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- PDB-5h3d: Helical structure of membrane tubules decorated by ACAP1 (BARPH d... -

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Entry
Database: PDB / ID: 5h3d
TitleHelical structure of membrane tubules decorated by ACAP1 (BARPH doamin) protein by cryo-electron microscopy and MD simulation
ComponentsArf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
KeywordsSIGNALING PROTEIN / ACAP1 BARPH domain / membrane remodeling / molecular dynamics simulation
Function / homologyBAR domain of APPL family / ARFGAP/RecO-like zinc finger / Ankyrin repeat region circular profile. / ARF GTPase-activating proteins domain profile. / Ankyrin repeat profile. / PH domain profile. / Ankyrin repeats (3 copies) / Putative GTPase activating protein for Arf / PH domain / ArfGAP domain superfamily ...BAR domain of APPL family / ARFGAP/RecO-like zinc finger / Ankyrin repeat region circular profile. / ARF GTPase-activating proteins domain profile. / Ankyrin repeat profile. / PH domain profile. / Ankyrin repeats (3 copies) / Putative GTPase activating protein for Arf / PH domain / ArfGAP domain superfamily / Ankyrin repeat-containing domain superfamily / AH/BAR domain superfamily / Ankyrin repeat-containing domain / PH-like domain superfamily / Ankyrin repeat / Pleckstrin homology domain / Arf GTPase activating protein / GTPase activator activity / recycling endosome membrane / protein transport / membrane / metal ion binding / Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 14 Å resolution
AuthorsChan, C. / Pang, X.Y. / Zhang, Y. / Sun, F. / Fan, J.
CitationJournal: To Be Published
Title: Electrostatic Interactions Dominated ACAP1BAR-PH Proteins Asymmetrical Membrane Binding and Lattice Assembly
Authors: Chan, C. / Pang, X. / Zhang, Y. / Niu, T. / Li, J. / Hsu, V.W. / Sun, F. / Fan, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 22, 2016 / Release: Jan 16, 2019

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Assembly

Deposited unit
A: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
B: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
C: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
D: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)173,3374
Polyers173,3374
Non-polymers00
Water0
1
A: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
B: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
C: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
D: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
x 9


Theoretical massNumber of molelcules
Total (without water)1,560,03736
Polyers1,560,03736
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation9
Buried area (Å2)25590
ΔGint (kcal/M)-150
Surface area (Å2)67660
2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
Helical symmetryCircular symmetry: 3 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 9 / Rise per n subunits: 23.198 Å / Rotation per n subunits: 42.693 deg.

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Components

#1: Protein/peptide
Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1 / Centaurin-beta-1 / Cnt-b1


Mass: 43334.348 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: ACAP1, CENTB1, KIAA0050 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15027

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical structure of ACAP1 BARPH domain on membrane tubules
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pGEX-6p-1 / Strain: BL21(DE3)
Buffer solutionDetails: 50mM HEPES, pH7.4, 100mM NaCl, pH 7.4 / pH: 7.4
Buffer component
IDConc.NameBuffer ID
150 mMHepes1
2100 mMNaCl1
SpecimenConc.: 4 mg/ml
Details: The ACAP1 BAR-PH protein (4 mg/ml) was incubated with liposomes(2 mg/ml)
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 42.72 deg. / Axial rise/subunit: 23.2 Å / Axial symmetry: C3
3D reconstructionMethod: HELICAL / Resolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 304 / Symmetry type: HELICAL
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: cross correlation

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