[English] 日本語
Yorodumi
- PDB-7p31: Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p31
TitlePlasmodium falciparum Hsp70-x chaperone nucleotide binding domain in complex with NCL-00023818
ComponentsHeat shock protein 70
KeywordsCHAPERONE / MALARIA EXPORTED CHAPERONE INTRA-ERYTHROCYTIC AMP-PNP / CHAPE
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
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
AMP PHOSPHORAMIDATE / IODIDE ION / PHOSPHATE ION / 4-IODOPYRAZOLE / Heat shock 70 kDa protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structures of the Plasmodium falciparum heat-shock protein 70-x ATPase domain in complex with chemical fragments identify conserved and unique binding sites.
Authors: Mohamad, N. / O'Donoghue, A. / Kantsadi, A.L. / Vakonakis, I.
History
DepositionJul 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 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
SupersessionSep 25, 2024ID: 7OOH
Revision 1.2Sep 25, 2024Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_PDB_obs_spr / pdbx_database_related
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 / _pdbx_database_related.content_type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,03218
Polymers85,6572
Non-polymers2,37516
Water2,306128
1
A: Heat shock protein 70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,08510
Polymers42,8281
Non-polymers1,2579
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein 70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9478
Polymers42,8281
Non-polymers1,1187
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.979, 102.575, 103.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K7NTP5

-
Non-polymers , 8 types, 144 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PYZ / 4-IODOPYRAZOLE


Mass: 193.974 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H3IN2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.52 %
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

-
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 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.36→79.98 Å / Num. obs: 35843 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 63.81 Å2 / CC1/2: 1 / Rrim(I) all: 0.13 / Net I/σ(I): 8
Reflection shellResolution: 2.36→2.4 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1745 / CC1/2: 0.5 / Rrim(I) all: 2.176 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (24-FEB-2021)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZQ

6rzq


Resolution: 2.36→72.97 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.379 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.38 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.229
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 1773 4.96 %RANDOM
Rwork0.2199 ---
obs0.2206 35772 99.9 %-
Displacement parametersBiso mean: 85.96 Å2
Baniso -1Baniso -2Baniso -3
1-11.6545 Å20 Å20 Å2
2---17.1539 Å20 Å2
3---5.4993 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.36→72.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5834 0 136 128 6098
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086049HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.978148HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2177SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1026HARMONIC5
X-RAY DIFFRACTIONt_it6049HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion16.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion812SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4688SEMIHARMONIC4
LS refinement shellResolution: 2.36→2.38 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3643 -3.91 %
Rwork0.3367 688 -
all0.3377 716 -
obs--97.47 %
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)
11.6987-0.2004-0.43171.37880.55721.4620.0329-0.0604-0.27440.05050.1062-0.10010.10720.0787-0.1392-0.7754-0.01180.0259-0.54320.0409-0.60530.156377.175954.6943
24.7055-0.6427-1.05252.88670.47993.95310.12220.99740.6028-0.4208-0.06410.0073-0.9997-0.5194-0.0581-0.44420.11440.017-0.48980.0484-0.631647.53475.160314.8315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more