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- PDB-3fp4: Crystal structure of Tom71 complexed with Ssa1 C-terminal fragment -

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Basic information

Entry
Database: PDB / ID: 3fp4
TitleCrystal structure of Tom71 complexed with Ssa1 C-terminal fragment
Components
  • Ssa1
  • TPR repeat-containing protein YHR117W
KeywordsTRANSPORT PROTEIN / Tom71 / Hsp70 / Mitochondria / translocation / Chaperone / Phosphoprotein / TPR repeat
Function / homology
Function and homology information


HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / Mitochondrial unfolded protein response (UPRmt) / protein aggregate center / Protein methylation / Regulation of HSF1-mediated heat shock response / Clathrin-mediated endocytosis / Neutrophil degranulation / nucleolar peripheral inclusion body / mRNA Splicing - Major Pathway ...HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / Mitochondrial unfolded protein response (UPRmt) / protein aggregate center / Protein methylation / Regulation of HSF1-mediated heat shock response / Clathrin-mediated endocytosis / Neutrophil degranulation / nucleolar peripheral inclusion body / mRNA Splicing - Major Pathway / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / protein targeting to mitochondrion / protein import into mitochondrial matrix / : / protein transmembrane transporter activity / heat shock protein binding / protein folding chaperone / ATP-dependent protein folding chaperone / protein catabolic process / unfolded protein binding / protein refolding / mitochondrial outer membrane / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Tetratricopeptide repeat / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Tetratricopeptide repeat / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein ...Tetratricopeptide repeat / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Tetratricopeptide repeat / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / ATPase, nucleotide binding domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Protein TOM71 / Probable heat shock protein ssa1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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: 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

Downloads & links

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Assembly

Deposited unit
A: TPR repeat-containing protein YHR117W
Q: Ssa1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,52119
Polymers61,7732
Non-polymers74717
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-2 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.820, 116.025, 150.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AQ

#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 Ssa1


Mass: 1202.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in yeast. / References: UniProt: Q10265*PLUS

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Non-polymers , 4 types, 281 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG6K, 5% Ethylene Glyco, 0.15M NaCl, 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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→8 Å / Num. obs: 39166 / % possible obs: 0.89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.14 Å / % possible all: 0.89

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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: 2.14→8 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.296 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.213 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26127 2100 5.1 %RANDOM
Rwork0.20768 ---
obs0.21036 39166 89.36 %-
all-39116 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.851 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.14→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 29 264 4391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224250
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9825792
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1225.598209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03115787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7511516
X-RAY DIFFRACTIONr_chiral_restr0.1270.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023239
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.22163
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22898
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9931.52581
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69824197
X-RAY DIFFRACTIONr_scbond_it3.0131692
X-RAY DIFFRACTIONr_scangle_it4.5224.51567
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.141→2.192 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 102 -
Rwork0.261 2029 -
obs--65.87 %

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