[English] 日本語
Yorodumi
- EMDB-30911: Human 46QHuntingtin-HAP40 complex structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30911
TitleHuman 46QHuntingtin-HAP40 complex structure
Map dataHuman 46QHuntingtin-HAP40 complex structure
Sample
  • Complex: Human 46QHuntingtin-HAP40 complex structure
    • Protein or peptide: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein
Function / homology
Function and homology information


vesicle cytoskeletal trafficking / regulation of cAMP-dependent protein kinase activity / regulation of phosphoprotein phosphatase activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / regulation of CAMKK-AMPK signaling cascade / negative regulation of proteasomal protein catabolic process / positive regulation of mitophagy / profilin binding ...vesicle cytoskeletal trafficking / regulation of cAMP-dependent protein kinase activity / regulation of phosphoprotein phosphatase activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / regulation of CAMKK-AMPK signaling cascade / negative regulation of proteasomal protein catabolic process / positive regulation of mitophagy / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly / presynaptic cytosol / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / positive regulation of aggrephagy / postsynaptic cytosol / positive regulation of lipophagy / dynein intermediate chain binding / beta-tubulin binding / Golgi organization / dynactin binding / establishment of mitotic spindle orientation / Regulation of MECP2 expression and activity / autophagosome / inclusion body / heat shock protein binding / centriole / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / cytoplasmic vesicle membrane / kinase binding / p53 binding / late endosome / transmembrane transporter binding / nuclear body / early endosome / 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: 3.6 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 6, 2021-
Current statusOct 6, 2021Processing 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-7dxj
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30911.png

Downloads & links

-
Map

FileDownload / File: emd_30911.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman 46QHuntingtin-HAP40 complex structure
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.36667737 - 0.5486653
Average (Standard dev.)5.1469153e-05 (±0.018514901)
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-0.3670.5490.000

-
Supplemental data

-
Sample components

-
Entire : Human 46QHuntingtin-HAP40 complex structure

EntireName: Human 46QHuntingtin-HAP40 complex structure
Components
  • Complex: Human 46QHuntingtin-HAP40 complex structure
    • Protein or peptide: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein

-
Supramolecule #1: Human 46QHuntingtin-HAP40 complex structure

SupramoleculeName: Human 46QHuntingtin-HAP40 complex structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)

-
Macromolecule #1: Huntingtin

MacromoleculeName: Huntingtin / type: protein_or_peptide / ID: 1 / Details: 46Q-Huntingtin / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 351.191312 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MATLEKLMKA FESLKSFQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQPPPPPPP PPPPQLPQPP PQAQPLLPQ PQPPPPPPPP PPGPAVAEEP LHRPKKELSA TKKDRVNHCL TICENIVAQS VRNSPEFQKL LGIAMELFLL C SDDAESDV ...String:
MATLEKLMKA FESLKSFQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQPPPPPPP PPPPQLPQPP PQAQPLLPQ PQPPPPPPPP PPGPAVAEEP LHRPKKELSA TKKDRVNHCL TICENIVAQS VRNSPEFQKL LGIAMELFLL C SDDAESDV RMVADECLNK VIKALMDSNL PRLQLELYKE IKKNGAPRSL RAALWRFAEL AHLVRPQKCR PYLVNLLPCL TR TSKRPEE SVQETLAAAV PKIMASFGNF ANDNEIKVLL KAFIANLKSS SPTIRRTAAG SAVSICQHSR RTQYFYSWLL NVL LGLLVP VEDEHSTLLI LGVLLTLRYL VPLLQQQVKD TSLKGSFGVT RKEMEVSPSA EQLVQVYELT LHHTQHQDHN VVTG ALELL QQLFRTPPPE LLQTLTAVGG IGQLTAAKEE SGGRSRSGSI VELIAGGGSS CSPVLSRKQK GKVLLGEEEA LEDDS ESRS DVSSSALTAS VKDEISGELA ASSGVSTPGS AGHDIITEQP RSQHTLQADS VDLASCDLTS SATDGDEEDI LSHSSS QVS AVPSDPAMDL NDGTQASSPI SDSSQTTTEG PDSAVTPSDS SEIVLDGTDN QYLGLQIGQP QDEDEEATGI LPDEASE AF RNSSMALQQA HLLKNMSHCR QPSDSSVDKF VLRDEATEPG DQENKPCRIK GDIGQSTDDD SAPLVHCVRL LSASFLLT G GKNVLVPDRD VRVSVKALAL SCVGAAVALH PESFFSKLYK VPLDTTEYPE EQYVSDILNY IDHGDPQVRG ATAILCGTL ICSILSRSRF HVGDWMGTIR TLTGNTFSLA DCIPLLRKTL KDESSVTCKL ACTAVRNCVM SLCSSSYSEL GLQLIIDVLT LRNSSYWLV RTELLETLAE IDFRLVSFLE AKAENLHRGA HHYTGLLKLQ ERVLNNVVIH LLGDEDPRVR HVAAASLIRL V PKLFYKCD QGQADPVVAV ARDQSSVYLK LLMHETQPPS HFSVSTITRI YRGYNLLPSI TDVTMENNLS RVIAAVSHEL IT STTRALT FGCCEALCLL STAFPVCIWS LGWHCGVPPL SASDESRKSC TVGMATMILT LLSSAWFPLD LSAHQDALIL AGN LLAASA PKSLRSSWAS EEEANPAATK QEEVWPALGD RALVPMVEQL FSHLLKVINI CAHVLDDVAP GPAIKAALPS LTNP PSLSP IRRKGKEKEP GEQASVPLSP KKGSEASAAS RQSDTSGPVT TSKSSSLGSF YHLPSYLRLH DVLKATHANY KVTLD LQNS TEKFGGFLRS ALDVLSQILE LATLQDIGKC VEEILGYLKS CFSREPMMAT VCVQQLLKTL FGTNLASQFD GLSSNP SKS QGRAQRLGSS SVRPGLYHYC FMAPYTHFTQ ALADASLRNM VQAEQENDTS GWFDVLQKVS TQLKTNLTSV TKNRADK NA IHNHIRLFEP LVIKALKQYT TTTCVQLQKQ VLDLLAQLVQ LRVNYCLLDS DQVFIGFVLK QFEYIEVGQF RESEAIIP N IFFFLVLLSY ERYHSKQIIG IPKIIQLCDG IMASGRKAVT HAIPALQPIV HDLFVLRGTN KADAGKELET QKEVVVSML LRLIQYHQVL EMFILVLQQC HKENEDKWKR LSRQIADIIL PMLAKQQMHI DSHEALGVLN TLFEILAPSS LRPVDMLLRS MFVTPNTMA SVSTVQLWIS GILAILRVLI SQSTEDIVLS RIQELSFSPY LISCTVINRL RDGDSNSTLE EHSEGKQIKN L PEETFSRF LLQLVGILLE DIVTKQLKVE MSEQQHTFYC QELGTLLMCL IHIFKSGMFR RITAAATRLF RSDGCGGSFY TL DSLNLRA RSMITTHPAL VLLWCQILLL VNHTDYRWWA EVQQTPKRHS LSSTKLLSPQ MSGEEEDSDL AAKLGMCNRE IVR RGALIL FCDYVCQNLH DSEHLTWLIV NHIQDLISLS HEPPVQDFIS AVHRNSAASG LFIQAIQSRC ENLSTPTMLK KTLQ CLEGI HLSQSGAVLT LYVDRLLCTP FRVLARMVDI LACRRVEMLL AANLQSSMAQ LPMEELNRIQ EYLQSSGLAQ RHQRL YSLL DRFRLSTMQD SLSPSPPVSS HPLDGDGHVS LETVSPDKDW YVHLVKSQCW TRSDSALLEG AELVNRIPAE DMNAFM MNS EFNLSLLAPC LSLGMSEISG GQKSALFEAA REVTLARVSG TVQQLPAVHH VFQPELPAEP AAYWSKLNDL FGDAALY QS LPTLARALAQ YLVVVSKLPS HLHLPPEKEK DIVKFVVATL EALSWHLIHE QIPLSLDLQA GLDCCCLALQ LPGLWSVV S STEFVTHACS LIHCVHFILE AVAVQPGEQL LSPERRTNTP KAISEEEEEV DPNTQNPKYI TAACEMVAEM VESLQSVLA LGHKRNSGVP AFLTPLLRNI IISLARLPLV NSYTRVPPLV WKLGWSPKPG GDFGTAFPEI PVEFLQEKEV FKEFIYRINT LGWTSRTQF EETWATLLGV LVTQPLVMEQ EESPPEEDTE RTQINVLAVQ AITSLVLSAM TVPVAGNPAV SCLEQQPRNK P LKALDTRF GRKLSIIRGI VEQEIQAMVS KRENIATHHL YQAWDPVPSL SPATTGALIS HEKLLLQINP ERELGSMSYK LG QVSIHSV WLGNSITPLR EEEWDEEEEE EADAPAPSSP PTSPVNSRKH RAGVDIHSCS QFLLELYSRW ILPSSSARRT PAI LISEVV RSLLVVSDLF TERNQFELMY VTLTELRRVH PSEDEILAQY LVPATCKAAA VLGMDKAVAE PVSRLLESTL RSSH LPSRV GALHGVLYVL ECDLLDDTAK QLIPVISDYL LSNLKGIAHC VNIHSQQHVL VMCATAFYLI ENYPLDVGPE FSASI IQMC GVMLSGSEES TPSIIYHCAL RGLERLLLSE QLSRLDAESL VKLSVDRVNV HSPHRAMAAL GLMLTCMYTG KEKVSP GRT SDPNPAAPDS ESVIVAMERV SVLFDRIRKG FPCEARVVAR ILPQFLDDFF PPQDIMNKVI GEFLSNQQPY PQFMATV VY KVFQTLHSTG QSSMVRDWVM LSLSNFTQRA PVAMATWSLS CFFVSASTSP WVAAILPHVI SRMGKLEQVD VNLFCLVA T DFYRHQIEEE LDRRAFQSVL EVVAAPGSPY HRLLTCLRNV HKVTTC

-
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

-
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 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

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

-
Image processing

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192473

+
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