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- EMDB-39097: Cryo-ET structure of huntingtin actin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39097
TitleCryo-ET structure of huntingtin actin complex
Map data
Sample
  • Complex: Huntingtin-Actin complex
    • Protein or peptide: Huntingtin
    • Protein or peptide: Actin, alpha skeletal muscle
KeywordsHuntington's disease / cytoskeleton / CYTOSOLIC PROTEIN / CYTOSOLIC PROTEIN-CONTRACTILE PROTEIN complex
Function / homology
Function and homology information


positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / 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 inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / 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 / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / Golgi organization / troponin I binding / filamentous actin / mesenchyme migration / dynein intermediate chain binding / establishment of mitotic spindle orientation / dynactin binding / actin filament bundle assembly / phosphoprotein phosphatase activity / skeletal muscle myofibril / striated muscle thin filament / Regulation of MECP2 expression and activity / skeletal muscle thin filament assembly / actin monomer binding / postsynaptic cytosol / beta-tubulin binding / presynaptic cytosol / skeletal muscle fiber development / stress fiber / titin binding / inclusion body / heat shock protein binding / actin filament polymerization / centriole / autophagosome / cytoplasmic vesicle membrane / negative regulation of extrinsic apoptotic signaling pathway / actin filament / filopodium / protein destabilization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinase binding / calcium-dependent protein binding / p53 binding / late endosome / lamellipodium / cell body / transmembrane transporter binding / early endosome / hydrolase activity / positive regulation of apoptotic process / axon / protein domain specific binding / apoptotic process / dendrite / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT ...Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Huntingtin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsubtomogram averaging / cryo EM / Resolution: 10.08 Å
AuthorsSong JJ
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Cryo-ET Structure of Huntingtin and Actin complex
Authors: Song JJ
History
DepositionFeb 9, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39097.png

Downloads & links

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Map

FileDownload / File: emd_39097.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.)
2.76 Å/pix.
x 160 pix.
= 441.92 Å		2.76 Å/pix.
x 160 pix.
= 441.92 Å		2.76 Å/pix.
x 160 pix.
= 441.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.762 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-0.20463535 - 0.90686774
Average (Standard dev.)0.013686844 (±0.07353659)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 441.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39097_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39097_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 : Huntingtin-Actin complex

EntireName: Huntingtin-Actin complex
Components
  • Complex: Huntingtin-Actin complex
    • Protein or peptide: Huntingtin
    • Protein or peptide: Actin, alpha skeletal muscle

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Supramolecule #1: Huntingtin-Actin complex

SupramoleculeName: Huntingtin-Actin 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: 348.128094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAMATLEKLM KAFESLKSFQ QQQQQQQQQQ QQQQQQQQQQ PPPPPPPPPP PQLPQPPPQA QPLLPQPQPP PPPPPPPPGP AVAEEPLHR PKKELSATKK DRVNHCLTIC ENIVAQSVRN SPEFQKLLGI AMELFLLCSD DAESDVRMVA DECLNKVIKA L MDSNLPRL ...String:
GAMATLEKLM KAFESLKSFQ QQQQQQQQQQ QQQQQQQQQQ PPPPPPPPPP PQLPQPPPQA QPLLPQPQPP PPPPPPPPGP AVAEEPLHR PKKELSATKK DRVNHCLTIC ENIVAQSVRN SPEFQKLLGI AMELFLLCSD DAESDVRMVA DECLNKVIKA L MDSNLPRL QLELYKEIKK NGAPRSLRAA LWRFAELAHL VRPQKCRPYL VNLLPCLTRT SKRPEESVQE TLAAAVPKIM AS FGNFAND NEIKVLLKAF IANLKSSSPT IRRTAAGSAV SICQHSRRTQ YFYSWLLNVL LGLLVPVEDE HSTLLILGVL LTL RYLVPL LQQQVKDTSL KGSFGVTRKE MEVSPSAEQL VQVYELTLHH TQHQDHNVVT GALELLQQLF RTPPPELLQT LTAV GGIGQ LTAAKEESGG RSRSGSIVEL IAGGGSSCSP VLSRKQKGKV LLGEEEALED DSESRSDVSS SALTASVKDE ISGEL AASS GVSTPGSAGH DIITEQPRSQ HTLQADSVDL ASCDLTSSAT DGDEEDILSH SSSQVSAVPS DPAMDLNDGT QASSPI SDS SQTTTEGPDS AVTPSDSSEI VLDGTDNQYL GLQIGQPQDE DEEATGILPD EASEAFRNSS MALQQAHLLK NMSHCRQ PS DSSVDKFVLR DEATEPGDQE NKPCRIKGDI GQSTDDDSAP LVHCVRLLSA SFLLTGGKNV LVPDRDVRVS VKALALSC V GAAVALHPES FFSKLYKVPL DTTEYPEEQY VSDILNYIDH GDPQVRGATA ILCGTLICSI LSRSRFHVGD WMGTIRTLT GNTFSLADCI PLLRKTLKDE SSVTCKLACT AVRNCVMSLC SSSYSELGLQ LIIDVLTLRN SSYWLVRTEL LETLAEIDFR LVSFLEAKA ENLHRGAHHY TGLLKLQERV LNNVVIHLLG DEDPRVRHVA AASLIRLVPK LFYKCDQGQA DPVVAVARDQ S SVYLKLLM HETQPPSHFS VSTITRIYRG YNLLPSITDV TMENNLSRVI AAVSHELITS TTRALTFGCC EALCLLSTAF PV CIWSLGW HCGVPPLSAS DESRKSCTVG MATMILTLLS SAWFPLDLSA HQDALILAGN LLAASAPKSL RSSWASEEEA NPA ATKQEE VWPALGDRAL VPMVEQLFSH LLKVINICAH VLDDVAPGPA IKAALPSLTN PPSLSPIRRK GKEKEPGEQA SVPL SPKKG SEASAASRQS DTSGPVTTSK SSSLGSFYHL PSYLRLHDVL KATHANYKVT LDLQNSTEKF GGFLRSALDV LSQIL ELAT LQDIGKCVEE ILGYLKSCFS REPMMATVCV QQLLKTLFGT NLASQFDGLS SNPSKSQGRA QRLGSSSVRP GLYHYC FMA PYTHFTQALA DASLRNMVQA EQENDTSGWF DVLQKVSTQL KTNLTSVTKN RADKNAIHNH IRLFEPLVIK ALKQYTT TT CVQLQKQVLD LLAQLVQLRV NYCLLDSDQV FIGFVLKQFE YIEVGQFRES EAIIPNIFFF LVLLSYERYH SKQIIGIP K IIQLCDGIMA SGRKAVTHAI PALQPIVHDL FVLRGTNKAD AGKELETQKE VVVSMLLRLI QYHQVLEMFI LVLQQCHKE NEDKWKRLSR QIADIILPML AKQQMHIDSH EALGVLNTLF EILAPSSLRP VDMLLRSMFV TPNTMASVST VQLWISGILA ILRVLISQS TEDIVLSRIQ ELSFSPYLIS CTVINRLRDG DSTSTLEEHS EGKQIKNLPE ETFSRFLLQL VGILLEDIVT K QLKVEMSE QQHTFYCQEL GTLLMCLIHI FKSGMFRRIT AAATRLFRSD GCGGSFYTLD SLNLRARSMI TTHPALVLLW CQ ILLLVNH TDYRWWAEVQ QTPKRHSLSS TKLLSPQMSG EEEDSDLAAK LGMCNREIVR RGALILFCDY VCQNLHDSEH LTW LIVNHI QDLISLSHEP PVQDFISAVH RNSAASGLFI QAIQSRCENL STPTMLKKTL QCLEGIHLSQ SGAVLTLYVD RLLC TPFRV LARMVDILAC RRVEMLLAAN LQSSMAQLPM EELNRIQEYL QSSGLAQRHQ RLYSLLDRFR LSTMQDSLSP SPPVS SHPL DGDGHVSLET VSPDKDWYVH LVKSQCWTRS DSALLEGAEL VNRIPAEDMN AFMMNSEFNL SLLAPCLSLG MSEISG GQK SALFEAAREV TLARVSGTVQ QLPAVHHVFQ PELPAEPAAY WSKLNDLFGD AALYQSLPTL ARALAQYLVV VSKLPSH LH LPPEKEKDIV KFVVATLEAL SWHLIHEQIP LSLDLQAGLD CCCLALQLPG LWSVVSSTEF VTHACSLIYC VHFILEAV A VQPGEQLLSP ERRTNTPKAI SEEEEEVDPN TQNPKYITAA CEMVAEMVES LQSVLALGHK RNSGVPAFLT PLLRNIIIS LARLPLVNSY TRVPPLVWKL GWSPKPGGDF GTAFPEIPVE FLQEKEVFKE FIYRINTLGW TSRTQFEETW ATLLGVLVTQ PLVMEQEES PPEEDTERTQ INVLAVQAIT SLVLSAMTVP VAGNPAVSCL EQQPRNKPLK ALDTRFGRKL SIIRGIVEQE I QAMVSKRE NIATHHLYQA WDPVPSLSPA TTGALISHEK LLLQINPERE LGSMSYKLGQ VSIHSVWLGN SITPLREEEW DE EEEEEAD APAPSSPPTS PVNSRKHRAG VDIHSCSQFL LELYSRWILP SSSARRTPAI LISEVVRSLL VVSDLFTERN QFE LMYVTL TELRRVHPSE DEILAQYLVP ATCKAAAVLG MDKAVAEPVS RLLESTLRSS HLPSRVGALH GVLYVLECDL LDDT AKQLI PVISDYLLSN LKGIAHCVNI HSQQHVLVMC ATAFYLIENY PLDVGPEFSA SIIQMCGVML SGSEESTPSI IYHCA LRGL ERLLLSEQLS RLDAESLVKL SVDRVNVHSP HRAMAALGLM LTCMYTGKEK VSPGRTSDPN PAAPDSESVI VAMERV SVL FDRIRKGFPC EARVVARILP QFLDDFFPPQ DIMNKVIGEF LSNQQPYPQF MATVVYKVFQ TLHSTGQSSM VRDWVML SL SNFTQRAPVA MATWSLSCFF VSASTSPWVA AILPHVISRM GKLEQVDVNL FCLVATDFYR HQIEEELDRR AFQSVLEV V AAPGSPYHRL LTCLRNVHKV TTC

UniProtKB: Huntingtin

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.862613 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 170.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 22664
ExtractionNumber tomograms: 42 / Number images used: 84019
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8yae:
Cryo-ET structure of huntingtin actin complex

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