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

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Basic information

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 / homology
Function and homology information


GTPase activator activity / recycling endosome membrane / protein transport / membrane / metal ion binding
Similarity search - Function
ArfGAP ACAP1/2/3-like / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / BAR domain / ARFGAP/RecO-like zinc finger / AH/BAR domain superfamily ...ArfGAP ACAP1/2/3-like / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / BAR domain / ARFGAP/RecO-like zinc finger / AH/BAR domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 14 Å
AuthorsChan, C. / Pang, X.Y. / Zhang, Y. / Sun, F. / Fan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: PLoS Comput Biol / Year: 2019
Title: ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages.
Authors: Chun Chan / Xiaoyun Pang / Yan Zhang / Tongxin Niu / Shengjiang Yang / Daohui Zhao / Jian Li / Lanyuan Lu / Victor W Hsu / Jian Zhou / Fei Sun / Jun Fan /
Abstract: Studies on the Bin-Amphiphysin-Rvs (BAR) domain have advanced a fundamental understanding of how proteins deform membrane. We previously showed that a BAR domain in tandem with a Pleckstrin Homology ...Studies on the Bin-Amphiphysin-Rvs (BAR) domain have advanced a fundamental understanding of how proteins deform membrane. We previously showed that a BAR domain in tandem with a Pleckstrin Homology (PH domain) underlies the assembly of ACAP1 (Arfgap with Coil-coil, Ankryin repeat, and PH domain I) into an unusual lattice structure that also uncovers a new paradigm for how a BAR protein deforms membrane. Here, we initially pursued computation-based refinement of the ACAP1 lattice to identify its critical protein contacts. Simulation studies then revealed how ACAP1, which dimerizes into a symmetrical structure in solution, is recruited asymmetrically to the membrane through dynamic behavior. We also pursued electron microscopy (EM)-based structural studies, which shed further insight into the dynamic nature of the ACAP1 lattice assembly. As ACAP1 is an unconventional BAR protein, our findings broaden the understanding of the mechanistic spectrum by which proteins assemble into higher-ordered structures to achieve membrane deformation.
History
DepositionOct 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.2Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as representative helical assembly
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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
Polymers173,3374
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
Polymers1,560,03736
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation8
identity operation1_555x,y,z1
Buried area25590 Å2
ΔGint-150 kcal/mol
Surface area67660 Å2
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))
Helical symmetry: (Circular symmetry: 3 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 9 / Rise per n subunits: 23.198 Å / Rotation per n subunits: 42.693 °)

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Components

#1: Protein
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 method: isolated from a genetically manipulated source
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 / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical structure of ACAP1 BARPH domain on membrane tubules
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: pGEX-6p-1
Buffer solutionpH: 7.4 / Details: 50mM HEPES, pH7.4, 100mM NaCl, pH 7.4
Buffer component
IDConc.NameBuffer-ID
150 mMHepes1
2100 mMNaClSodium chloride1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The ACAP1 BAR-PH protein (4 mg/ml) was incubated with liposomes(2 mg/ml)
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: 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 X / 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 ° / Axial rise/subunit: 23.2 Å / Axial symmetry: C3
3D reconstructionMethod: HELICAL / Resolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross correlation

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