[English] 日本語
Yorodumi
- EMDB-28766: Huntingtin C-HEAT domain in complex with HAP40 -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of cAMP-dependent protein kinase activity / : / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / negative regulation of proteasomal protein catabolic process / regulation of CAMKK-AMPK signaling cascade / positive regulation of mitophagy / profilin binding ...vesicle cytoskeletal trafficking / regulation of cAMP-dependent protein kinase activity / : / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / negative regulation of proteasomal protein catabolic process / regulation of CAMKK-AMPK signaling cascade / positive regulation of mitophagy / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / presynaptic cytosol / positive regulation of aggrephagy / positive regulation of lipophagy / dynein intermediate chain binding / postsynaptic cytosol / Golgi organization / beta-tubulin binding / establishment of mitotic spindle orientation / dynactin binding / Regulation of MECP2 expression and activity / inclusion body / heat shock protein binding / centriole / autophagosome / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / cytoplasmic vesicle membrane / kinase binding / p53 binding / late endosome / transmembrane transporter binding / early endosome / nuclear body / positive regulation of apoptotic process / axon / dendrite / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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

-
Structure visualization

Supplemental images

emd_28766.png

Downloads & links

-
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 °

-
Supplemental data

-
Mask #1

Fileemd_28766_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Additional Map

Fileemd_28766_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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)

-
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)

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more