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- PDB-9jih: Crystal structure of BAR domain of ACAP4 -

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Basic information

Entry
Database: PDB / ID: 9jih
TitleCrystal structure of BAR domain of ACAP4
ComponentsArf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3
KeywordsSIGNALING PROTEIN / ArfGAP / tumor-associated / membrane bind cell migration / cancer metastasis
Function / homology
Function and homology information


regulation of stress fiber assembly / positive regulation of GTPase activity / ruffle / GTPase activator activity / cell migration / focal adhesion / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
Arf GTPase activating protein, ASAP3 / : / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / 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 ...Arf GTPase activating protein, ASAP3 / : / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / 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 SH3 domain, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsHuang, S. / Chen, J.S. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: J Mol Cell Biol / Year: 2025
Title: BAR-PH tandem of ACAP4 remodels membranes to drive migration via Ezrin-dependent activation.
Authors: Huang, S. / Chen, J. / Wang, X. / Song, X. / Zhu, X. / Fu, C. / Zhang, X. / Liu, X. / Wang, C.
History
DepositionSep 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3
B: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)63,5782
Polymers63,5782
Non-polymers00
Water00
1
A: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3

B: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)63,5782
Polymers63,5782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area8780 Å2
ΔGint-92 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.023, 189.975, 43.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 / Development and differentiation-enhancing factor-like 1 / Protein up-regulated in liver cancer 1


Mass: 31788.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASAP3, DDEFL1, UPLC1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8TDY4
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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate monohydrate 0.1M Tris ph8.5 25%w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.8→47.84 Å / Num. obs: 15659 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.035 / Rrim(I) all: 0.105 / Χ2: 1 / Net I/σ(I): 14.9 / Num. measured all: 140851
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 99.9 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.592 / Num. measured all: 19231 / Num. unique obs: 2241 / CC1/2: 0.944 / Rpim(I) all: 0.215 / Rrim(I) all: 0.631 / Χ2: 1 / Net I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
PHENIX5.8.0267refinement
autoPROCdata scaling
autoPROCdata reduction
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→47.84 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 766 4.92 %
Rwork0.2402 --
obs0.2419 15560 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4175 0 0 0 4175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034249
X-RAY DIFFRACTIONf_angle_d0.5445699
X-RAY DIFFRACTIONf_dihedral_angle_d13.8891605
X-RAY DIFFRACTIONf_chiral_restr0.034611
X-RAY DIFFRACTIONf_plane_restr0.006753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.36071550.29592893X-RAY DIFFRACTION100
3.02-3.320.35961610.28632909X-RAY DIFFRACTION99
3.32-3.80.29151590.24622890X-RAY DIFFRACTION100
3.8-4.790.24521350.22342984X-RAY DIFFRACTION100
4.79-47.840.23661560.21953118X-RAY DIFFRACTION99

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