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- PDB-7f50: X-ray crystal structure of Y149A mutated Hsp72-NBD in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7f50
TitleX-ray crystal structure of Y149A mutated Hsp72-NBD in complex with AMPPnP
ComponentsHeat shock 70 kDa protein 1B
KeywordsHYDROLASE / Complex / Chaperone / nuclueotide-binding domain
Function / homology
Function and homology information


cellular heat acclimation / negative regulation of inclusion body assembly / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / aggresome / cellular response to steroid hormone stimulus ...cellular heat acclimation / negative regulation of inclusion body assembly / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / aggresome / cellular response to steroid hormone stimulus / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / Attenuation phase / ATP metabolic process / protein folding chaperone / inclusion body / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of erythrocyte differentiation / positive regulation of interleukin-8 production / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / vesicle / ficolin-1-rich granule lumen / protein stabilization / blood microparticle / nuclear speck / ribonucleoprotein complex / negative regulation of cell population proliferation / focal adhesion / signaling receptor binding / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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, nucleotide binding domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock 70 kDa protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsYokoyama, T. / Fujii, S. / Nabeshima, Y. / Mizuguchi, M.
CitationJournal: Iucrj / Year: 2022
Title: Neutron crystallographic analysis of the nucleotide-binding domain of Hsp72 in complex with ADP.
Authors: Yokoyama, T. / Fujii, S. / Ostermann, A. / Schrader, T.E. / Nabeshima, Y. / Mizuguchi, M.
History
DepositionJun 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock 70 kDa protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2635
Polymers42,6731
Non-polymers5904
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-23 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.827, 61.968, 142.779
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 Heat shock 70 kDa protein 1B / Heat shock 70 kDa protein 2 / HSP70-2 / HSP70.2


Mass: 42673.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1B, HSP72 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DMV9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 29% PEG550 MME, 200 mM MgCl2 and 100 mM Tris-HCl pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→37.75 Å / Num. obs: 44823 / % possible obs: 98.8 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rpim(I) all: 0.034 / Rrim(I) all: 0.074 / Net I/σ(I): 13.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4381 / CC1/2: 0.771 / Rpim(I) all: 0.337 / Rrim(I) all: 0.713 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AQZ

5aqz


Resolution: 1.703→36.846 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 2241 5 %
Rwork0.1855 --
obs0.1876 44814 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.703→36.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 34 328 3285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063008
X-RAY DIFFRACTIONf_angle_d0.8124077
X-RAY DIFFRACTIONf_dihedral_angle_d19.7261112
X-RAY DIFFRACTIONf_chiral_restr0.081468
X-RAY DIFFRACTIONf_plane_restr0.006530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7034-1.74040.35831350.32342547X-RAY DIFFRACTION96
1.7404-1.78090.34511390.29762646X-RAY DIFFRACTION100
1.7809-1.82540.30131410.25422673X-RAY DIFFRACTION100
1.8254-1.87480.25131380.21962633X-RAY DIFFRACTION100
1.8748-1.930.25371400.19342654X-RAY DIFFRACTION100
1.93-1.99220.20071400.19122662X-RAY DIFFRACTION100
1.9922-2.06340.21461390.18642641X-RAY DIFFRACTION100
2.0634-2.14610.22191380.17942646X-RAY DIFFRACTION99
2.1461-2.24370.2491390.17772633X-RAY DIFFRACTION99
2.2437-2.3620.24391400.19022663X-RAY DIFFRACTION99
2.362-2.50990.25371400.20032653X-RAY DIFFRACTION99
2.5099-2.70370.20091420.19192709X-RAY DIFFRACTION100
2.7037-2.97570.22881410.18872671X-RAY DIFFRACTION99
2.9757-3.4060.24221420.18432701X-RAY DIFFRACTION99
3.406-4.29010.20261410.15512683X-RAY DIFFRACTION97
4.2901-36.8460.19931460.16922758X-RAY DIFFRACTION95

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