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- PDB-6zhi: Structure of the Plasmodium falciparum Hsp70-x substrate binding ... -

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Basic information

Entry
Database: PDB / ID: 6zhi
TitleStructure of the Plasmodium falciparum Hsp70-x substrate binding domain in complex with hydrophobic peptide
Components
  • ASN-ARG-LEU-LEU-LEU-THR-GLY
  • Heat shock protein 70
KeywordsCHAPERONE / malaria / erythrocyte remodelling / PfHsp70-x / complex
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
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein 70
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsSchmidt, J. / Vakonakis, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N009274/1 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structure of the substrate-binding domain of Plasmodium falciparum heat-shock protein 70-x.
Authors: Schmidt, J. / Vakonakis, I.
History
DepositionJun 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Revision 1.2Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 70
B: Heat shock protein 70
C: Heat shock protein 70
D: Heat shock protein 70
E: ASN-ARG-LEU-LEU-LEU-THR-GLY
F: ASN-ARG-LEU-LEU-LEU-THR-GLY
G: ASN-ARG-LEU-LEU-LEU-THR-GLY
H: ASN-ARG-LEU-LEU-LEU-THR-GLY


Theoretical massNumber of molelcules
Total (without water)106,4928
Polymers106,4928
Non-polymers00
Water00
1
D: Heat shock protein 70
H: ASN-ARG-LEU-LEU-LEU-THR-GLY


Theoretical massNumber of molelcules
Total (without water)26,6232
Polymers26,6232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heat shock protein 70
E: ASN-ARG-LEU-LEU-LEU-THR-GLY


Theoretical massNumber of molelcules
Total (without water)26,6232
Polymers26,6232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7 kcal/mol
Surface area13370 Å2
MethodPISA
3
B: Heat shock protein 70
G: ASN-ARG-LEU-LEU-LEU-THR-GLY


Theoretical massNumber of molelcules
Total (without water)26,6232
Polymers26,6232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-7 kcal/mol
Surface area13680 Å2
MethodPISA
4
C: Heat shock protein 70
F: ASN-ARG-LEU-LEU-LEU-THR-GLY


Theoretical massNumber of molelcules
Total (without water)26,6232
Polymers26,6232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.069, 93.853, 85.296
Angle α, β, γ (deg.)90.00, 99.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25835.967 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_0831700 / Plasmid: pFLOAT
Details (production host): pET30a derivative with His-tag and 3C cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: K7NTP5
#2: Protein/peptide
ASN-ARG-LEU-LEU-LEU-THR-GLY


Mass: 786.941 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)

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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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M bicine/2-Amino-2-(hydroxymethyl)propane-1,3-diol base 10% w/v PEG 20,000 20% w/v PEG MME 550 0.03 M of each of di- to penta-ethyleneglycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.25→93.89 Å / Num. obs: 17457 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 94.35 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.048 / Rrim(I) all: 0.125 / Net I/σ(I): 8.7
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 1.5 % / Rmerge(I) obs: 1.857 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 796 / CC1/2: 0.568 / Rpim(I) all: 0.777 / Rrim(I) all: 2.016 / % possible all: 94.09

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PO2

4po2


Resolution: 3.25→84.13 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.635
RfactorNum. reflection% reflectionSelection details
Rfree0.321 843 4.83 %RANDOM
Rwork0.297 ---
obs0.298 17437 99.7 %-
Displacement parametersBiso mean: 152.49 Å2
Baniso -1Baniso -2Baniso -3
1--15.8165 Å20 Å2-11.221 Å2
2---11.4099 Å20 Å2
3---27.2264 Å2
Refine analyzeLuzzati coordinate error obs: 0.81 Å
Refinement stepCycle: 1 / Resolution: 3.25→84.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 0 0 7012
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097088HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.129562HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2644SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1226HARMONIC5
X-RAY DIFFRACTIONt_it7088HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion11.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion976SEMIHARMONIC5
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_contact7927SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.28 Å / Total num. of bins used: 42
RfactorNum. reflection% reflection
Rfree0.2994 -4.09 %
Rwork0.2892 399 -
all0.2896 416 -
obs--90.27 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
120.0262-33.67060.2351
22.7493-16.7489-29.0483
319.6701-40.8956-36.0555
441.3168-13.138-9.2657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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