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- EMDB-28766: Huntingtin C-HEAT domain in complex with HAP40 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-28766
TitleHuntingtin C-HEAT domain in complex with HAP40
Map dataSharpened map used for modelling
Sample
  • Complex: Full-length Huntingtin-HAP40 complex from subdomain fragments
    • Protein or peptide: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein
KeywordsScaffold protein / HTT / Huntingtin / HAP40 / Huntingtin-associated protein 40 kDa / STRUCTURAL PROTEIN
Function / homology
Function and homology information


vesicle cytoskeletal trafficking / : / positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / negative regulation of proteasomal protein catabolic process / positive regulation of mitophagy / regulation of CAMKK-AMPK signaling cascade / profilin binding / positive regulation of cilium assembly ...vesicle cytoskeletal trafficking / : / positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / negative regulation of proteasomal protein catabolic process / positive regulation of mitophagy / regulation of CAMKK-AMPK signaling cascade / profilin binding / positive regulation of cilium assembly / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / vesicle transport along microtubule / positive regulation of aggrephagy / positive regulation of lipophagy / Golgi organization / dynein intermediate chain binding / establishment of mitotic spindle orientation / dynactin binding / phosphoprotein phosphatase activity / Regulation of MECP2 expression and activity / postsynaptic cytosol / beta-tubulin binding / presynaptic cytosol / heat shock protein binding / inclusion body / centriole / autophagosome / cytoplasmic vesicle membrane / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / kinase binding / p53 binding / late endosome / transmembrane transporter binding / early endosome / nuclear body / positive regulation of apoptotic process / axon / apoptotic process / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Factor VIII intron 22 protein / Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 ...Factor VIII intron 22 protein / Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
40-kDa huntingtin-associated protein / Huntingtin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHarding RJ / Deme JC / Alteen MG / Arrowsmith CH / Lea SM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Other government
Other private
CitationJournal: Biorxiv / Year: 2022
Title: Expanding the Huntingtons disease research toolbox; validated huntingtin subdomain constructs for biochemical and structural investigation of the huntingtin protein
Authors: Alteen MG / Deme JC / Alvarez CP / Loppnau P / Hutchinson A / Seitova A / Chandrasekaran R / Silva Ramos E / Secker C / Alqazzaz M / Wanker EE / Lea SM / Arrowsmith CH / Harding RJ
History
DepositionNov 3, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28766.png

Downloads & links

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Map

FileDownload / File: emd_28766.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map used for modelling
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 288 pix.
= 233.28 Å		0.81 Å/pix.
x 288 pix.
= 233.28 Å		0.81 Å/pix.
x 288 pix.
= 233.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.49
Minimum - Maximum-2.9018176 - 4.7637725
Average (Standard dev.)-0.008127706 (±0.12979236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 233.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28766_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map

Fileemd_28766_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_28766_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_28766_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full-length Huntingtin-HAP40 complex from subdomain fragments

EntireName: Full-length Huntingtin-HAP40 complex from subdomain fragments
Components
  • Complex: Full-length Huntingtin-HAP40 complex from subdomain fragments
    • Protein or peptide: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein

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Supramolecule #1: Full-length Huntingtin-HAP40 complex from subdomain fragments

SupramoleculeName: Full-length Huntingtin-HAP40 complex from subdomain fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 390 KDa

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Macromolecule #1: Huntingtin

MacromoleculeName: Huntingtin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MVSPDKDWYV HLVKSQCWTR SDSALLEGAE LVNRIPAEDM NAFMMNSEFN LSLLAPCLSL GMSEISGGQK SALFEAAREV TLARVSGTVQ QLPAVHHVFQ PELPAEPAAY WSKLNDLFGD AALYQSLPTL ARALAQYLVV VSKLPSHLHL PPEKEKDIVK FVVATLEALS ...String:
MVSPDKDWYV HLVKSQCWTR SDSALLEGAE LVNRIPAEDM NAFMMNSEFN LSLLAPCLSL GMSEISGGQK SALFEAAREV TLARVSGTVQ QLPAVHHVFQ PELPAEPAAY WSKLNDLFGD AALYQSLPTL ARALAQYLVV VSKLPSHLHL PPEKEKDIVK FVVATLEALS WHLIHEQIPL SLDLQAGLDC CCLALQLPGL WSVVSSTEFV THACSLIHCV HFILEAVAVQ PGEQLLSPER RTNTPKAISE EEEEVDPNTQ NPKYITAACE MVAEMVESLQ SVLALGHKRN SGVPAFLTPL LRNIIISLAR LPLVNSYTRV PPLVWKLGWS PKPGGDFGTA FPEIPVEFLQ EKEVFKEFIY RINTLGWTSR TQFEETWATL LGVLVTQPLV MEQEESPPEE DTERTQINVL AVQAITSLVL SAMTVPVAGN PAVSCLEQQP RNKPLKALDT RFGRKLSIIR GIVEQEIQAM VSKRENIATH HLYQAWDPVP SLSPATTGAL ISHEKLLLQI NPERELGSMS YKLGQVSIHS VWLGNSITPL REEEWDEEEE EEADAPAPSS PPTSPVNSRK HRAGVDIHSC SQFLLELYSR WILPSSSARR TPAILISEVV RSLLVVSDLF TERNQFELMY VTLTELRRVH PSEDEILAQY LVPATCKAAA VLGMDKAVAE PVSRLLESTL RSSHLPSRVG ALHGILYVLE CDLLDDTAKQ LIPVISDYLL SNLKGIAHCV NIHSQQHVLV MCATAFYLIE NYPLDVGPEF SASIIQMCGV MLSGSEESTP SIIYHCALRG LERLLLSEQL SRLDAESLVK LSVDRVNVHS PHRAMAALGL MLTCMYTGKE KVSPGRTSDP NPAAPDSESV IVAMERVSVL FDRIRKGFPC EARVVARILP QFLDDFFPPQ DIMNKVIGEF LSNQQPYPQF MATVVYKVFQ TLHSTGQSSM VRDWVMLSLS NFTQRAPVAM ATWSLSCFFV SASTSPWVAA ILPHVISRMG KLEQVDVNLF CLVATDFYRH QIEEELDRRA FQSVLEVVAA PGSPYHRLLT CLRNVGGSGD YKDDDDK

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Macromolecule #2: 40-kDa huntingtin-associated protein

MacromoleculeName: 40-kDa huntingtin-associated protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHSSG RENLYFQGMA AAAAGLGGGG AGPGPEAGDF LARYRLVSNK LKKRFLRKPN VAEAGEQFGQ LGRELRAQEC LPYAAWCQLA VARCQQALFH GPGEALALTE AARLFLRQER DARQRLVCPA AYGEPLQAAA SALGAAVRLH LELGQPAAAA ALCLELAAAL ...String:
MHHHHHHSSG RENLYFQGMA AAAAGLGGGG AGPGPEAGDF LARYRLVSNK LKKRFLRKPN VAEAGEQFGQ LGRELRAQEC LPYAAWCQLA VARCQQALFH GPGEALALTE AARLFLRQER DARQRLVCPA AYGEPLQAAA SALGAAVRLH LELGQPAAAA ALCLELAAAL RDLGQPAAAA GHFQRAAQLQ LPQLPLAALQ ALGEAASCQL LARDYTGALA VFTRMQRLAR EHGSHPVQSL PPPPPPAPQP GPGATPALPA ALLPPNSGSA APSPAALGAF SDVLVRCEVS RVLLLLLLQP PPAKLLPEHA QTLEKYSWEA FDSHGQESSG QLPEELFLLL QSLVMATHEK DTEAIKSLQV EMWPLLTAEQ NHLLHLVLQE TISPSGQGV

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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: 7.4
Component:
ConcentrationFormulaName
300.0 mMNaClSodium chloride
25.0 mMHEPES
0.025 % (v/v)CHAPS
1.0 mMDTT
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.4 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6x9o

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134849
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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