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- EMDB-43715: HTT in complex with HAP40 in the apo state. -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-43715
TitleHTT in complex with HAP40 in the apo state.
Map data
Sample
  • Complex: HTT and HAP40 complex
    • Protein or peptide: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein
KeywordsHuntington's Disease / neurodegenerative disease / UNKNOWN FUNCTION
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 / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / presynaptic cytosol / 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: 2.72 Å
AuthorsPoweleit N / Boudet J / Doherty E
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Discovery of a Small Molecule Ligand to the Huntingtin/HAP40 complex
Authors: Poweleit N / Boudet J / Doherty E
History
DepositionFeb 15, 2024-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43715.png

Downloads & links

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Map

FileDownload / File: emd_43715.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.46023434 - 1.1786351
Average (Standard dev.)0.00022835458 (±0.045129005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43715_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43715_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 : HTT and HAP40 complex

EntireName: HTT and HAP40 complex
Components
  • Complex: HTT and HAP40 complex
    • Protein or peptide: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein

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Supramolecule #1: HTT and HAP40 complex

SupramoleculeName: HTT and HAP40 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Huntingtin

MacromoleculeName: Huntingtin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 353.493656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATLEKLMKA FESLKSFQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQPPPPP PPPPPPQLPQ PPPQAQPLL PQPQPPPPPP PPPPGPAVAE EPLHRPKKEL SATKKDRVNH CLTICENIVA QSVRNSPEFQ KLLGIAMELF L LCSDDAES ...String:
MATLEKLMKA FESLKSFQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQPPPPP PPPPPPQLPQ PPPQAQPLL PQPQPPPPPP PPPPGPAVAE EPLHRPKKEL SATKKDRVNH CLTICENIVA QSVRNSPEFQ KLLGIAMELF L LCSDDAES DVRMVADECL NKVIKALMDS NLPRLQLELY KEIKKNGAPR SLRAALWRFA ELAHLVRPQK CRPYLVNLLP CL TRTSKRP EESVQETLAA AVPKIMASFG NFANDNEIKV LLKAFIANLK SSSPTIRRTA AGSAVSICQH SRRTQYFYSW LLN VLLGLL VPVEDEHSTL LILGVLLTLR YLVPLLQQQV KDTSLKGSFG VTRKEMEVSP SAEQLVQVYE LTLHHTQHQD HNVV TGALE LLQQLFRTPP PELLQTLTAV GGIGQLTAAK EESGGRSRSG SIVELIAGGG SSCSPVLSRK QKGKVLLGEE EALED DSES RSDVSSSALT ASVKDEISGE LAASSGVSTP GSAGHDIITE QPRSQHTLQA DSVDLASCDL TSSATDGDEE DILSHS SSQ VSAVPSDPAM DLNDGTQASS PISDSSQTTT EGPDSAVTPS DSSEIVLDGT DNQYLGLQIG QPQDEDEEAT GILPDEA SE AFRNSSMALQ QAHLLKNMSH CRQPSDSSVD KFVLRDEATE PGDQENKPCR IKGDIGQSTD DDSAPLVHCV RLLSASFL L TGGKNVLVPD RDVRVSVKAL ALSCVGAAVA LHPESFFSKL YKVPLDTTEY PEEQYVSDIL NYIDHGDPQV RGATAILCG TLICSILSRS RFHVGDWMGT IRTLTGNTFS LADCIPLLRK TLKDESSVTC KLACTAVRNC VMSLCSSSYS ELGLQLIIDV LTLRNSSYW LVRTELLETL AEIDFRLVSF LEAKAENLHR GAHHYTGLLK LQERVLNNVV IHLLGDEDPR VRHVAAASLI R LVPKLFYK CDQGQADPVV AVARDQSSVY LKLLMHETQP PSHFSVSTIT RIYRGYNLLP SITDVTMENN LSRVIAAVSH EL ITSTTRA LTFGCCEALC LLSTAFPVCI WSLGWHCGVP PLSASDESRK SCTVGMATMI LTLLSSAWFP LDLSAHQDAL ILA GNLLAA SAPKSLRSSW ASEEEANPAA TKQEEVWPAL GDRALVPMVE QLFSHLLKVI NICAHVLDDV APGPAIKAAL PSLT NPPSL SPIRRKGKEK EPGEQASVPL SPKKGSEASA ASRQSDTSGP VTTSKSSSLG SFYHLPSYLK LHDVLKATHA NYKVT LDLQ NSTEKFGGFL RSALDVLSQI LELATLQDIG KCVEEILGYL KSCFSREPMM ATVCVQQLLK TLFGTNLASQ FDGLSS NPS KSQGRAQRLG SSSVRPGLYH YCFMAPYTHF TQALADASLR NMVQAEQEND TSGWFDVLQK VSTQLKTNLT SVTKNRA DK NAIHNHIRLF EPLVIKALKQ YTTTTCVQLQ KQVLDLLAQL VQLRVNYCLL DSDQVFIGFV LKQFEYIEVG QFRESEAI I PNIFFFLVLL SYERYHSKQI IGIPKIIQLC DGIMASGRKA VTHAIPALQP IVHDLFVLRG TNKADAGKEL ETQKEVVVS MLLRLIQYHQ VLEMFILVLQ QCHKENEDKW KRLSRQIADI ILPMLAKQQM HIDSHEALGV LNTLFEILAP SSLRPVDMLL RSMFVTPNT MASVSTVQLW ISGILAILRV LISQSTEDIV LSRIQELSFS PYLISCTVIN RLRDGDSTST LEEHSEGKQI K NLPEETFS RFLLQLVGIL LEDIVTKQLK VEMSEQQHTF YCQELGTLLM CLIHIFKSGM FRRITAAATR LFRSDGCGGS FY TLDSLNL RARSMITTHP ALVLLWCQIL LLVNHTDYRW WAEVQQTPKR HSLSSTKLLS PQMSGEEEDS DLAAKLGMCN REI VRRGAL ILFCDYVCQN LHDSEHLTWL IVNHIQDLIS LSHEPPVQDF ISAVHRNSAA SGLFIQAIQS RCENLSTPTM LKKT LQCLE GIHLSQSGAV LTLYVDRLLC TPFRVLARMV DILACRRVEM LLAANLQSSM AQLPMEELNR IQEYLQSSGL AQRHQ RLYS LLDRFRLSTM QDSLSPSPPV SSHPLDGDGH VSLETVSPDK DWYVHLVKSQ CWTRSDSALL EGAELVNRIP AEDMNA FMM NSEFNLSLLA PCLSLGMSEI SGGQKSALFE AAREVTLARV SGTVQQLPAV HHVFQPELPA EPAAYWSKLN DLFGDAA LY QSLPTLARAL AQYLVVVSKL PSHLHLPPEK EKDIVKFVVA TLEALSWHLI HEQIPLSLDL QAGLDCCCLA LQLPGLWS V VSSTEFVTHA CSLIYCVHFI LEAVAVQPGE QLLSPERRTN TPKAISEEEE EVDPNTQNPK YITAACEMVA EMVESLQSV LALGHKRNSG VPAFLTPLLR NIIISLARLP LVNSYTRVPP LVWKLGWSPK PGGDFGTAFP EIPVEFLQEK EVFKEFIYRI NTLGWTSRT QFEETWATLL GVLVTQPLVM EQEESPPEED TERTQINVLA VQAITSLVLS AMTVPVAGNP AVSCLEQQPR N KPLKALDT RFGRKLSIIR GIVEQEIQAM VSKRENIATH HLYQAWDPVP SLSPATTGAL ISHEKLLLQI NPERELGSMS YK LGQVSIH SVWLGNSITP LREEEWDEEE EEEADAPAPS SPPTSPVNSR KHRAGVDIHS CSQFLLELYS RWILPSSSAR RTP AILISE VVRSLLVVSD LFTERNQFEL MYVTLTELRR VHPSEDEILA QYLVPATCKA AAVLGMDKAV AEPVSRLLES TLRS SHLPS RVGALHGVLY VLECDLLDDT AKQLIPVISD YLLSNLKGIA HCVNIHSQQH VLVMCATAFY LIENYPLDVG PEFSA SIIQ MCGVMLSGSE ESTPSIIYHC ALRGLERLLL SEQLSRLDAE SLVKLSVDRV NVHSPHRAMA ALGLMLTCMY TGKEKV SPG RTSDPNPAAP DSESVIVAME RVSVLFDRIR KGFPCEARVV ARILPQFLDD FFPPQDIMNK VIGEFLSNQQ PYPQFMA TV VYKVFQTLHS TGQSSMVRDW VMLSLSNFTQ RAPVAMATWS LSCFFVSAST SPWVAAILPH VISRMGKLEQ VDVNLFCL V ATDFYRHQIE EELDRRAFQS VLEVVAAPGS PYHRLLTCLR NVHKVTTCAA AENLYFQGDY KDDDDK

UniProtKB: Huntingtin

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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: 41.342254 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHSSG RENLYFQGMA AAAAGLGGGG AGPGPEAGDF LARYRLVSNK LKKRFLRKPN VAEAGEQFGQ LGRELRAQEC LPYAAWCQL AVARCQQALF HGPGEALALT EAARLFLRQE RDARQRLVCP AAYGEPLQAA ASALGAAVRL HLELGQPAAA A ALCLELAA ...String:
MHHHHHHSSG RENLYFQGMA AAAAGLGGGG AGPGPEAGDF LARYRLVSNK LKKRFLRKPN VAEAGEQFGQ LGRELRAQEC LPYAAWCQL AVARCQQALF HGPGEALALT EAARLFLRQE RDARQRLVCP AAYGEPLQAA ASALGAAVRL HLELGQPAAA A ALCLELAA ALRDLGQPAA AAGHFQRAAQ LQLPQLPLAA LQALGEAASC QLLARDYTGA LAVFTRMQRL AREHGSHPVQ SL PPPPPPA PQPGPGATPA LPAALLPPNS GSAAPSPAAL GAFSDVLVRC EVSRVLLLLL LQPPPAKLLP EHAQTLEKYS WEA FDSHGQ ESSGQLPEEL FLLLQSLVMA THEKDTEAIK SLQVEMWPLL TAEQNHLLHL VLQETISPSG QGV

UniProtKB: 40-kDa huntingtin-associated protein

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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
Details: 25 mM Hepes, 300 mM NaCl, 0.025%CHAPS, 1mM DTT, 1% DMSO
GridModel: Quantifoil R2/4 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6788 / Average exposure time: 1.4 sec. / Average electron dose: 50.48 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4700000
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 352043

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8w15:
HTT in complex with HAP40 in the apo state.

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