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- PDB-3gdq: Crystal structure of the human 70kDa heat shock protein 1-like AT... -

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Basic information

Entry
Database: PDB / ID: 3gdq
TitleCrystal structure of the human 70kDa heat shock protein 1-like ATPase domain in complex with ADP and inorganic phosphate
ComponentsHeat shock 70 kDa protein 1-like
KeywordsCHAPERONE / helix / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / TRANSCRIPTION
Function / homology
Function and homology information


zona pellucida receptor complex / binding of sperm to zona pellucida / positive regulation of protein targeting to mitochondrion / : / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / response to unfolded protein / Attenuation phase / heat shock protein binding / protein folding chaperone ...zona pellucida receptor complex / binding of sperm to zona pellucida / positive regulation of protein targeting to mitochondrion / : / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / response to unfolded protein / Attenuation phase / heat shock protein binding / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ATP-dependent protein folding chaperone / PKR-mediated signaling / unfolded protein binding / cell body / protein refolding / blood microparticle / mitochondrial matrix / ubiquitin protein ligase binding / ATP hydrolysis activity / nucleoplasm / ATP binding / 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 70 kDa protein 1-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWisniewska, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Wisniewska, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Schutz, P. / Siponen, M. / 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. / Schuler, H.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer 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 / 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 70 kDa protein 1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6585
Polymers44,9891
Non-polymers6694
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.070, 70.700, 97.500
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 70 kDa protein 1-like / Heat shock 70 kDa protein 1L / Heat shock 70 kDa protein 1-Hom / HSP70-Hom


Mass: 44988.910 Da / Num. of mol.: 1 / Fragment: ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: P34931

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Non-polymers , 5 types, 313 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 26% PEG monomethyl ether 2000, 0.1M Tris, 0.2M trimethylamine n-oxide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2008
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 45423 / Num. obs: 45400
Reflection shellResolution: 1.8→1.85 Å

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0035refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BA0

1ba0


Resolution: 1.8→23.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.898 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20249 2255 5 %RANDOM
Rwork0.17071 ---
obs0.17224 42856 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 39 309 3246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223025
X-RAY DIFFRACTIONr_bond_other_d0.0010.022044
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.974099
X-RAY DIFFRACTIONr_angle_other_deg0.85634979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0855382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75824.101139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20715517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2951523
X-RAY DIFFRACTIONr_chiral_restr0.0810.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023392
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02617
X-RAY DIFFRACTIONr_mcbond_it0.7921.51884
X-RAY DIFFRACTIONr_mcbond_other0.1941.5777
X-RAY DIFFRACTIONr_mcangle_it1.47223034
X-RAY DIFFRACTIONr_scbond_it2.28731141
X-RAY DIFFRACTIONr_scangle_it3.8494.51065
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 155 -
Rwork0.206 2951 -
obs--100 %

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