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- EMDB-76511: CryoEM structure of the 41-kDa Thermus thermophilus HSP70 nucleot... -

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Basic information

Entry
Database: EMDB / ID: EMD-76511
TitleCryoEM structure of the 41-kDa Thermus thermophilus HSP70 nucleotide-binding domain at 3.79 Angstrom resolution reveals the bound AMP-PNP and large-scale domain rearrangement
Map datafinal masked map after post processing
Sample
  • Complex: HSP70:HSP40:DafA
    • Protein or peptide: HSP70 nucleotide-binding domain
KeywordsHSP70 / nucleotide-binding domain / ATPase / chaperone
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / : / ATP binding
Similarity search - Function
Chaperone DnaK / 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
Chaperone protein DnaK
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsTang L / Jiang Y / Kalodimos CG
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CryoEM structure of the 41-kDa Thermus thermophilus HSP70 nucleotide-binding domain at 3.79 Angstrom resolution reveals the bound AMP-PNP and large-scale domain rearrangement
Authors: Tang L
History
DepositionApr 9, 2026-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76511.png

Downloads & links

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Map

FileDownload / File: emd_76511.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal masked map after post processing
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 192 pix.
= 155.52 Å		0.81 Å/pix.
x 192 pix.
= 155.52 Å		0.81 Å/pix.
x 192 pix.
= 155.52 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.09979273 - 0.14694712
Average (Standard dev.)0.00006107076 (±0.0037929635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 155.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76511_msk_1.map
Projections & Slices
AxesZYX

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Mask #2

Fileemd_76511_msk_2.map
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Half map: half map 2

Fileemd_76511_half_map_1.map
Annotationhalf map 2
Projections & Slices
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Half map: half map 1

Fileemd_76511_half_map_2.map
Annotationhalf map 1
Projections & Slices
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Sample components

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Entire : HSP70:HSP40:DafA

EntireName: HSP70:HSP40:DafA
Components
  • Complex: HSP70:HSP40:DafA
    • Protein or peptide: HSP70 nucleotide-binding domain

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Supramolecule #1: HSP70:HSP40:DafA

SupramoleculeName: HSP70:HSP40:DafA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The cryoEM map of this entry was obtained from a data set of the HSP70:HSP40:DafA ternary complex, which failed to generate the ternary complex structure due to high heterogeneity. Instead, ...Details: The cryoEM map of this entry was obtained from a data set of the HSP70:HSP40:DafA ternary complex, which failed to generate the ternary complex structure due to high heterogeneity. Instead, the cryoEM images were processed so that particles for the HSP70 nucleotide-binding domain were picked and a map was obtained.
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 40.6 KDa

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Macromolecule #1: HSP70 nucleotide-binding domain

MacromoleculeName: HSP70 nucleotide-binding domain / type: protein_or_peptide / ID: 1
Details: the N-terminal nucleotide-binding domain of heat shock protein HSP70 from Thermus thermophilus
Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKAVGIDLG TTNSVIAVLE GGKPVVLENA EGERVTPSVV AFRDGETLVG RMAKRQAVLN PEGTIFEIK RFIGRRFEEV QEEAKRVPYK VVPGPDGGVR VEVKGKLYTP EEISAMILRK L VEDASKKL GEKITKAVIT VPAYFNNAQR EATANAGRIA GLEVLRIINE ...String:
MAKAVGIDLG TTNSVIAVLE GGKPVVLENA EGERVTPSVV AFRDGETLVG RMAKRQAVLN PEGTIFEIK RFIGRRFEEV QEEAKRVPYK VVPGPDGGVR VEVKGKLYTP EEISAMILRK L VEDASKKL GEKITKAVIT VPAYFNNAQR EATANAGRIA GLEVLRIINE PTAAALAYGL DK KGNETVL VFDLGGGTFD VTILEIGEGV FEVKATSGDT HLGGSDMDHA IVNWLAEEFK KEH GVDLKA DRQALQRLIE AAEKAKIELS STLETTISLP FIALDPASKT PLHLEKKLTR AKFE ELIQP LLKRLRGPVE QALKDAGLTP AQIDEVILVG GATRVPAVQQ VVRELLGKEP NRSVN PDEV VAMGAAIQAG VLM

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

BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsArctica at 200 keV K3/BioQuantum 0.81 A/pixel 60 frames/image 40ms/frame Total dose 87.8 e-/A2
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 7680 pixel / Digitization - Dimensions - Height: 5456 pixel / Number grids imaged: 1 / Number real images: 2000 / Average exposure time: 2.4 sec. / Average electron dose: 87.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2624324
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: The initial model was generated with the Initial Model function in Relion
Final reconstructionNumber classes used: 11 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4)
Details: 3.79A resolution was based on Fourier shell correlation of masked half maps with Relion. If using corrected Fourier shell correlation, the resolution value would be 4 A. ResMap reported MEAN ...Details: 3.79A resolution was based on Fourier shell correlation of masked half maps with Relion. If using corrected Fourier shell correlation, the resolution value would be 4 A. ResMap reported MEAN RESOLUTION in MASK = 3.97 and MEDIAN RESOLUTION in MASK = 3.50. Nevertheless, maps low-pass-filtered with these resolution values show similar and consistent detailed map features.
Number images used: 158351
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationNumber classes: 20 / Avg.num./class: 8500 / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Details: the initial model was built with phenix.map_to_model
DetailsThe initial model was built with phenix.map_to_model, which covered 65% of the protein (245 out of 377 residues), followed by manual building using pdb entries 1dkg and 5oby as references and manual modeling of the bound ligand AMP-PNP.
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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