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- PDB-7nqu: Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain... -

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Basic information

Entry
Database: PDB / ID: 7nqu
TitlePlasmodium falciparum Hsp70-x chaperone nucleotide binding domain in complex with Z396380540
ComponentsHeat shock protein 70
KeywordsCHAPERONE / Intra-erythrocytic / AMP-PNP / Ligand
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / mRNA Splicing - Major Pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AUF1 (hnRNP D0) binds and destabilizes mRNA / Neutrophil degranulation / : / heat shock protein binding / protein folding chaperone / ATP-dependent protein folding chaperone / protein refolding ...Regulation of HSF1-mediated heat shock response / mRNA Splicing - Major Pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AUF1 (hnRNP D0) binds and destabilizes mRNA / Neutrophil degranulation / : / heat shock protein binding / protein folding chaperone / ATP-dependent protein folding chaperone / protein refolding / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 ...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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
AMP PHOSPHORAMIDATE / Chem-HR5 / PHOSPHATE ION / Heat shock 70 kDa protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsMohamad, N. / O'Donoghue, A. / Kantsadi, A.L. / Vakonakis, I.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021759/1 United Kingdom
H2020 Marie Curie Actions of the European Commission752069European Union
CitationJournal: To Be Published
Title: Structures of P. falciparum Hsp70-x nucleotide binding domain with small molecule ligands
Authors: Mohamad, N. / O'Donoghue, A. / Kantsadi, A.L. / Vakonakis, I.
History
DepositionMar 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,49625
Polymers85,6572
Non-polymers2,84023
Water3,423190
1
A: Heat shock protein 70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,29514
Polymers42,8281
Non-polymers1,46613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein 70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,20211
Polymers42,8281
Non-polymers1,37310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.89, 102.45, 103.69
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Heat shock protein 70 / Hsp70-x


Mass: 42828.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0831700 / Plasmid: pFLOAT
Details (production host): pET30a derivative with N-terminal His6-tag and HRV 3C cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K7NTP5

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Non-polymers , 7 types, 213 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-HR5 / ~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide


Mass: 207.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3O / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20 mM HEPES pH 7.4 50 mM NaCl 1 mM DTT 3.5 mM AMP-PNP 24% w/v PEG 1500 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.13→63.28 Å / Num. obs: 48320 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Rrim(I) all: 0.071 / Net I/σ(I): 13.6
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2383 / CC1/2: 0.8 / Rrim(I) all: 1.601 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZQ

6rzq


Resolution: 2.13→63.28 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 2316 -RANDOM
Rwork0.2203 ---
obs0.2211 48256 99.9 %-
Displacement parametersBiso mean: 85.93 Å2
Baniso -1Baniso -2Baniso -3
1-16.7356 Å20 Å20 Å2
2---22.2275 Å20 Å2
3---5.4918 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.13→63.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5869 0 176 190 6235
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086139HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.978260HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2225SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1037HARMONIC5
X-RAY DIFFRACTIONt_it6139HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion816SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4950SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion16.26
LS refinement shellResolution: 2.13→2.15 Å
RfactorNum. reflection% reflection
Rfree0.4198 47 -
Rwork0.3487 --
obs0.3522 966 100 %
Refinement TLS params.

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)
12.8572-0.0903-0.17452.22810.78252.92380.0330.0211-0.01080.02110.0925-0.023-0.0108-0.023-0.1255-0.6759-0.00720.0455-0.41880.0341-0.553230.156377.175954.6943
25.2420.1917-1.43022.5255-0.67484.24860.1412-0.085-1.4258-0.0850.0342-0.4416-1.4258-0.4416-0.1754-0.22230.1115-0.0059-0.39230.0677-0.373447.53475.160314.8315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A33 - 418
2X-RAY DIFFRACTION1{ A|* }A504
3X-RAY DIFFRACTION1{ A|* }A601 - 803
4X-RAY DIFFRACTION1{ A|* }A1301 - 3001
5X-RAY DIFFRACTION2{ B|* }B33 - 414
6X-RAY DIFFRACTION2{ B|* }B503
7X-RAY DIFFRACTION2{ B|* }B604 - 703
8X-RAY DIFFRACTION2{ B|* }B1101 - 2301

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