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- PDB-7q4r: Crystal structure of human HSP72-NBD in complex with fragment 1 -

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Basic information

Entry
Database: PDB / ID: 7q4r
TitleCrystal structure of human HSP72-NBD in complex with fragment 1
ComponentsHeat shock 70 kDa protein 1A
KeywordsCHAPERONE / Inhibitor / ATPase
Function / homology
Function and homology information


positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / death receptor agonist activity / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity ...positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / death receptor agonist activity / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / inclusion body / heat shock protein binding / protein folding chaperone / negative regulation of protein ubiquitination / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / vesicle / blood microparticle / ficolin-1-rich granule lumen / protein stabilization / receptor ligand activity / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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
Chem-8X6 / PHOSPHATE ION / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsLe Bihan, Y.V. / Westwood, I.M. / van Montfort, R.L.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC309/A11566 United Kingdom
CitationJournal: Molecules / Year: 2022
Title: Discovery and Characterization of a Cryptic Secondary Binding Site in the Molecular Chaperone HSP70.
Authors: O'Connor, S. / Le Bihan, Y.V. / Westwood, I.M. / Liu, M. / Mak, O.W. / Zazeri, G. / Povinelli, A.P.R. / Jones, A.M. / van Montfort, R. / Reynisson, J. / Collins, I.
History
DepositionNov 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,6044
Polymers43,1961
Non-polymers4083
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-18 kcal/mol
Surface area16840 Å2
Unit cell
Length a, b, c (Å)47.465, 78.473, 93.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heat shock 70 kDa protein 1A / Heat shock 70 kDa protein 1 / HSP70.1


Mass: 43195.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSPA1, HSX70 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P0DMV8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-8X6 / 4-(4-phenyl-1,3-thiazol-2-yl)piperazine-1-carboxamide


Mass: 288.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N4OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18 to 28 % PEG 3350, 0.1 M HEPES pH 7.5, 2 mM MgCl2 and 2 mM NaH2PO4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.79→47.47 Å / Num. obs: 32590 / % possible obs: 96.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 23.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.028 / Rrim(I) all: 0.069 / Net I/σ(I): 15.7 / Num. measured all: 179702 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.79-1.833.40.406504914700.8640.2280.472.275
8.95-47.475.30.0317473310.9990.0140.03339.199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.1data scaling
PHASERphasing
BUSTER2.10.4 (24-FEB-2021)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s3x

1s3x


Resolution: 1.79→46.75 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.166 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 1645 5.09 %RANDOM
Rwork0.1917 ---
obs0.1939 32323 96 %-
Displacement parametersBiso max: 64.33 Å2 / Biso mean: 26.3 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.5311 Å20 Å20 Å2
2--2.2364 Å20 Å2
3----4.7675 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.79→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 26 421 3358
Biso mean--21.81 38.45 -
Num. residues----383
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1061SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes545HARMONIC5
X-RAY DIFFRACTIONt_it3039HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion412SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies18HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3081SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3039HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4128HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion15.03
LS refinement shellResolution: 1.79→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3522 28 4.33 %
Rwork0.2805 619 -
all0.2835 647 -
obs--73.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8841-0.1932-0.51440.7477-0.19761.7197-0.0174-0.12490.1477-0.01030.01780.05060.1945-0.1757-0.0005-0.0721-0.01940.02390.0731-0.01360.0125-19.88774.33176.9399
21.2775-0.03180.23180.52750.23800.00810.0712-0.0193-0.02410.00510.0301-0.05160.0568-0.0132-0.0635-0.00840.0150.0239-0.00370.02731.05437.5437-2.5741
30.87510.1772-0.31380-0.17690.30710.0924-0.05910.02220.0621-0.0507-0.0962-0.0203-0.0166-0.0417-0.048-0.00770.0090.03-0.02490.0209-7.40473.72777.3314
41.23940.3674-0.52080.47790.341800.1404-0.0295-0.1210.117-0.089-0.08080.1368-0.0371-0.0514-0.0254-0.0152-0.01690.03140.0041-0.0006-10.9669-6.12075.7885
50.4691-0.4748-0.02651.9339-0.5270.96720.0208-0.03770.0262-0.0004-0.02350.00060.13790.08740.0027-0.0347-0.029-0.0030.0036-0.0054-0.0006-21.2289-10.4623-7.0583
61.04540.8130.59094.6102-2.91041.812-0.1135-0.05360.0061-0.0752-0.1075-0.1356-0.00590.06810.221-0.0618-0.0261-0.02020.08390.0256-0.0277-8.561814.1877-25.2713
72.42411.462-0.86130.814-0.36091.7993-0.04190.05020.04590.09180.1012-0.1556-0.0333-0.1207-0.0593-0.0475-0.0211-0.02680.0776-0.0009-0.0524-6.29116.4397-18.599
81.56120.57650.380.6835-0.66751.3246-0.1745-0.0670.246-0.1160.12230.1631-0.0779-0.15720.0521-0.0709-0.0018-0.03710.04-0.004-0.009-13.841719.3771-21.7787
90.49140.9863-0.04841.8087-0.55811.32490.01880.1167-0.0958-0.0712-0.015-0.0179-0.0486-0.0356-0.0039-0.0615-0.0101-0.00880.0545-0.0151-0.0319-21.9703-8.6174-16.7522
100.13380.598-0.12810.52190.76911.6680.00650.09810.04820.0735-0.06270.1654-0.0427-0.09610.0563-0.0906-0.0079-0.00090.1068-0.0252-0.0137-26.2317-2.5731-6.1702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 28}A2 - 28
2X-RAY DIFFRACTION2{A|29 - 109}A29 - 109
3X-RAY DIFFRACTION3{A|110 - 151}A110 - 151
4X-RAY DIFFRACTION4{A|152 - 182}A152 - 182
5X-RAY DIFFRACTION5{A|183 - 229}A183 - 229
6X-RAY DIFFRACTION6{A|230 - 249}A230 - 249
7X-RAY DIFFRACTION7{A|250 - 275}A250 - 275
8X-RAY DIFFRACTION8{A|276 - 306}A276 - 306
9X-RAY DIFFRACTION9{A|307 - 343}A307 - 343
10X-RAY DIFFRACTION10{A|344 - 384}A344 - 384

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