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- PDB-3i33: Crystal structure of the human 70kDa heat shock protein 2 (Hsp70-... -

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Basic information

Entry
Database: PDB / ID: 3i33
TitleCrystal structure of the human 70kDa heat shock protein 2 (Hsp70-2) ATPase domain in complex with ADP and inorganic phosphate
ComponentsHeat shock-related 70 kDa protein 2
KeywordsCHAPERONE / protein-ADP complex / ATP-binding / Nucleotide-binding / Phosphoprotein / Stress response / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / spermatid development / chaperone cofactor-dependent protein refolding ...CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / spermatid development / chaperone cofactor-dependent protein refolding / response to unfolded protein / Regulation of HSF1-mediated heat shock response / Attenuation phase / protein folding chaperone / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of G2/M transition of mitotic cell cycle / Meiotic synapsis / response to cold / male germ cell nucleus / ATP-dependent protein folding chaperone / tau protein binding / PKR-mediated signaling / disordered domain specific binding / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / spermatogenesis / blood microparticle / positive regulation of protein phosphorylation / enzyme binding / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Defensin A-like - #30 / Defensin A-like / 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 / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily ...Defensin A-like - #30 / Defensin A-like / 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 / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Heat shock-related 70 kDa protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWisniewska, M. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Wisniewska, M. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Kotzsch, A. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Moche, M. / Persson, C. / Roos, A.K. / Sagemark, J. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van den Berg, S. / Weigelt, J. / Welin, M. / Schueler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Crystal structures of the ATPase domains of four human Hsp70 isoforms: HSPA1L/Hsp70-hom, HSPA2/Hsp70-2, HSPA6/Hsp70B', and HSPA5/BiP/GRP78
Authors: Wisniewska, M. / Karlberg, T. / Lehtio, L. / Johansson, I. / Kotenyova, T. / Moche, M. / Schueler, H.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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 / 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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: Heat shock-related 70 kDa protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0845
Polymers44,4451
Non-polymers6394
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.180, 78.600, 93.990
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 , 1 types, 1 molecules A

#1: Protein Heat shock-related 70 kDa protein 2 / Heat shock 70 kDa protein 2 / Hsp70-2


Mass: 44445.215 Da / Num. of mol.: 1 / Fragment: ATP-ase domain, residues 6-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA2 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3pRARE / References: UniProt: P54652

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Non-polymers , 5 types, 349 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M ammonium acetate, 0.1M bis-tris, 25% PEG 3350 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å
DetectorType: ADSC / Detector: CCD / Date: Jan 30, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.3→26.26 Å / Num. obs: 87721 / % possible obs: 99.3 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 11.6 / Num. measured all: 604452
Reflection shellResolution: 1.3→1.37 Å / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0035refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FE1

3fe1


Resolution: 1.3→25.56 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.693 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19854 4419 5 %RANDOM
Rwork0.18278 ---
all0.18358 83300 --
obs0.18358 83300 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.869 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→25.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 39 345 3286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223023
X-RAY DIFFRACTIONr_bond_other_d0.0010.022047
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9754094
X-RAY DIFFRACTIONr_angle_other_deg0.78135010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1685389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53224.462130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4315529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1211519
X-RAY DIFFRACTIONr_chiral_restr0.0670.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02599
X-RAY DIFFRACTIONr_mcbond_it0.61.51899
X-RAY DIFFRACTIONr_mcbond_other0.1411.5787
X-RAY DIFFRACTIONr_mcangle_it1.14923059
X-RAY DIFFRACTIONr_scbond_it1.75731124
X-RAY DIFFRACTIONr_scangle_it2.8814.51032
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 308 -
Rwork0.197 6095 -
obs--98.96 %

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