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- PDB-8ze8: Arf-GTPase activating protein Asap1 SH3 domain in complex with 44... -

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Basic information

Entry
Database: PDB / ID: 8ze8
TitleArf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment
Components
  • Ankyrin-2
  • Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
KeywordsPROTEIN BINDING / complex
Function / homology
Function and homology information


VxPx cargo-targeting to cilium / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / T-tubule organization / positive regulation of membrane tubulation / protein localization to M-band / atrial septum development / SA node cell action potential / membrane depolarization during SA node cell action potential ...VxPx cargo-targeting to cilium / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / T-tubule organization / positive regulation of membrane tubulation / protein localization to M-band / atrial septum development / SA node cell action potential / membrane depolarization during SA node cell action potential / paranodal junction assembly / negative regulation of dendritic spine development / potassium channel activator activity / regulation of atrial cardiac muscle cell action potential / positive regulation of podosome assembly / positive regulation of potassium ion import across plasma membrane / channel activator activity / atrial cardiac muscle cell action potential / phosphorylation-dependent protein binding / sarcoplasmic reticulum calcium ion transport / regulation of SA node cell action potential / cell projection membrane / protein localization to endoplasmic reticulum / A band / protein localization to cilium / cytoskeletal adaptor activity / costamere / ventricular cardiac muscle cell action potential / response to methylmercury / regulation of ventricular cardiac muscle cell membrane repolarization / positive regulation of calcium ion transport / regulation of release of sequestered calcium ion into cytosol / protein localization to cell surface / podosome / regulation of cardiac muscle cell contraction / M band / regulation of postsynapse organization / regulation of cardiac muscle contraction by calcium ion signaling / Interaction between L1 and Ankyrins / centriolar satellite / phosphatidylserine binding / spectrin binding / regulation of calcium ion transport / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of heart rate by cardiac conduction / intercalated disc / regulation of cardiac muscle contraction / cilium assembly / COPI-mediated anterograde transport / regulation of heart rate / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / phosphatidylinositol-4,5-bisphosphate binding / T-tubule / protein localization to plasma membrane / trans-Golgi network membrane / GTPase activator activity / regulation of protein stability / SH3 domain binding / sarcolemma / recycling endosome / intracellular calcium ion homeostasis / endocytosis / intracellular protein localization / Z disc / structural constituent of cytoskeleton / protein transport / ATPase binding / dendritic spine / basolateral plasma membrane / early endosome / cytoskeleton / transmembrane transporter binding / protein-macromolecule adaptor activity / postsynaptic membrane / lysosome / protein stabilization / apical plasma membrane / neuron projection / Golgi membrane / positive regulation of gene expression / protein kinase binding / glutamatergic synapse / Golgi apparatus / enzyme binding / mitochondrion / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / BAR domain of APPL family / Ankyrin, UPA domain / UPA domain / : / Arf GTPase activating protein / ArfGAP domain superfamily ...ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / BAR domain of APPL family / Ankyrin, UPA domain / UPA domain / : / 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 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeats (many copies) / PH domain / Death-like domain superfamily / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Src homology 3 domains / Ankyrin repeat-containing domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
Ankyrin-2 / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsChen, K. / Li, Y. / Zhao, Y. / He, Y. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: New targets and designed inhibitors of ASAP Arf-GAPs derived from structural characterization of the ASAP1/440-kD ankyrin-B interaction.
Authors: Li, Y. / Zhao, Y. / He, Y. / Liu, F. / Xia, L. / Liu, K. / Zhang, M. / Chen, K.
History
DepositionMay 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
E: Ankyrin-2
B: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
C: Ankyrin-2
D: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
F: Ankyrin-2
G: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
H: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1029
Polymers37,0108
Non-polymers921
Water5,585310
1
A: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
E: Ankyrin-2


Theoretical massNumber of molelcules
Total (without water)9,2522
Polymers9,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-1 kcal/mol
Surface area4330 Å2
MethodPISA
2
B: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
C: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3453
Polymers9,2522
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-1 kcal/mol
Surface area4520 Å2
MethodPISA
3
D: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
F: Ankyrin-2


Theoretical massNumber of molelcules
Total (without water)9,2522
Polymers9,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-2 kcal/mol
Surface area4290 Å2
MethodPISA
4
G: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
H: Ankyrin-2


Theoretical massNumber of molelcules
Total (without water)9,2522
Polymers9,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-1 kcal/mol
Surface area4260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.922, 52.074, 56.909
Angle α, β, γ (deg.)111.42, 90.16, 112.46
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1 / 130 kDa phosphatidylinositol 4 / 5-bisphosphate-dependent ARF1 GTPase-activating protein / ADP- ...130 kDa phosphatidylinositol 4 / 5-bisphosphate-dependent ARF1 GTPase-activating protein / ADP-ribosylation factor-directed GTPase-activating protein 1 / ARF GTPase-activating protein 1 / Development and differentiation-enhancing factor 1 / DEF-1 / Differentiation-enhancing factor 1 / PIP2-dependent ARF1 GAP


Mass: 7794.611 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Asap1, Ddef1, Kiaa1249, Shag1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QWY8
#2: Protein/peptide
Ankyrin-2 / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 1457.849 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01484
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.07→32.49 Å / Num. obs: 23173 / % possible obs: 97.6 % / Redundancy: 3.2 % / CC1/2: 0.941 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.08 / Rrim(I) all: 0.146 / Χ2: 0.77 / Net I/σ(I): 8.1 / Num. measured all: 75254
Reflection shellResolution: 2.07→2.12 Å / % possible obs: 95.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.213 / Num. measured all: 4758 / Num. unique obs: 1695 / CC1/2: 0.674 / Rpim(I) all: 0.153 / Rrim(I) all: 0.264 / Χ2: 0.7 / Net I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JV3

3jv3


Resolution: 2.07→32.4 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1131 4.89 %
Rwork0.1838 --
obs0.1859 23128 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 6 310 2547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132280
X-RAY DIFFRACTIONf_angle_d1.2843079
X-RAY DIFFRACTIONf_dihedral_angle_d6.45291
X-RAY DIFFRACTIONf_chiral_restr0.066337
X-RAY DIFFRACTIONf_plane_restr0.013398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.160.2711270.19882716X-RAY DIFFRACTION96
2.16-2.280.24411640.19682721X-RAY DIFFRACTION96
2.28-2.420.24591300.18372697X-RAY DIFFRACTION97
2.42-2.610.2291460.19462776X-RAY DIFFRACTION97
2.61-2.870.24591480.18652740X-RAY DIFFRACTION98
2.87-3.290.25851230.1832773X-RAY DIFFRACTION98
3.29-4.140.17251470.16252787X-RAY DIFFRACTION99
4.14-32.40.21131460.1892787X-RAY DIFFRACTION99

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