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- PDB-6rzq: Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain... -

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Basic information

Entry
Database: PDB / ID: 6rzq
TitlePlasmodium falciparum Hsp70-x chaperone nucleotide binding domain - ANP-PnP bound state
ComponentsHeat shock protein 70
KeywordsCHAPERONE / Malaria Exported chaperone Intra-erythrocytic AMP-PnP
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / AUF1 (hnRNP D0) binds and destabilizes mRNA / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / chaperone cofactor-dependent protein refolding / heat shock protein binding / protein folding chaperone / ATP-dependent protein folding chaperone / protein refolding / ATP hydrolysis activity ...Regulation of HSF1-mediated heat shock response / AUF1 (hnRNP D0) binds and destabilizes mRNA / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / chaperone cofactor-dependent protein refolding / heat shock protein binding / protein folding chaperone / ATP-dependent protein folding chaperone / protein refolding / ATP hydrolysis activity / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Defensin A-like - #30 / Defensin A-like / 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 ...Defensin A-like - #30 / Defensin A-like / 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, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock 70 kDa protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsVakonakis, I. / Day, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Medical Research Council (United Kingdom)MR/N009274/1 United Kingdom
CitationJournal: Faseb J. / Year: 2019
Title: ThePlasmodium falciparumHsp70-x chaperone assists the heat stress response of the malaria parasite.
Authors: Day, J. / Passecker, A. / Beck, H.P. / Vakonakis, I.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,45514
Polymers85,6572
Non-polymers1,79812
Water6,431357
1
A: Heat shock protein 70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8198
Polymers42,8281
Non-polymers9917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein 70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6356
Polymers42,8281
Non-polymers8075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.290, 102.710, 103.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 33 - 414 / Label seq-ID: 7 - 388

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K7NTP5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 50.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.81→43.26 Å / Num. obs: 78727 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 38.74 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Net I/σ(I): 12.65
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.523 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3870 / CC1/2: 0.72 / Rpim(I) all: 0.63 / Rrim(I) all: 1.65 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mkr

5mkr


Resolution: 1.81→37.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.71 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22403 3923 5 %RANDOM
Rwork0.19217 ---
obs0.19381 74723 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.732 Å2
Baniso -1Baniso -2Baniso -3
1--3.74 Å20 Å2-0 Å2
2--4.55 Å2-0 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.81→37.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5829 0 112 357 6298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136060
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175723
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.6498174
X-RAY DIFFRACTIONr_angle_other_deg1.2961.58813338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78423.784296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.312151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9411531
X-RAY DIFFRACTIONr_chiral_restr0.0730.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026701
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021158
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1235.1063048
X-RAY DIFFRACTIONr_mcbond_other4.1235.1043047
X-RAY DIFFRACTIONr_mcangle_it5.5237.633803
X-RAY DIFFRACTIONr_mcangle_other5.5227.6323804
X-RAY DIFFRACTIONr_scbond_it5.1185.7053012
X-RAY DIFFRACTIONr_scbond_other5.1175.7063013
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4998.2814365
X-RAY DIFFRACTIONr_long_range_B_refined9.10160.0596490
X-RAY DIFFRACTIONr_long_range_B_other9.09359.9146430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11539 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 258 -
Rwork0.378 5491 -
obs--99.74 %

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