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- EMDB-4937: Cryo-EM 3D map of normal Huntingtin -

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Basic information

Entry
Database: EMDB / ID: EMD-4937
TitleCryo-EM 3D map of normal Huntingtin
Map data
Sample
  • Organelle or cellular component: normal-type human huntingtin
    • Protein or peptide: Huntingtin
Keywordsmultivalent scaffold platform / PROTEIN BINDING
Function / homology
Function and homology information


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 / regulation of CAMKK-AMPK signaling cascade / positive regulation of mitophagy / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly ...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 / 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 / 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
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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsJung T / Tamo G
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2016-K1A1A2912057 Korea, Republic Of
National Research Foundation (NRF, Korea)2016R1A2B3006293 Korea, Republic Of
CitationJournal: Structure / Year: 2020
Title: The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain.
Authors: Taeyang Jung / Baehyun Shin / Giorgio Tamo / Hyeongju Kim / Ravi Vijayvargia / Alexander Leitner / Maria J Marcaida / Juan Astorga-Wells / Roy Jung / Ruedi Aebersold / Matteo Dal Peraro / ...Authors: Taeyang Jung / Baehyun Shin / Giorgio Tamo / Hyeongju Kim / Ravi Vijayvargia / Alexander Leitner / Maria J Marcaida / Juan Astorga-Wells / Roy Jung / Ruedi Aebersold / Matteo Dal Peraro / Hans Hebert / Ihn Sik Seong / Ji-Joon Song /
Abstract: The polyQ expansion in huntingtin protein (HTT) is the prime cause of Huntington's disease (HD). The recent cryoelectron microscopy (cryo-EM) structure of HTT-HAP40 complex provided the structural ...The polyQ expansion in huntingtin protein (HTT) is the prime cause of Huntington's disease (HD). The recent cryoelectron microscopy (cryo-EM) structure of HTT-HAP40 complex provided the structural information on its HEAT-repeat domains. Here, we present analyses of the impact of polyQ length on the structure and function of HTT via an integrative structural and biochemical approach. The cryo-EM analysis of normal (Q23) and disease (Q78) type HTTs shows that the structures of apo HTTs significantly differ from the structure of HTT in a HAP40 complex and that the polyQ expansion induces global structural changes in the relative movements among the HTT domains. In addition, we show that the polyQ expansion alters the phosphorylation pattern across HTT and that Ser2116 phosphorylation in turn affects the global structure and function of HTT. These results provide a molecular basis for the effect of the polyQ segment on HTT structure and activity, which may be important for HTT pathology.
History
DepositionMay 6, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseJun 3, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0117
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0117
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rmh
  • Surface level: 0.0117
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4937.png

Downloads & links

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Map

FileDownload / File: emd_4937.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0117 / Movie #1: 0.0117
Minimum - Maximum-0.0037352745 - 0.03649042
Average (Standard dev.)0.0003055958 (±0.0030137054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 265.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z265.000265.000265.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0040.0360.000

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Supplemental data

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Sample components

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Entire : normal-type human huntingtin

EntireName: normal-type human huntingtin
Components
  • Organelle or cellular component: normal-type human huntingtin
    • Protein or peptide: Huntingtin

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Supramolecule #1: normal-type human huntingtin

SupramoleculeName: normal-type human huntingtin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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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: 347.974906 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATLEKLMKA FESLKSFQQQ QQQQQQQQQQ QQQQQQQQPP PPPPPPPPPQ LPQPPPQAQP LLPQPQPPPP PPPPPPGPAV AEEPLHRPK KELSATKKDR VNHCLTICEN IVAQSVRNSP EFQKLLGIAM ELFLLCSDDA ESDVRMVADE CLNKVIKALM D SNLPRLQL ...String:
MATLEKLMKA FESLKSFQQQ QQQQQQQQQQ QQQQQQQQPP PPPPPPPPPQ LPQPPPQAQP LLPQPQPPPP PPPPPPGPAV AEEPLHRPK KELSATKKDR VNHCLTICEN IVAQSVRNSP EFQKLLGIAM ELFLLCSDDA ESDVRMVADE CLNKVIKALM D SNLPRLQL ELYKEIKKNG APRSLRAALW RFAELAHLVR PQKCRPYLVN LLPCLTRTSK RPEESVQETL AAAVPKIMAS FG NFANDNE IKVLLKAFIA NLKSSSPTIR RTAAGSAVSI CQHSRRTQYF YSWLLNVLLG LLVPVEDEHS TLLILGVLLT LRY LVPLLQ QQVKDTSLKG SFGVTRKEME VSPSAEQLVQ VYELTLHHTQ HQDHNVVTGA LELLQQLFRT PPPELLQTLT AVGG IGQLT AAKEESGGRS RSGSIVELIA GGGSSCSPVL SRKQKGKVLL GEEEALEDDS ESRSDVSSSA LTASVKDEIS GELAA SSGV STPGSAGHDI ITEQPRSQHT LQADSVDLAS CDLTSSATDG DEEDILSHSS SQVSAVPSDP AMDLNDGTQA SSPISD SSQ TTTEGPDSAV TPSDSSEIVL DGTDNQYLGL QIGQPQDEDE EATGILPDEA SEAFRNSSMA LQQAHLLKNM SHCRQPS DS SVDKFVLRDE ATEPGDQENK PCRIKGDIGQ STDDDSAPLV HCVRLLSASF LLTGGKNVLV PDRDVRVSVK ALALSCVG A AVALHPESFF SKLYKVPLDT TEYPEEQYVS DILNYIDHGD PQVRGATAIL CGTLICSILS RSRFHVGDWM GTIRTLTGN TFSLADCIPL LRKTLKDESS VTCKLACTAV RNCVMSLCSS SYSELGLQLI IDVLTLRNSS YWLVRTELLE TLAEIDFRLV SFLEAKAEN LHRGAHHYTG LLKLQERVLN NVVIHLLGDE DPRVRHVAAA SLIRLVPKLF YKCDQGQADP VVAVARDQSS V YLKLLMHE TQPPSHFSVS TITRIYRGYN LLPSITDVTM ENNLSRVIAA VSHELITSTT RALTFGCCEA LCLLSTAFPV CI WSLGWHC GVPPLSASDE SRKSCTVGMA TMILTLLSSA WFPLDLSAHQ DALILAGNLL AASAPKSLRS SWASEEEANP AAT KQEEVW PALGDRALVP MVEQLFSHLL KVINICAHVL DDVAPGPAIK AALPSLTNPP SLSPIRRKGK EKEPGEQASV PLSP KKGSE ASAASRQSDT SGPVTTSKSS SLGSFYHLPS YLRLHDVLKA THANYKVTLD LQNSTEKFGG FLRSALDVLS QILEL ATLQ DIGKCVEEIL GYLKSCFSRE PMMATVCVQQ LLKTLFGTNL ASQFDGLSSN PSKSQGRAQR LGSSSVRPGL YHYCFM APY THFTQALADA SLRNMVQAEQ ENDTSGWFDV LQKVSTQLKT NLTSVTKNRA DKNAIHNHIR LFEPLVIKAL KQYTTTT CV QLQKQVLDLL AQLVQLRVNY CLLDSDQVFI GFVLKQFEYI EVGQFRESEA IIPNIFFFLV LLSYERYHSK QIIGIPKI I QLCDGIMASG RKAVTHAIPA LQPIVHDLFV LRGTNKADAG KELETQKEVV VSMLLRLIQY HQVLEMFILV LQQCHKENE DKWKRLSRQI ADIILPMLAK QQMHIDSHEA LGVLNTLFEI LAPSSLRPVD MLLRSMFVTP NTMASVSTVQ LWISGILAIL RVLISQSTE DIVLSRIQEL SFSPYLISCT VINRLRDGDS TSTLEEHSEG KQIKNLPEET FSRFLLQLVG ILLEDIVTKQ L KVEMSEQQ HTFYCQELGT LLMCLIHIFK SGMFRRITAA ATRLFRSDGC GGSFYTLDSL NLRARSMITT HPALVLLWCQ IL LLVNHTD YRWWAEVQQT PKRHSLSSTK LLSPQMSGEE EDSDLAAKLG MCNREIVRRG ALILFCDYVC QNLHDSEHLT WLI VNHIQD LISLSHEPPV QDFISAVHRN SAASGLFIQA IQSRCENLST PTMLKKTLQC LEGIHLSQSG AVLTLYVDRL LCTP FRVLA RMVDILACRR VEMLLAANLQ SSMAQLPMEE LNRIQEYLQS SGLAQRHQRL YSLLDRFRLS TMQDSLSPSP PVSSH PLDG DGHVSLETVS PDKDWYVHLV KSQCWTRSDS ALLEGAELVN RIPAEDMNAF MMNSEFNLSL LAPCLSLGMS EISGGQ KSA LFEAAREVTL ARVSGTVQQL PAVHHVFQPE LPAEPAAYWS KLNDLFGDAA LYQSLPTLAR ALAQYLVVVS KLPSHLH LP PEKEKDIVKF VVATLEALSW HLIHEQIPLS LDLQAGLDCC CLALQLPGLW SVVSSTEFVT HACSLIHCVH FILEAVAV Q PGEQLLSPER RTNTPKAISE EEEEVDPNTQ NPKYITAACE MVAEMVESLQ SVLALGHKRN SGVPAFLTPL LRNIIISLA RLPLVNSYTR VPPLVWKLGW SPKPGGDFGT AFPEIPVEFL QEKEVFKEFI YRINTLGWTS RTQFEETWAT LLGVLVTQPL VMEQEESPP EEDTERTQIN VLAVQAITSL VLSAMTVPVA GNPAVSCLEQ QPRNKPLKAL DTRFGRKLSI IRGIVEQEIQ A MVSKRENI ATHHLYQAWD PVPSLSPATT GALISHEKLL LQINPERELG SMSYKLGQVS IHSVWLGNSI TPLREEEWDE EE EEEADAP APSSPPTSPV NSRKHRAGVD IHSCSQFLLE LYSRWILPSS SARRTPAILI SEVVRSLLVV SDLFTERNQF ELM YVTLTE LRRVHPSEDE ILAQYLVPAT CKAAAVLGMD KAVAEPVSRL LESTLRSSHL PSRVGALHGV LYVLECDLLD DTAK QLIPV ISDYLLSNLK GIAHCVNIHS QQHVLVMCAT AFYLIENYPL DVGPEFSASI IQMCGVMLSG SEESTPSIIY HCALR GLER LLLSEQLSRL DAESLVKLSV DRVNVHSPHR AMAALGLMLT CMYTGKEKVS PGRTSDPNPA APDSESVIVA MERVSV LFD RIRKGFPCEA RVVARILPQF LDDFFPPQDI MNKVIGEFLS NQQPYPQFMA TVVYKVFQTL HSTGQSSMVR DWVMLSL SN FTQRAPVAMA TWSLSCFFVS ASTSPWVAAI LPHVISRMGK LEQVDVNLFC LVATDFYRHQ IEEELDRRAF QSVLEVVA A PGSPYHRLLT CLRNVHKVTT C

UniProtKB: Huntingtin

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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

Concentration0.06 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK I / Details: blot 9 seconds incubate 30 seconds.
DetailsHTT was mixed with final 0.05% of Octyl glucoside.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-40 / Number real images: 2331 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.0 µm / Calibrated magnification: 47170 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.4 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

6ez8

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 20825
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1 / Avg.num./class: 20825 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ez8


Chain - Chain ID: A / Chain - Residue range: 91-3198 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Overall B value: 800 / Target criteria: CC=0.88
Output model

PDB-6rmh:
The Rigid-body refined model of the normal Huntingtin.

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