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- PDB-3fp2: Crystal structure of Tom71 complexed with Hsp82 C-terminal fragment -

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Basic information

Entry
Database: PDB / ID: 3fp2
TitleCrystal structure of Tom71 complexed with Hsp82 C-terminal fragment
Components
  • ATP-dependent molecular chaperone HSP82
  • TPR repeat-containing protein YHR117W
KeywordsTRANSPORT PROTEIN / Tom71 / mitochondria translocation / chaperone / allosteric regulation / Phosphoprotein / TPR repeat / ATP-binding / Nucleotide-binding / Stress response
Function / homology
Function and homology information


mitochondrion targeting sequence binding / The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein insertion into mitochondrial inner membrane ...mitochondrion targeting sequence binding / The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein insertion into mitochondrial inner membrane / protein import into mitochondrial matrix / HSF1 activation / response to oxygen levels / : / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / protein transmembrane transporter activity / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / mitochondrial outer membrane / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein ...Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSP82 / Protein TOM71
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLi, J. / Qian, X. / Hu, J. / Sha, B.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Molecular chaperone Hsp70/Hsp90 prepares the mitochondrial outer membrane translocon receptor Tom71 for preprotein loading.
Authors: Li, J. / Qian, X. / Hu, J. / Sha, B.
History
DepositionJan 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TPR repeat-containing protein YHR117W
Q: ATP-dependent molecular chaperone HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9944
Polymers61,9352
Non-polymers602
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-4 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.863, 116.288, 150.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TPR repeat-containing protein YHR117W


Mass: 60571.273 Da / Num. of mol.: 1 / Fragment: UNP residues 107-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YHR117W / Production host: Escherichia coli (E. coli) / References: UniProt: P38825
#2: Protein/peptide ATP-dependent molecular chaperone HSP82 / Heat shock protein Hsp90 heat-inducible isoform / 82 kDa heat shock protein


Mass: 1363.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in yeast. / References: UniProt: P02829
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG6K, Ethylene Glyco 5%, NaCl 0.15M, Tris 10mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→7.99 Å / Num. all: 53827 / Num. obs: 53827 / % possible obs: 0.96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 1.98 Å / % possible all: 0.96

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FP3

3fp3


Resolution: 1.98→7.99 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.387 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.145 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23645 2858 5 %RANDOM
Rwork0.19917 ---
obs0.20107 53827 96.83 %-
all-53827 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.98→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 2 434 4335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224201
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.975704
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02125.686204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90115760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2011514
X-RAY DIFFRACTIONr_chiral_restr0.1120.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023215
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.22088
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22971
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2378
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0941.52665
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58624196
X-RAY DIFFRACTIONr_scbond_it2.99831708
X-RAY DIFFRACTIONr_scangle_it4.4884.51508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.028 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 154 -
Rwork0.247 3165 -
obs--81.55 %
Refinement TLS params.Method: refined / Origin x: 9.238 Å / Origin y: 44.822 Å / Origin z: 21.145 Å
111213212223313233
T-0.1059 Å2-0.008 Å20.0143 Å2--0.0946 Å20.0526 Å2---0.1138 Å2
L0.1764 °20.1025 °2-0.2722 °2-0.294 °2-0.1488 °2--0.4202 °2
S0.0458 Å °-0.1299 Å °-0.1152 Å °0.1439 Å °-0.0061 Å °0.054 Å °-0.0311 Å °0.0509 Å °-0.0397 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A110 - 222
2X-RAY DIFFRACTION1A234 - 252
3X-RAY DIFFRACTION1A262 - 411
4X-RAY DIFFRACTION1A412 - 532
5X-RAY DIFFRACTION1A546 - 617

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