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- EMDB-28767: Full-length Huntingtin-HAP40 complex from subdomain fragments -

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Basic information

Entry
Database: EMDB / ID: EMD-28767
TitleFull-length Huntingtin-HAP40 complex from subdomain fragments
Map dataSharpened map used for modelling
Sample
  • Complex: Full-length Huntingtin-HAP40 complex from subdomain fragments
    • Protein or peptide: Huntingtin
    • Protein or peptide: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein
KeywordsScaffold protein / HTT / Huntingtin / HAP40 / Huntingtin-associated protein 40 kDa / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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

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Structure visualization

Supplemental images

emd_28767.png

Downloads & links

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Map

FileDownload / File: emd_28767.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-1.973562 - 2.8791296
Average (Standard dev.)0.005420622 (±0.10471574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 233.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28767_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map

Fileemd_28767_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_28767_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_28767_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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: Huntingtin
    • Protein or peptide: 40-kDa huntingtin-associated protein

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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

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Macromolecule #1: Huntingtin

MacromoleculeName: Huntingtin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTKKDRVNHC LTICENIVAQ SVRNSPEFQK LLGIAMELFL LCSDDAESDV RMVADECLNK VIKALMDSNL PRLQLELYKE IKKNGAPRSL RAALWRFAEL AHLVRPQKCR PYLVNLLPCL TRTSKRPEES VQETLAAAVP KIMASFGNFA NDNEIKVLLK AFIANLKSSS ...String:
MTKKDRVNHC LTICENIVAQ SVRNSPEFQK LLGIAMELFL LCSDDAESDV RMVADECLNK VIKALMDSNL PRLQLELYKE IKKNGAPRSL RAALWRFAEL AHLVRPQKCR PYLVNLLPCL TRTSKRPEES VQETLAAAVP KIMASFGNFA NDNEIKVLLK AFIANLKSSS PTIRRTAAGS AVSICQHSRR TQYFYSWLLN VLLGLLVPVE DEHSTLLILG VLLTLRYLVP LLQQQVKDTS LKGSFGVTRK EMEVSPSAEQ LVQVYELTLH HTQHQDHNVV TGALELLQQL FRTPPPELLQ TLTAVGGIGQ LTAAKEESGG RSRSGSIVEL IAGGGSSCSP VLSRKQKGKV LLGEEEALED DSESRSDVSS SALTASVKDE ISGELAASSG VSTPGSAGHD IITEQPRSQH TLQADSVDLA SCDLTSSATD GDEEDILSHS SSQVSAVPSD PAMDLNDGTQ ASSPISDSSQ TTTEGPDSAV TPSDSSEIVL DGTDNQYLGL QIGQPQDEDE EATGILPDEA SEAFRNSSMA LQQAHLLKNM SHCRQPSDSS VDKFVLRDEA TEPGDQENKP CRIKGDIGQS TDDDSAPLVH CVRLLSASFL LTGGKNVLVP DRDVRVSVKA LALSCVGAAV ALHPESFFSK LYKVPLDTTE YPEEQYVSDI LNYIDHGDPQ VRGATAILCG TLICSILSRS RFHVGDWMGT IRTLTGNTFS LADCIPLLRK TLKDESSVTC KLACTAVRNC VMSLCSSSYS ELGLQLIIDV LTLRNSSYWL VRTELLETLA EIDFRLVSFL EAKAENLHRG AHHYTGLLKL QERVLNNVVI HLLGDEDPRV RHVAAASLIR LVPKLFYKCD QGQADPVVAV ARDQSSVYLK LLMHETQPPS HFSVSTITRI YRGYNLLPSI TDVTMENNLS RVIAAVSHEL ITSTTRALTF GCCEALCLLS TAFPVCIWSL GWHCGVPPLS ASDESRKSCT VGMATMILTL LSSAWFPLDL SAHQDALILA GNLLAASAPK SLRSSWASEE EANPAATKQE EVWPALGDRA LVPMVEQLFS HLLKVINICA HVLDDVAPGP AIKAALPSLT NPPSLSPIRR KGKEKEPGEQ ASVPLSPKKG SEASAASRQS DTSGPVTTSK SSSLGSFYHL PSYLKLHDVL KATHANYKVT LDLQNSTEKF GGFLRSALDV LSQILELATL QDIGKCVEEI LGYLKSCFSR EPMMATVCVQ QLLKTLFGTN LASQFDGLSS NPSKSQGRAQ RLGSSSVRPG LYHYCFMAPY THFTQALADA SLRNMVQAEQ ENDTSGWFDV LQKVSTQLKT NLTSVTKNRA DKNAIHNHIR LFEPLVIKAL KQYTTTTCVQ LQKQVLDLLA QLVQLRVNYC LLDSDQVFIG FVLKQFEYIE VGQFRESEAI IPNIFFFLVL LSYERYHSKQ IIGIPKIIQL CDGIMASGRK AVTHAIPALQ PIVHDLFVLR GTNKADAGKE LETQKEVVVS MLLRLIQYHQ VLEMFILVLQ QCHKENEDKW KRLSRQIADI ILPMLAKQQM HIDSHEALGV LNTLFEILAP SSLRPVDMLL RSMFVTPNTM ASVSTVQLWI SGILAILRVL ISQSTEDIVL SRIQELSFSP YLISCTVINR LRDGDSTSTL EEHSEGKQIK NLPEETFSRF LLQLVGILLE DIVTKQLKVE MSEQQHTFYC QELGTLLMCL IHIFKSGMFR RITAAATRLF RSDGCGGSFY TLDSLNLRAR SMITTHPALV LLWCQILLLV NHTDYRWWAE VQQTPKRHSL SSTKLLSPQM SGEEEDSDLA AKLGMCNREI VRRGALILFC DYVCQNLHDS EHLTWLIVNH IQDLISLSHE PPVQDFISAV HRNSAASGLF IQAIQSRCEN LSTPTMLKKT LQCLEGIHLS QSGAVLTLYV DRLLCTPFRV LARMVDILAC RRVEMLLAAN LQSSMAQLPM EELNRIQEYL QSSGLAQRHQ RLYSLLDRFR LSTMGGSGDY KDDDDK

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Macromolecule #2: Huntingtin

MacromoleculeName: Huntingtin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

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Macromolecule #3: 40-kDa huntingtin-associated protein

MacromoleculeName: 40-kDa huntingtin-associated protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

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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
Component:
ConcentrationFormulaName
300.0 mMNaClSodium chloride
25.0 mMHEPES
0.025 % (v/v)CHAPS
1.0 mMDTT
VitrificationCryogen name: ETHANE

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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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6x9o

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64597
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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