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- PDB-4ckh: Helical reconstruction of ACAP1(BAR-PH domain) decorated membrane... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ckh | ||||||
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Title | Helical reconstruction of ACAP1(BAR-PH domain) decorated membrane tubules by cryo-electron microscopy | ||||||
![]() | ARF-GAP WITH COILED-COIL, ANK REPEAT AND PH DOMAIN-CONTAINING PROTEIN 1 | ||||||
![]() | SIGNALING PROTEIN / MEMBRANE REMODELING | ||||||
Function / homology | ![]() GTPase activator activity / recycling endosome membrane / protein transport / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 17 Å | ||||||
![]() | Pang, 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. | ||||||
![]() | ![]() 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 |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 258.3 KB | Display | ![]() |
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PDB format | ![]() | 202 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2547MC ![]() 2546C ![]() 4ckgC ![]() 4nswC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | 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.) ![]() ![]() ![]() Sequence details | PFAM PF03114 | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: BAR-PH DOMAIN OF ACAP1 / Type: COMPLEX / Details: MICROGRAPHS SELECTED MANUALLY |
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Buffer solution | Name: 50MM HEPES, PH7.4, 100MM NACL / pH: 7.4 / Details: 50MM HEPES, PH7.4, 100MM NACL |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: 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 |
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Microscopy | Model: 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 gun | Electron source: ![]() |
Electron lens | Mode: 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 holder | Temperature: 98 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 259 |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: CTFFIND3 | ||||||||||||
3D reconstruction | Method: HELICAL RECONSTRUCTION USING IHRSR WITH THE PARTICLES SHRUNK 4 TIMES TO IMPROVE THE ACCURACY OF ALIGNMENT. Resolution: 17 Å / Num. of particles: 352 / Nominal pixel size: 4.8 Å / Actual pixel size: 4.8 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-2547. (DEPOSITION ID: 12222). Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--RIGID BODY FITTING AND MANUALLY DOCKING REFINEMENT PROTOCOL--X-RAY | ||||||||||||
Atomic model building | PDB-ID: 4NSW Accession code: 4NSW / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 17 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 14 Å
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