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- EMDB-47203: Hetero-hexameric Hsp70-Hsp40-DafA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-47203
TitleHetero-hexameric Hsp70-Hsp40-DafA complex
Map data
Sample
  • Complex: hetero-hexameric Hsp70-Hsp40-DafA complex
    • Protein or peptide: Hsp70-Hsp40-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 / Chaperone protein DnaK
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsIbrahim Z / Kalodimos C
Funding support United States, 2 items
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 7, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47203.png

Downloads & links

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Map

FileDownload / File: emd_47203.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 256 pix.
= 422.912 Å		1.65 Å/pix.
x 256 pix.
= 422.912 Å		1.65 Å/pix.
x 256 pix.
= 422.912 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.116
Minimum - Maximum-3.337662 - 3.7853384
Average (Standard dev.)0.0018860322 (±0.054438893)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47203_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47203_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47203_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : hetero-hexameric Hsp70-Hsp40-DafA complex

EntireName: hetero-hexameric Hsp70-Hsp40-DafA complex
Components
  • Complex: hetero-hexameric Hsp70-Hsp40-DafA complex
    • Protein or peptide: Hsp70-Hsp40-DafA

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Supramolecule #1: hetero-hexameric Hsp70-Hsp40-DafA complex

SupramoleculeName: hetero-hexameric Hsp70-Hsp40-DafA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: it is a heterohexameric complex containing two copies of each of the chaperone proteins: Hsp70, Hsp40 and DafA
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 211.1 KDa

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Macromolecule #1: Hsp70-Hsp40-DafA

MacromoleculeName: Hsp70-Hsp40-DafA / type: protein_or_peptide / ID: 1
Details: it is a heterohexameric complex containing two copies of each of the proteins: Hsp70, Hsp40 and DafA
Enantiomer: DEXTRO
Source (natural)Organism: Thermus thermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKAVGIDLG TTNSVIAVLE GGKPVVLENA EGERVTPSVV AFRDGETLVG RMAKRQAVLN PEGTIFEIKR FIGRRFEEVQ EEAKRVPYKV VPGPDGGVRV EVKGKLYTPE EISAMILRKL VEDASKKLGE KITKAVITVP AYFNNAQREA TANAGRIAGL EVLRIINEPT ...String:
MAKAVGIDLG TTNSVIAVLE GGKPVVLENA EGERVTPSVV AFRDGETLVG RMAKRQAVLN PEGTIFEIKR FIGRRFEEVQ EEAKRVPYKV VPGPDGGVRV EVKGKLYTPE EISAMILRKL VEDASKKLGE KITKAVITVP AYFNNAQREA TANAGRIAGL EVLRIINEPT AAALAYGLDK KGNETVLVFD LGGGTFDVTI LEIGEGVFEV KATSGDTHLG GSDMDHAIVN WLAEEFKKEH GVDLKADRQA LQRLIEAAEK AKIELSSTLE TTISLPFIAL DPASKTPLHL EKKLTRAKFE ELIQPLLKRL RGPVEQALKD AGLTPAQIDE VILVGGATRV PAVQQVVREL LGKEPNRSVN PDEVVAMGAA IQAGVLMGEV RDVVLLDVTP LSLGVETKGG VMTVLIPRNT TIPTRKCEIF TTAEHNQTAV EIHVLQGERP MAQDNKSLGR FRLEGIPPMP AGVPQIEVCF DIDANGILHV TAKERSTGRE ASITIQNTTT LSEEEIQRII EEAKRHAEED RRRREHAELK NALDSARVQA ERVLQERQGA PEARARLEAA IGKAKELVER DAPDPELKAA TEELLKAVEE YEKGAQAASG KGPDDVIDAD YKPAD MAAK KDYYAILGVP RNATQEEIKR AYKRLARQYH PDVNKSPEAE EKFKEINEAY AVLSDPEKRR IYDTYGTTEA PPPPPPGGYD FSGFDVEDFS EFFQELFGPG LFGGFGRRSR KGRDLRAELP LTLEEAFHGG ERVVEVAGRR VSVRIPPGVR EGSVIRVPGM GGQGNPPGDL LLVVRLLPHP VFRLEGQDLY ATLDVPAPIA VVGGKVRAMT LEGPVEVAVP PRTQAGRKLR LKGKGFPGPA GRGDLYLEVR ITIPERLTPE EEALWKKLAE AYYARA MLA RSGWLSLEAL SEYGLSLAAV RAYVEIGFVE PLEVGGAWYF REEDLLRMAK AERIRKDLGA NLIGAALVVE ILERT

UniProtKB: Chaperone protein DnaK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 50 mM HEPES, 75 mM NaCl at pH 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsGradient Fixation method was used to stabilize the Hsp70-Hsp40-DafA complex for single particle cryoEM

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 77.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 175874
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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