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- PDB-4ckg: Helical reconstruction of ACAP1(BAR-PH domain) decorated membrane... -

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Basic information

Entry
Database: PDB / ID: 4ckg
TitleHelical reconstruction of ACAP1(BAR-PH domain) decorated membrane tubules by cryo-electron microscopy
ComponentsARF-GAP WITH COILED-COIL, ANK REPEAT AND PH DOMAIN-CONTAINING PROTEIN 1
KeywordsSIGNALING PROTEIN / MEMBRANE REMODELING
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 / ARFGAP/RecO-like zinc finger / BAR domain / 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 / ARFGAP/RecO-like zinc finger / BAR domain / 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: 15 Å
AuthorsPang, X.Y. / Fan, J. / Zhang, Y. / Zhang, K. / Gao, B.Q. / Ma, J. / Li, J. / Deng, Y.C. / Zhou, Q.J. / Hsu, V. / Sun, F.
CitationJournal: Dev Cell / Year: 2014
Title: A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature.
Authors: Xiaoyun Pang / Jun Fan / Yan Zhang / Kai Zhang / Bingquan Gao / Jun Ma / Jian Li / Yuchen Deng / Qiangjun Zhou / Edward H Egelman / Victor W Hsu / Fei Sun /
Abstract: The BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane ...The BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane curvature. In some cases, a BAR domain also possesses an amphipathic helix that inserts into the membrane to induce curvature. ACAP1 (Arfgap with Coil coil, Ankyrin repeat, and PH domain protein 1) contains a BAR domain. Here, we show that this BAR domain can neither bind membrane nor impart curvature, but instead requires a neighboring PH (Pleckstrin Homology) domain to achieve these functions. Specific residues within the PH domain are responsible for both membrane binding and curvature generation. The BAR domain adjacent to the PH domain instead interacts with the BAR domains of neighboring ACAP1 proteins to enable clustering at the membrane. Thus, we have uncovered the molecular basis for an unexpected and unconventional collaboration between PH and BAR domains in membrane bending.
History
DepositionJan 6, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Derived calculations / Refinement description
Category: em_3d_fitting / em_software ...em_3d_fitting / em_software / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _refine.ls_d_res_high

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Structure visualization

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  • Biological unit as author_and_software_defined_assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-2546
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  • Superimposition on EM map
  • EMDB-2546
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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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
Water00
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 10


Theoretical massNumber of molelcules
Total (without water)1,733,37440
Polymers1,733,37440
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation9
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.735, 0.6781), (-0.6781, 0.735), (1)-23.1982
3given(0.735, -0.6781), (0.6781, 0.735), (1)23.1982
4given(-0.5, -0.8666), (0.8666, -0.5), (1)
5given(0.2208, -0.9753), (0.9753, 0.2208), (1)-23.1982
6given(-0.9544, -0.2985), (0.2985, -0.9544), (1)23.1982
7given(-0.5, 0.865), (-0.865, -0.5), (1)
8given(-0.9554, 0.2955), (-0.2955, -0.9554), (1)-23.1982
9given(0.2177, 0.976), (-0.976, 0.2177), (1)23.1982
10given(0.0804, -0.9968), (0.9968, 0.0804), (1)46.3964

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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 / BAR-PH DOMAIN OF ACAP1


Mass: 43334.348 Da / Num. of mol.: 4 / Fragment: BAR-PH DOMAIN, RESIDUES 1-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15027
Sequence detailsPFAM PF03114

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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: BAR-PH DOMAIN OF ACAP1 / Type: COMPLEX / Details: MICROGRAPHS SELECTED MANUALLY
Buffer solutionName: 50MM HEPES, PH7.4, 100MM NACL / pH: 7.4 / Details: 50MM HEPES, PH7.4, 100MM NACL
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 16, 2012
Details: GOOD MICROGRAPHS (VERIFIED BY HELICAL DIFFRACTION PATTERN) WERE SELECTED MANUALLY. THE ELECTRON DOSE IS 2000 ELECTRON PER NANOMETER SQUARE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 125418 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm
Specimen holderTemperature: 98 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 259
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1UCSF Chimeramodel fittingChimera plus manual docking
2IHRSR3D reconstruction
CTF correctionDetails: CTFFIND3
3D reconstructionMethod: HELICAL RECONSTRUCTION USING IHRSR WITH THE PARTICLES SHRUNK 4 TIMES TO IMPROVE THE ACCURACY OF ALIGNMENT.
Resolution: 15 Å / Num. of particles: 367 / Nominal pixel size: 3.6 Å / Actual pixel size: 3.6 Å
Details: PARTICLES WERE CLASSIFIED BY THEIR DIAMETERS, THEN SHRUNK 4 TIMES TO PERFORM SINGLE PARTICLE RECONSTRUCTION USING IHRSR. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2546. (DEPOSITION ID: 12221).
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--RIGID BODY FITTING AND MANUALLY DOCKING REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 4NSW

4nsw


Accession code: 4NSW / Source name: PDB / Type: experimental model
RefinementHighest resolution: 15 Å
Refinement stepCycle: LAST / Highest resolution: 12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11682 0 0 0 11682

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