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- PDB-7f4x: Joint neutron and X-ray crystal structure of the nucleotide-bindi... -

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Basic information

Entry
Database: PDB / ID: 7f4x
TitleJoint neutron and X-ray crystal structure of the nucleotide-binding domain of Hsp72 in complex with ADP
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 / blood microparticle / protein stabilization / 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
ADENOSINE-5'-DIPHOSPHATE / Heat shock 70 kDa protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYokoyama, T. / Ostermann, A. / Schrader, T.E.
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 1.2Apr 3, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,2404
Polymers42,7651
Non-polymers4743
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-31 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.677, 64.618, 145.593
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: 42765.281 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-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20-25% PEG 2000 MME, 90 mMsodium acetate, 10 mM acetic acid, 200 mM MgCl2, 10%(v/v) glycerol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12981N
22981N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
NUCLEAR REACTORFRM II BIODIFF23.98
Detector
TypeIDDetectorDate
DECTRIS PILATUS 12M1PIXELMay 14, 2017
MAATEL IMAGINE2IMAGE PLATEJun 26, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
23.981
Reflection

Entry-ID: 7F4X

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rrim(I) allDiffraction-IDNet I/σ(I)
1.6-44.455763997.55.70.081113.5
2.2-39.32095290.42.30.11728.1
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRrim(I) allDiffraction-ID% possible all
1.6-1.665.92.455790.733195.4
2.2-2.262.12.916730.374288.5

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
Refinement

SU ML: 0.14 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 19.04 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5AQZ

5aqz

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)
1.6-37.838X-RAY DIFFRACTION0.18980.16550.1667288157604597.561.37
2.199-38.805NEUTRON DIFFRACTION0.2220.18410.1861053209355.0390.42
Refinement stepCycle: LAST / Resolution: 1.6→37.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 29 85 3044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076814
X-RAY DIFFRACTIONf_angle_d0.99212111
X-RAY DIFFRACTIONf_dihedral_angle_d16.3091846
X-RAY DIFFRACTIONf_chiral_restr0.074467
X-RAY DIFFRACTIONf_plane_restr0.0051359
NEUTRON DIFFRACTIONf_bond_d0.0076814
NEUTRON DIFFRACTIONf_angle_d0.99212111
NEUTRON DIFFRACTIONf_dihedral_angle_d16.3091846
NEUTRON DIFFRACTIONf_chiral_restr0.074467
NEUTRON DIFFRACTIONf_plane_restr0.0051359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62620.26551320.23052518X-RAY DIFFRACTION95
1.6262-1.65430.26351330.2292516X-RAY DIFFRACTION96
1.6543-1.68440.24541320.20862522X-RAY DIFFRACTION96
1.6844-1.71680.23491350.20292553X-RAY DIFFRACTION96
1.7168-1.75180.24081340.20072555X-RAY DIFFRACTION97
1.7518-1.78990.22011340.19522536X-RAY DIFFRACTION96
1.7899-1.83150.24951360.18592581X-RAY DIFFRACTION98
1.8315-1.87730.24451340.1852544X-RAY DIFFRACTION97
1.8773-1.92810.20031350.17862572X-RAY DIFFRACTION97
1.9281-1.98480.18911370.17222597X-RAY DIFFRACTION98
1.9848-2.04890.18631350.17272573X-RAY DIFFRACTION97
2.0489-2.12210.24451360.17432583X-RAY DIFFRACTION97
2.1221-2.2070.20731370.17432609X-RAY DIFFRACTION99
2.207-2.30750.17941390.1752630X-RAY DIFFRACTION99
2.3075-2.42910.22131380.16982623X-RAY DIFFRACTION98
2.4291-2.58130.18871380.17422632X-RAY DIFFRACTION98
2.5813-2.78050.18441390.16862637X-RAY DIFFRACTION99
2.7805-3.06020.1971410.17362681X-RAY DIFFRACTION99
3.0602-3.50280.20621410.1692679X-RAY DIFFRACTION99
3.5028-4.41210.14321440.13412736X-RAY DIFFRACTION99
4.4121-37.8380.15281510.13882846X-RAY DIFFRACTION99
2.1994-2.29950.24141350.22352357NEUTRON DIFFRACTION88
2.2995-2.42070.24641230.19462476NEUTRON DIFFRACTION91
2.4207-2.57230.22911290.19682511NEUTRON DIFFRACTION92
2.5723-2.77090.20831320.19112448NEUTRON DIFFRACTION91
2.7709-3.04970.24991240.19982442NEUTRON DIFFRACTION90
3.0497-3.49070.24651280.1992386NEUTRON DIFFRACTION87
3.4907-4.39690.2141360.16472532NEUTRON DIFFRACTION91
4.3969-38.8050.18831460.15972730NEUTRON DIFFRACTION93

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