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- EMDB-3984: Human Huntingtin-HAP40 complex structure -

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Basic information

Entry
Database: EMDB / ID: 3984
TitleHuman Huntingtin-HAP40 complex structure
Map dataHuntingtin-HAP40 complex
SampleHuntingtin-HAP40 complex:
Huntingtin / Factor VIII intron 22 protein
Function / homologyArmadillo-type fold / Regulation of MECP2 expression and activity / Huntingtin protein region / Factor VIII intron 22 protein / Huntingtin family / Huntingtin, middle-repeat / Huntingtin / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / positive regulation of aggrephagy ...Armadillo-type fold / Regulation of MECP2 expression and activity / Huntingtin protein region / Factor VIII intron 22 protein / Huntingtin family / Huntingtin, middle-repeat / Huntingtin / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / positive regulation of aggrephagy / regulation of cAMP-dependent protein kinase activity / regulation of CAMKK-AMPK signaling cascade / positive regulation of cilium assembly / regulation of phosphoprotein phosphatase activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / positive regulation of lipophagy / vocal learning / vesicle transport along microtubule / profilin binding / positive regulation of autophagy of mitochondrion / presynaptic cytosol / dynactin binding / beta-tubulin binding / establishment of mitotic spindle orientation / dynein intermediate chain binding / Golgi organization / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / autophagosome / postsynaptic cytosol / inclusion body / centriole / heat shock protein binding / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / cytoplasmic vesicle membrane / kinase binding / p53 binding / late endosome / ion channel binding / positive regulation of apoptotic process / axon / apoptotic process / dendrite / endoplasmic reticulum / Golgi apparatus / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm / Factor VIII intron 22 protein / Huntingtin
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsGuo Q / Bin H / Cheng J / Pfeifer G / Baumeister W / Fernandez-Busnadiego R / Kochanek S
CitationJournal: Nature / Year: 2018
Title: The cryo-electron microscopy structure of huntingtin.
Authors: Qiang Guo / Bin Huang / Jingdong Cheng / Manuel Seefelder / Tatjana Engler / Günter Pfeifer / Patrick Oeckl / Markus Otto / Franziska Moser / Melanie Maurer / Alexander Pautsch / Wolfgang Baumeister / Rubén Fernández-Busnadiego / Stefan Kochanek
Validation ReportPDB-ID: 6ez8

SummaryFull reportAbout validation report
DateDeposition: Nov 14, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Feb 21, 2018 / Last update: Mar 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ez8
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3984.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.35 Å/pix.
= 216. Å
160 pix
1.35 Å/pix.
= 216. Å
160 pix
1.35 Å/pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.3883469 - 0.47479543
Average (Standard dev.)0.000055755136 (0.023309596)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin0.00.00.0
Limit159.0159.0159.0
Spacing160160160
CellA=B=C: 216.0 Å
α=β=γ: 90.0 deg.

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/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.3880.4750.000

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Supplemental data

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Sample components

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Entire Huntingtin-HAP40 complex

EntireName: Huntingtin-HAP40 complex / Number of components: 3

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Component #1: protein, Huntingtin-HAP40 complex

ProteinName: Huntingtin-HAP40 complex / Recombinant expression: No
MassExperimental: 352 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293

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Component #2: protein, Huntingtin

ProteinName: Huntingtin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 347.475375 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Factor VIII intron 22 protein

ProteinName: Factor VIII intron 22 protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.141879 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 32 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 98310
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

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