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- PDB-1nlt: The crystal structure of Hsp40 Ydj1 -

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Basic information

Entry
Database: PDB / ID: 1nlt
TitleThe crystal structure of Hsp40 Ydj1
Components
  • Mitochondrial protein import protein MAS5Mitochondrion
  • Seven residue peptide
KeywordsPROTEIN TRANSPORT / beta-strands / chaperone / heat shock / mitochondrion
Function / homology
Function and homology information


tRNA import into nucleus / TRC complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to oxygen levels / protein targeting to ER / protein targeting to mitochondrion / 'de novo' protein folding / ATPase activator activity / chaperone-mediated protein complex assembly / : ...tRNA import into nucleus / TRC complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to oxygen levels / protein targeting to ER / protein targeting to mitochondrion / 'de novo' protein folding / ATPase activator activity / chaperone-mediated protein complex assembly / : / Hsp70 protein binding / transcription repressor complex / unfolded protein binding / protein transport / response to heat / ubiquitin-dependent protein catabolic process / protein-folding chaperone binding / protein refolding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Chaperone, DNAj Protein; Chain A / Heat shock protein DnaJ, cysteine-rich domain / DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / Heat shock protein DnaJ, cysteine-rich domain superfamily ...Chaperone, DNAj Protein; Chain A / Heat shock protein DnaJ, cysteine-rich domain / DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / Heat shock protein DnaJ, cysteine-rich domain superfamily / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Ribbon / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mitochondrial protein import protein MAS5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsLi, J. / Sha, B.
CitationJournal: Structure / Year: 2003
Title: The crystal structure of the yeast Hsp40 Ydj1 complexed with its peptide substrate.
Authors: Li, J. / Qian, X. / Sha, B.
History
DepositionJan 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _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: Mitochondrial protein import protein MAS5
B: Seven residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3864
Polymers28,2562
Non-polymers1312
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.025, 55.025, 161.870
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Mitochondrial protein import protein MAS5 / Mitochondrion / Protein YDJ1


Mass: 27388.627 Da / Num. of mol.: 1 / Fragment: C terminal domain / Mutation: no
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAS5 OR YDJ1 OR YNL064C OR N2418 OR YNL2418C / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25491
#2: Protein/peptide Seven residue peptide


Mass: 866.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
2100 mMTris1reservoirpH7.0
315 %ethylene glycol1reservoir
45 %PEG40001reservoir
510 mMMES1droppH6.0
6150 mM1dropNaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F211.2828,1.2894, 1.244, 1.3237
SYNCHROTRONAPS 14-BM-D21.2828,1.2894, 1.244, 1.3237
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 20, 2002
ADSC QUANTUM 42CCDAug 30, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1sagitally focused SiMADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.28281
21.28941
31.2441
41.32371
ReflectionResolution: 2.7→27.5 Å / Num. all: 7827 / Num. obs: 7827 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.33 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.3
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.01145 / Mean I/σ(I) obs: 8.67 / % possible all: 73.1
Reflection
*PLUS
% possible obs: 95 % / Redundancy: 5.22 %
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 73.1 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 8.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→27.5 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 278924.7 / Data cutoff high rms absF: 278924.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 786 10 %RANDOM
Rwork0.269 ---
obs0.269 7827 93.6 %-
all-7827 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.0786 Å2 / ksol: 0.332447 e/Å3
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å26.7 Å20 Å2
2--3.7 Å20 Å2
3----7.4 Å2
Refine analyzeLuzzati coordinate error free: 0.47 Å / Luzzati sigma a free: 0.51 Å
Refinement stepCycle: LAST / Resolution: 2.7→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 2 147 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it3.22
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 37 3.9 %
Rwork0.326 906 -
obs--69.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 3 Å / Rfactor Rwork: 0.268
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.91
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.329 / Rfactor Rwork: 0.325 / Num. reflection Rwork: 786

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