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- PDB-9dvi: Hetero-hexameric Hsp70-Hsp40-DafA complex -

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Basic information

Entry
Database: PDB / ID: 9dvi
TitleHetero-hexameric Hsp70-Hsp40-DafA complex
Components
  • Chaperone protein DnaJ 2
  • Chaperone protein DnaK
  • Protein DafA
KeywordsCHAPERONE / Hsp70 / Hsp40 / protein folding
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / DNA replication / ATP binding / cytoplasm
Similarity search - Function
MerR HTH family regulatory protein / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Chaperone DnaK / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / Putative DNA-binding domain superfamily / DnaJ molecular chaperone homology domain ...MerR HTH family regulatory protein / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Chaperone DnaK / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / Putative DNA-binding domain superfamily / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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 / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Protein DafA / Chaperone protein DnaK / Chaperone protein DnaJ 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsIbrahim, Z. / Kalodimos, C.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentNIH grant R35 GM12246 United States
Other privateALSAC United States
CitationJournal: To Be Published
Title: hetero-hexameric Hsp70-Hsp40-DafA complex
Authors: Ibrahim, Z. / Kalodimos, C.
History
DepositionOct 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein DnaJ 2
B: Chaperone protein DnaK
C: Chaperone protein DnaJ 2
D: Chaperone protein DnaK
S: Protein DafA
T: Protein DafA


Theoretical massNumber of molelcules
Total (without water)216,8036
Polymers216,8036
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Chaperone protein DnaJ 2


Mass: 31023.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: dnaJ2, TthHB5018_15880 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7R7YIH9
#2: Protein Chaperone protein DnaK / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 66915.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: dnaK, TthHB5018_15900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7R7TFM0
#3: Protein Protein DafA


Mass: 10463.015 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: dafA, TthAA11_16070, TthHB5018_15870 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A510INE8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: hetero-hexameric Hsp70-Hsp40-DafA complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermus thermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 77.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175874 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029160
ELECTRON MICROSCOPYf_angle_d0.60312399
ELECTRON MICROSCOPYf_dihedral_angle_d4.9061281
ELECTRON MICROSCOPYf_chiral_restr0.0441366
ELECTRON MICROSCOPYf_plane_restr0.0051659

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