[English] 日本語
Yorodumi
- EMDB-30912: Human 128QHuntingtin-HAP40 complex structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30912
TitleHuman 128QHuntingtin-HAP40 complex structure
Map data
Sample
  • Complex: Human 128QHuntingtin-HAP40 complex structure
    • Protein or peptide: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein
KeywordsHuntingtin / 128Q / HAP40 / 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 / cytoplasmic vesicle membrane / protein destabilization / 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: 4.1 Å
AuthorsGuo Q / Fernandez-Busnadiego R
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)412854449 Germany
European CommissionERC-2012-SyG 318987-ToPAGEuropean Union
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
German Research Foundation (DFG)STE 2517/1-1 Germany
CitationJournal: Structure / Year: 2021
Title: Pathological polyQ expansion does not alter the conformation of the Huntingtin-HAP40 complex.
Authors: Bin Huang / Qiang Guo / Marie L Niedermeier / Jingdong Cheng / Tatjana Engler / Melanie Maurer / Alexander Pautsch / Wolfgang Baumeister / Florian Stengel / Stefan Kochanek / Rubén Fernández-Busnadiego /
Abstract: The abnormal amplification of a CAG repeat in the gene coding for huntingtin (HTT) leads to Huntington's disease (HD). At the protein level, this translates into the expansion of a polyglutamine ...The abnormal amplification of a CAG repeat in the gene coding for huntingtin (HTT) leads to Huntington's disease (HD). At the protein level, this translates into the expansion of a polyglutamine (polyQ) stretch located at the HTT N terminus, which renders HTT aggregation prone by unknown mechanisms. Here we investigated the effects of polyQ expansion on HTT in a complex with its stabilizing interaction partner huntingtin-associated protein 40 (HAP40). Surprisingly, our comprehensive biophysical, crosslinking mass spectrometry and cryo-EM experiments revealed no major differences in the conformation of HTT-HAP40 complexes of various polyQ length, including 17QHTT-HAP40 (wild type), 46QHTT-HAP40 (typical polyQ length in HD patients), and 128QHTT-HAP40 (extreme polyQ length). Thus, HTT polyQ expansion does not alter the global conformation of HTT when associated with HAP40.
History
DepositionJan 19, 2021-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7dxk
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30912.png

Downloads & links

-
Map

FileDownload / File: emd_30912.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 160 pix.
= 216. Å		1.35 Å/pix.
x 160 pix.
= 216. Å		1.35 Å/pix.
x 160 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.24996099 - 0.41230744
Average (Standard dev.)0.0012422163 (±0.016350696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.2500.4120.001

-
Supplemental data

-
Sample components

-
Entire : Human 128QHuntingtin-HAP40 complex structure

EntireName: Human 128QHuntingtin-HAP40 complex structure
Components
  • Complex: Human 128QHuntingtin-HAP40 complex structure
    • Protein or peptide: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein

-
Supramolecule #1: Human 128QHuntingtin-HAP40 complex structure

SupramoleculeName: Human 128QHuntingtin-HAP40 complex structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Huntingtin

MacromoleculeName: Huntingtin / type: protein_or_peptide / ID: 1 / Details: 128Q-Huntingtin / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 361.698406 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MATLEKLMKA FESLKSFQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQPPPP PPPPPPPQLP Q PPPQAQPL ...String:
MATLEKLMKA FESLKSFQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQPPPP PPPPPPPQLP Q PPPQAQPL LPQPQPPPPP PPPPPGPAVA EEPLHRPKKE LSATKKDRVN HCLTICENIV AQSVRNSPEF QKLLGIAMEL FL LCSDDAE SDVRMVADEC LNKVIKALMD SNLPRLQLEL YKEIKKNGAP RSLRAALWRF AELAHLVRPQ KCRPYLVNLL PCL TRTSKR PEESVQETLA AAVPKIMASF GNFANDNEIK VLLKAFIANL KSSSPTIRRT AAGSAVSICQ HSRRTQYFYS WLLN VLLGL LVPVEDEHST LLILGVLLTL RYLVPLLQQQ VKDTSLKGSF GVTRKEMEVS PSAEQLVQVY ELTLHHTQHQ DHNVV TGAL ELLQQLFRTP PPELLQTLTA VGGIGQLTAA KEESGGRSRS GSIVELIAGG GSSCSPVLSR KQKGKVLLGE EEALED DSE SRSDVSSSAL TASVKDEISG ELAASSGVST PGSAGHDIIT EQPRSQHTLQ ADSVDLASCD LTSSATDGDE EDILSHS SS QVSAVPSDPA MDLNDGTQAS SPISDSSQTT TEGPDSAVTP SDSSEIVLDG TDNQYLGLQI GQPQDEDEEA TGILPDEA S EAFRNSSMAL QQAHLLKNMS HCRQPSDSSV DKFVLRDEAT EPGDQENKPC RIKGDIGQST DDDSAPLVHC VRLLSASFL LTGGKNVLVP DRDVRVSVKA LALSCVGAAV ALHPESFFSK LYKVPLDTTE YPEEQYVSDI LNYIDHGDPQ VRGATAILCG TLICSILSR SRFHVGDWMG TIRTLTGNTF SLADCIPLLR KTLKDESSVT CKLACTAVRN CVMSLCSSSY SELGLQLIID V LTLRNSSY WLVRTELLET LAEIDFRLVS FLEAKAENLH RGAHHYTGLL KLQERVLNNV VIHLLGDEDP RVRHVAAASL IR LVPKLFY KCDQGQADPV VAVARDQSSV YLKLLMHETQ PPSHFSVSTI TRIYRGYNLL PSITDVTMEN NLSRVIAAVS HEL ITSTTR ALTFGCCEAL CLLSTAFPVC IWSLGWHCGV PPLSASDESR KSCTVGMATM ILTLLSSAWF PLDLSAHQDA LILA GNLLA ASAPKSLRSS WASEEEANPA ATKQEEVWPA LGDRALVPMV EQLFSHLLKV INICAHVLDD VAPGPAIKAA LPSLT NPPS LSPIRRKGKE KEPGEQASVP LSPKKGSEAS AASRQSDTSG PVTTSKSSSL GSFYHLPSYL RLHDVLKATH ANYKVT LDL QNSTEKFGGF LRSALDVLSQ ILELATLQDI GKCVEEILGY LKSCFSREPM MATVCVQQLL KTLFGTNLAS QFDGLSS NP SKSQGRAQRL GSSSVRPGLY HYCFMAPYTH FTQALADASL RNMVQAEQEN DTSGWFDVLQ KVSTQLKTNL TSVTKNRA D KNAIHNHIRL FEPLVIKALK QYTTTTCVQL QKQVLDLLAQ LVQLRVNYCL LDSDQVFIGF VLKQFEYIEV GQFRESEAI IPNIFFFLVL LSYERYHSKQ IIGIPKIIQL CDGIMASGRK AVTHAIPALQ PIVHDLFVLR GTNKADAGKE LETQKEVVVS MLLRLIQYH QVLEMFILVL QQCHKENEDK WKRLSRQIAD IILPMLAKQQ MHIDSHEALG VLNTLFEILA PSSLRPVDML L RSMFVTPN TMASVSTVQL WISGILAILR VLISQSTEDI VLSRIQELSF SPYLISCTVI NRLRDGDSNS TLEEHSEGKQ IK NLPEETF SRFLLQLVGI LLEDIVTKQL KVEMSEQQHT FYCQELGTLL MCLIHIFKSG MFRRITAAAT RLFRSDGCGG SFY TLDSLN LRARSMITTH PALVLLWCQI LLLVNHTDYR WWAEVQQTPK RHSLSSTKLL SPQMSGEEED SDLAAKLGMC NREI VRRGA LILFCDYVCQ NLHDSEHLTW LIVNHIQDLI SLSHEPPVQD FISAVHRNSA ASGLFIQAIQ SRCENLSTPT MLKKT LQCL EGIHLSQSGA VLTLYVDRLL CTPFRVLARM VDILACRRVE MLLAANLQSS MAQLPMEELN RIQEYLQSSG LAQRHQ RLY SLLDRFRLST MQDSLSPSPP VSSHPLDGDG HVSLETVSPD KDWYVHLVKS QCWTRSDSAL LEGAELVNRI PAEDMNA FM MNSEFNLSLL APCLSLGMSE ISGGQKSALF EAAREVTLAR VSGTVQQLPA VHHVFQPELP AEPAAYWSKL NDLFGDAA L YQSLPTLARA LAQYLVVVSK LPSHLHLPPE KEKDIVKFVV ATLEALSWHL IHEQIPLSLD LQAGLDCCCL ALQLPGLWS VVSSTEFVTH ACSLIHCVHF ILEAVAVQPG EQLLSPERRT NTPKAISEEE EEVDPNTQNP KYITAACEMV AEMVESLQSV LALGHKRNS GVPAFLTPLL RNIIISLARL PLVNSYTRVP PLVWKLGWSP KPGGDFGTAF PEIPVEFLQE KEVFKEFIYR I NTLGWTSR TQFEETWATL LGVLVTQPLV MEQEESPPEE DTERTQINVL AVQAITSLVL SAMTVPVAGN PAVSCLEQQP RN KPLKALD TRFGRKLSII RGIVEQEIQA MVSKRENIAT HHLYQAWDPV PSLSPATTGA LISHEKLLLQ INPERELGSM SYK LGQVSI HSVWLGNSIT PLREEEWDEE EEEEADAPAP SSPPTSPVNS RKHRAGVDIH SCSQFLLELY SRWILPSSSA RRTP AILIS EVVRSLLVVS DLFTERNQFE LMYVTLTELR RVHPSEDEIL AQYLVPATCK AAAVLGMDKA VAEPVSRLLE STLRS SHLP SRVGALHGVL YVLECDLLDD TAKQLIPVIS DYLLSNLKGI AHCVNIHSQQ HVLVMCATAF YLIENYPLDV GPEFSA SII QMCGVMLSGS EESTPSIIYH CALRGLERLL LSEQLSRLDA ESLVKLSVDR VNVHSPHRAM AALGLMLTCM YTGKEKV SP GRTSDPNPAA PDSESVIVAM ERVSVLFDRI RKGFPCEARV VARILPQFLD DFFPPQDIMN KVIGEFLSNQ QPYPQFMA T VVYKVFQTLH STGQSSMVRD WVMLSLSNFT QRAPVAMATW SLSCFFVSAS TSPWVAAILP HVISRMGKLE QVDVNLFCL VATDFYRHQI EEELDRRAFQ SVLEVVAAPG SPYHRLLTCL RNVHKVTTC

UniProtKB: Huntingtin, Huntingtin

-
Macromolecule #2: 40-kDa huntingtin-associated protein

MacromoleculeName: 40-kDa huntingtin-associated protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.141879 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MAAAAAGLGG GGAGPGPEAG DFLARYRLVS NKLKKRFLRK PNVAEAGEQF GQLGRELRAQ ECLPYAAWCQ LAVARCQQAL FHGPGEALA LTEAARLFLR QERDARQRLV CPAAYGEPLQ AAASALGAAV RLHLELGQPA AAAALCLELA AALRDLGQPA A AAGHFQRA ...String:
MAAAAAGLGG GGAGPGPEAG DFLARYRLVS NKLKKRFLRK PNVAEAGEQF GQLGRELRAQ ECLPYAAWCQ LAVARCQQAL FHGPGEALA LTEAARLFLR QERDARQRLV CPAAYGEPLQ AAASALGAAV RLHLELGQPA AAAALCLELA AALRDLGQPA A AAGHFQRA AQLQLPQLPL AALQALGEAA SCQLLARDYT GALAVFTRMQ RLAREHGSHP VQSLPPPPPP APQPGPGATP AL PAALLPP NSGSAAPSPA ALGAFSDVLV RCEVSRVLLL LLLQPPPAKL LPEHAQTLEK YSWEAFDSHG QESSGQLPEE LFL LLQSLV MATHEKDTEA IKSLQVEMWP LLTAEQNHLL HLVLQETISP SGQGV

UniProtKB: 40-kDa huntingtin-associated protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil / Material: GOLD / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 122992
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

+
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