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- EMDB-14706: 3D reconstruction of the cylindrical assembly of DnaJA2 delta G/F... -

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Basic information

Entry
Database: EMDB / ID: EMD-14706
Title3D reconstruction of the cylindrical assembly of DnaJA2 delta G/F without symmetry imposition
Map data
Sample
  • Complex: Oligomeric structure of DnaJA2 delta G/F
    • Protein or peptide: DnaJA2 delta G/F
Keywordsoligomer / helix / filaments / holdase / foldase / Hsp40 / Hsp70 co-chaperone / CHAPERONE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.2 Å
AuthorsCuellar J / Velasco-Carneros L / Santiago C / Martin-Benito J / Muga A / Valpuesta JM
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-105872GB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-111068GB-I00 Spain
CitationJournal: Nat Commun / Year: 2023
Title: The self-association equilibrium of DNAJA2 regulates its interaction with unfolded substrate proteins and with Hsc70.
Authors: Lorea Velasco-Carneros / Jorge Cuéllar / Leire Dublang / César Santiago / Jean-Didier Maréchal / Jaime Martín-Benito / Moisés Maestro / José Ángel Fernández-Higuero / Natalia Orozco ...Authors: Lorea Velasco-Carneros / Jorge Cuéllar / Leire Dublang / César Santiago / Jean-Didier Maréchal / Jaime Martín-Benito / Moisés Maestro / José Ángel Fernández-Higuero / Natalia Orozco / Fernando Moro / José María Valpuesta / Arturo Muga /
Abstract: J-domain proteins tune the specificity of Hsp70s, engaging them in precise functions. Despite their essential role, the structure and function of many J-domain proteins remain largely unknown. We ...J-domain proteins tune the specificity of Hsp70s, engaging them in precise functions. Despite their essential role, the structure and function of many J-domain proteins remain largely unknown. We explore human DNAJA2, finding that it reversibly forms highly-ordered, tubular structures that can be dissociated by Hsc70, the constitutively expressed Hsp70 isoform. Cryoelectron microscopy and mutational studies reveal that different domains are involved in self-association. Oligomer dissociation into dimers potentiates its interaction with unfolded client proteins. The J-domains are accessible to Hsc70 within the tubular structure. They allow binding of closely spaced Hsc70 molecules that could be transferred to the unfolded substrate for its cooperative remodelling, explaining the efficient recovery of DNAJA2-bound clients. The disordered C-terminal domain, comprising the last 52 residues, regulates its holding activity and productive interaction with Hsc70. These in vitro findings suggest that the association equilibrium of DNAJA2 could regulate its interaction with client proteins and Hsc70.
History
DepositionApr 2, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14706.png

Downloads & links

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Map

FileDownload / File: emd_14706.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.43 Å
Density
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.002399181 - 0.02611526
Average (Standard dev.)0.0011633327 (±0.0029541827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 314.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_14706_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14706_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Oligomeric structure of DnaJA2 delta G/F

EntireName: Oligomeric structure of DnaJA2 delta G/F
Components
  • Complex: Oligomeric structure of DnaJA2 delta G/F
    • Protein or peptide: DnaJA2 delta G/F

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Supramolecule #1: Oligomeric structure of DnaJA2 delta G/F

SupramoleculeName: Oligomeric structure of DnaJA2 delta G/F / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DnaJA2 delta G/F

MacromoleculeName: DnaJA2 delta G/F / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANVADTKLY DILGVPPGAS ENELKKAYRK LAKEYHPDKN PNAGDKFKEI SFAYEVLSNP EKRELYDRY GEQGLREGNQ SRSRNGRRRG EDMMHPL KV SLEDLYNGKT TKLQLSKNVL CSACSGQGGK SGAVQKCSAC RGRGVRIMIR QLAPGMVQ Q MQSVCSDCNG ...String:
MANVADTKLY DILGVPPGAS ENELKKAYRK LAKEYHPDKN PNAGDKFKEI SFAYEVLSNP EKRELYDRY GEQGLREGNQ SRSRNGRRRG EDMMHPL KV SLEDLYNGKT TKLQLSKNVL CSACSGQGGK SGAVQKCSAC RGRGVRIMIR QLAPGMVQ Q MQSVCSDCNG EGEVINEKDR CKKCEGKKVI KEVKILEVHV DKGMKHGQRI TFTGEADQA PGVEPGDIVL LLQEKEHEVF QRDGNDLHMT YKIGLVEALC GFQFTFKHLD GRQIVVKYPP GKVIEPGCV RVVRGEGMPQ YRNPFEKGDL YIKFDVQFPE NNWINPDKLS ELEDLLPSRP E VPNIIGET EEVELQEFDS TRGSGGGQRR EAYNDSSDEE SSSHHGPGVQ CAHQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsPreliminary grid screening was performed manually
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 10714 / Average exposure time: 2.0 sec. / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 288620
Startup modelType of model: INSILICO MODEL
In silico model: Some of the best 2D classes were used as a template to generate an initial model using RANSAC
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 47396

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