Reflection shellResolution: 2.14→2.22 Å / Num. unique obs: 8330 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
iMOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IPE

4ipe


Resolution: 2.5→39.894 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 2670 5.07 %
Rwork0.1897 --
obs0.1922 52681 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9548 0 62 183 9793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039853
X-RAY DIFFRACTIONf_angle_d0.59513285
X-RAY DIFFRACTIONf_dihedral_angle_d15.4146029
X-RAY DIFFRACTIONf_chiral_restr0.0411477
X-RAY DIFFRACTIONf_plane_restr0.0041700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54550.32411810.25262610X-RAY DIFFRACTION100
2.5455-2.59440.2765990.23682648X-RAY DIFFRACTION100
2.5944-2.64740.29141280.22942611X-RAY DIFFRACTION100
2.6474-2.70490.33751220.22522668X-RAY DIFFRACTION99
2.7049-2.76780.28441020.2272638X-RAY DIFFRACTION99
2.7678-2.8370.29661690.21892630X-RAY DIFFRACTION99
2.837-2.91370.26781130.22332663X-RAY DIFFRACTION100
2.9137-2.99940.28741260.22532641X-RAY DIFFRACTION99
2.9994-3.09620.28621450.22252616X-RAY DIFFRACTION99
3.0962-3.20680.2641440.21852616X-RAY DIFFRACTION99
3.2068-3.33520.27491460.22212609X-RAY DIFFRACTION99
3.3352-3.48690.28191720.21682630X-RAY DIFFRACTION99
3.4869-3.67060.24911350.19742603X-RAY DIFFRACTION99
3.6706-3.90040.21151400.18292675X-RAY DIFFRACTION99
3.9004-4.20120.20991520.16432616X-RAY DIFFRACTION99
4.2012-4.62350.20791700.15082611X-RAY DIFFRACTION99
4.6235-5.29120.17911570.1562608X-RAY DIFFRACTION99
5.2912-6.66130.26271160.18912668X-RAY DIFFRACTION99
6.6613-39.89890.19921530.15982650X-RAY DIFFRACTION97
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)
12.09090.07560.03153.31680.54861.90750.0557-0.3028-0.07870.08560.012-0.31250.0510.1095-0.05340.2574-0.0336-0.01480.31320.00010.310410.25815.6672236.7142
21.8446-0.59261.43021.4385-0.32184.93260.01130.2068-0.0436-0.3658-0.07580.29250.0809-0.08260.1310.4066-0.0401-0.04150.3307-0.05890.3994-5.885429.6187210.6584
30.6388-0.0398-0.09430.0706-0.34241.8103-0.3267-0.1251.0192-0.55760.00690.7005-0.5759-1.10570.11520.9650.1282-0.52240.8357-0.02431.1108-26.828439.0579190.523
41.6255-2.0042-0.81892.69860.31392.8059-0.19980.3117-0.01080.0204-0.24490.749-0.0275-1.0623-0.15510.7828-0.1483-0.38930.92140.13990.7681-31.074718.7166167.6565
53.85930.4452-0.18281.1346-0.071.99950.1283-0.73970.21870.352-0.25210.3835-0.07180.00940.01290.3779-0.13250.18230.5868-0.13530.6689-26.047918.3131245.0119
60.9294-0.1644-0.31831.70080.54033.15650.10470.07310.2941-0.0697-0.08630.0871-0.12360.0077-0.02340.30050.01830.05350.36190.09480.5257-23.21753.0115213.3898
72.4404-0.0325-0.8831.7556-0.56295.3659-0.38030.1527-0.2542-0.50750.41650.39450.52590.0686-0.01390.4644-0.1261-0.03980.3260.09130.2353-13.7991-6.6958184.7891
80.6749-0.07920.22960.683-0.18812.8114-0.18370.40030.1755-0.39230.1270.2522-0.0344-0.0919-0.08240.7994-0.2945-0.23720.58090.21780.1487-9.71817.2977164.5933
94.67131.82641.334.89585.6697.6824-0.12610.08810.5706-0.1294-0.8723-0.691-0.0270.4050.11460.2424-0.0068-0.04380.4220.19550.3827.437220.4981240.2012
106.8276-2.9769-1.85791.554-0.5688.17310.3080.4585-0.02640.0652-0.0171-0.4642-0.2755-0.1743-0.10540.3738-0.130.18950.5878-0.09070.6223-21.406612.6574246.1074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 109:302 )A109 - 302
2X-RAY DIFFRACTION2( CHAIN A AND RESID 323:482 )A323 - 482
3X-RAY DIFFRACTION3( CHAIN A AND RESID 497:564 )A497 - 564
4X-RAY DIFFRACTION4( CHAIN A AND RESID 593:717 )A593 - 717
5X-RAY DIFFRACTION5( CHAIN B AND RESID 109:301 )B109 - 301
6X-RAY DIFFRACTION6( CHAIN B AND RESID 318:482 )B318 - 482
7X-RAY DIFFRACTION7( CHAIN B AND RESID 498:573 )B498 - 573
8X-RAY DIFFRACTION8( CHAIN B AND RESID 585:717 )B585 - 717
9X-RAY DIFFRACTION9( CHAIN A AND RESID 801:801 )A801
10X-RAY DIFFRACTION10( CHAIN B AND RESID 803:803 )B803

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