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- PDB-7gyn: Crystal Structure of HSP72 in complex with ligand 11 at 7.15 MGy ... -

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Basic information

Entry
Database: PDB / ID: 7gyn
TitleCrystal Structure of HSP72 in complex with ligand 11 at 7.15 MGy X-ray dose
ComponentsHeat shock 70 kDa protein 1A
KeywordsCHAPERONE / HSP70 / HSP72 / HEAT SHOCK PROTEIN / radiation damage / ligand
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 / C3HC4-type RING finger domain binding / Viral RNP Complexes in the Host Cell Nucleus / 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 / C3HC4-type RING finger domain binding / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / transcription regulator inhibitor activity / 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 / ATP metabolic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / heat shock protein binding / inclusion body / negative regulation of protein ubiquitination / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein folding chaperone / centriole / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / ATP-dependent protein folding chaperone / G protein-coupled receptor binding / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of cell growth / PKR-mediated signaling / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / cellular response to oxidative stress / cellular response to heat / positive regulation of NF-kappaB transcription factor activity / protein refolding / vesicle / blood microparticle / ficolin-1-rich granule lumen / protein stabilization / nuclear speck / cadherin binding / receptor ligand activity / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / 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
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.15 Å
AuthorsCabry, M. / Rodrigues, M.J. / Le Bihan, Y.V. / van Montfort, R.L.M.
CitationJournal: J.Appl.Crystallogr. / Year: 2024
Title: Specific radiation damage to halogenated inhibitors and ligands in protein-ligand crystal structures.
Authors: Rodrigues, M.J. / Cabry, M. / Collie, G. / Carter, M. / McAndrew, C. / Owen, R.L. / Bellenie, B.R. / Le Bihan, Y.V. / van Montfort, R.L.M.
History
DepositionJan 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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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 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,73016
Polymers43,1961
Non-polymers1,53415
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.100, 82.300, 93.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 1A / Heat shock 70 kDa protein 1 / HSP70-1 / HSP70.1


Mass: 43195.902 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDE BINDING DOMAIN, UNP RESIDUES 1-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSP72, HSPA1, HSX70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P0DMV8

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Non-polymers , 7 types, 325 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3S
#7: Chemical ChemComp-A1ACZ / 8-chloroadenosine


Mass: 301.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12ClN5O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES pH 7.5, 18-28% PEG 3350, 2 mM MgCL2, 2 mM NAH2PO4, 5 mM 8-CHLOROADENOSINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9192 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9192 Å / Relative weight: 1
ReflectionResolution: 2.15→39.83 Å / Num. obs: 22587 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 33.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Rrim(I) all: 0.078 / Net I/σ(I): 13.8 / Num. measured all: 142228 / Scaling rejects: 473
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
2.15-2.226.30.3331211419240.9530.1440.3634.8100
8.86-39.835.30.03220103780.9980.0150.03527.599.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
Aimless0.7.4data scaling
BUSTER2.10.3phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.15→23.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.245 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.174
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1097 4.87 %RANDOM
Rwork0.161 ---
obs0.164 22513 100 %-
Displacement parametersBiso max: 110.11 Å2 / Biso mean: 36.44 Å2 / Biso min: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.382 Å20 Å20 Å2
2--0.0715 Å20 Å2
3---5.3105 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 2.15→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 91 319 3342
Biso mean--52.26 48.03 -
Num. residues----385
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1087SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes556HARMONIC5
X-RAY DIFFRACTIONt_it3118HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion415SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3851SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3118HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4215HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion15.43
LS refinement shellResolution: 2.15→2.17 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2961 16 3.55 %
Rwork0.1583 435 -
all0.1623 451 -
obs--98.93 %
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)
11.99060.156-0.02932.79010.57233.99560.03680.12710.2211-0.12960.0392-0.2092-0.44910.3628-0.076-0.0144-0.05890.0135-0.06240.0233-0.067719.34566.1777-8.9257
22.3938-0.28640.27734.1097-1.05822.8097-0.0526-0.24560.0930.13820.04980.323-0.3034-0.54420.0027-0.07950.03610.00340.0058-0.0081-0.0642-1.54316.20331.4514
31.3194-0.16110.37251.12720.12892.3335-0.03340.06250.0622-0.04920.06790.1803-0.0986-0.1888-0.0344-0.0111-0.0289-0.0272-0.06490.0139-0.05288.71483.0684-9.9052
40.6118-0.05050.88270.99460.43562.21230.17110.0725-0.1431-0.0611-0.04170.09460.3606-0.0091-0.12940.0143-0.0056-0.0136-0.0130.0056-0.046512.349-6.7916-8.5033
52.4155-0.1563-0.32123.39350.52023.85180.17160.3012-0.2954-0.1773-0.1106-0.21160.50330.3362-0.0610.03290.0676-0.0775-0.0365-0.0201-0.060522.7153-10.58884.1941
60.5318-2.84430.38182.11861.80120.3017-0.00470.02010.02930.0526-0.06970.16640.1083-0.15130.07440.0211-0.05290.09-0.02790.02670.033713.371815.60922.819
73.5272-1.6716-0.41113.96341.91253.5947-0.0770.08650.2422-0.2341-0.06310.4253-0.3383-0.41190.14010.028-0.03520.0225-0.10030.0327-0.002214.397820.648816.7512
81.5085-0.415-0.14573.06560.5461.51170.1633-0.0955-0.00960.15980.0382-0.00770.10630.1994-0.2015-0.0077-0.0135-0.0162-0.02840.0158-0.065123.357-1.145716.6199
91.4992.53911.14821.86360.81513.70230.0793-0.032-0.19380.2823-0.0856-0.3735-0.02360.50160.0063-0.08140.0151-0.01960.031-0.0016-0.024130.2107-1.9611.3445
101.5911-1.0611-2.77763.5454-1.26051.86510.0480.1425-0.1115-0.22010.0739-0.03940.27940.163-0.1218-0.032-0.02440.00240.0538-0.0207-0.006923.5982-5.3455-14.0566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 41}A1 - 41
2X-RAY DIFFRACTION2{A|42 - 109}A42 - 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 - 292}A250 - 292
8X-RAY DIFFRACTION8{A|293 - 343}A293 - 343
9X-RAY DIFFRACTION9{A|344 - 367}A344 - 367
10X-RAY DIFFRACTION10{A|368 - 385}A368 - 385

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