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- EMDB-4371: Cryo-EM map of the FCHSD2 F-BAR domain + SH3-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-4371
TitleCryo-EM map of the FCHSD2 F-BAR domain + SH3-1
Map dataFCHSD2 F-BAR SH3-1 domains.
Sample
  • Organelle or cellular component: FCHSD2 F-BAR and SH3-1 domains
    • Protein or peptide: FCHSD2 F-BAR + SH3-1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.2 Å
AuthorsAlmeida-Souza L / Frank R / Garcia-Nafria J / Colussi A / Gunawardana N / Johnson CM / Yu M / Howard G / Andrews B / Vallis Y / McMahon HT
CitationJournal: Cell / Year: 2018
Title: A Flat BAR Protein Promotes Actin Polymerization at the Base of Clathrin-Coated Pits.
Authors: Leonardo Almeida-Souza / Rene A W Frank / Javier García-Nafría / Adeline Colussi / Nushan Gunawardana / Christopher M Johnson / Minmin Yu / Gillian Howard / Byron Andrews / Yvonne Vallis / Harvey T McMahon /
Abstract: Multiple proteins act co-operatively in mammalian clathrin-mediated endocytosis (CME) to generate endocytic vesicles from the plasma membrane. The principles controlling the activation and ...Multiple proteins act co-operatively in mammalian clathrin-mediated endocytosis (CME) to generate endocytic vesicles from the plasma membrane. The principles controlling the activation and organization of the actin cytoskeleton during mammalian CME are, however, not fully understood. Here, we show that the protein FCHSD2 is a major activator of actin polymerization during CME. FCHSD2 deletion leads to decreased ligand uptake caused by slowed pit maturation. FCHSD2 is recruited to endocytic pits by the scaffold protein intersectin via an unusual SH3-SH3 interaction. Here, its flat F-BAR domain binds to the planar region of the plasma membrane surrounding the developing pit forming an annulus. When bound to the membrane, FCHSD2 activates actin polymerization by a mechanism that combines oligomerization and recruitment of N-WASP to PI(4,5)P, thus promoting pit maturation. Our data therefore describe a molecular mechanism for linking spatiotemporally the plasma membrane to a force-generating actin platform guiding endocytic vesicle maturation.
History
DepositionApr 16, 2018-
Header (metadata) releaseApr 25, 2018-
Map releaseJun 13, 2018-
UpdateJul 25, 2018-
Current statusJul 25, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0123
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0123
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4371.png

Downloads & links

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Map

FileDownload / File: emd_4371.map.gz / Format: CCP4 / Size: 39.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFCHSD2 F-BAR SH3-1 domains.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 218 pix.
= 239.8 Å		1.1 Å/pix.
x 218 pix.
= 239.8 Å		1.1 Å/pix.
x 218 pix.
= 239.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0123 / Movie #1: 0.0123
Minimum - Maximum-0.0067462223 - 0.064117916
Average (Standard dev.)0.00032454843 (±0.0027927621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions218218218
Spacing218218218
CellA=B=C: 239.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z218218218
origin x/y/z0.0000.0000.000
length x/y/z239.800239.800239.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS218218218
D min/max/mean-0.0070.0640.000

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Supplemental data

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Sample components

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Entire : FCHSD2 F-BAR and SH3-1 domains

EntireName: FCHSD2 F-BAR and SH3-1 domains
Components
  • Organelle or cellular component: FCHSD2 F-BAR and SH3-1 domains
    • Protein or peptide: FCHSD2 F-BAR + SH3-1

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Supramolecule #1: FCHSD2 F-BAR and SH3-1 domains

SupramoleculeName: FCHSD2 F-BAR and SH3-1 domains / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 142 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 Rosetta (DE3)

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Macromolecule #1: FCHSD2 F-BAR + SH3-1

MacromoleculeName: FCHSD2 F-BAR + SH3-1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQPPPRKVKV TQELKNIQVE QMTKLQAKHQ AECDLLEDMR TFSQKKAAIE REYAQGMQKL ASQYLKRDWP GVKADDRNDY RSMYPVWKSF LEGTMQVAQS RMNICENYKN FISEPARTVR SLKEQQLKRC VDQLTKIQTE LQETVKDLAK GKKKYFETEQ MAHAVREKAD ...String:
MQPPPRKVKV TQELKNIQVE QMTKLQAKHQ AECDLLEDMR TFSQKKAAIE REYAQGMQKL ASQYLKRDWP GVKADDRNDY RSMYPVWKSF LEGTMQVAQS RMNICENYKN FISEPARTVR SLKEQQLKRC VDQLTKIQTE LQETVKDLAK GKKKYFETEQ MAHAVREKAD IEAKSKLSLF QSRISLQKAS VKLKARRSEC NSKATHARND YLLTLAAANA HQDRYYQTDL VNIMKALDGN VYDHLKDYLI AFSRTELETC QAVQNTFQFL LENSSKVVRD YNLQLFLQEN AVFHKPQPFQ FQPCDSDTSR QLESETGTTE EHSLNKEARK WATRVAREHK NIVHQQRVLN DLECHGAAVS EQSRAELEQK IDEARENIRK AEIIKLKAEA RLDLLKQIGV SVDTWLKSAM NQVMEELENE RWARPPAVTS NGTLHSLNAD TEREEGEEFE DNMDVFDDSS SSPSGTLRNY PLTCKVVYSY KASQPDELTI EEHEVLEVIE DGDMEDWVKA RNKVGQVGYV PEKYLQFPTS

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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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMC8H18N2O4SHEPES
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 766 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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

Particle selectionNumber selected: 230954
CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4dyl

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 30270
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.0)

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