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- PDB-8hlo: Crystal structure of ASAP1-SH3 and MICAL1-PRM complex -

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Basic information

Entry
Database: PDB / ID: 8hlo
TitleCrystal structure of ASAP1-SH3 and MICAL1-PRM complex
Components
  • Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
  • Proline rich motif from MICAL1
KeywordsPROTEIN BINDING / SH3 / Proline-rich motif / high-affinity
Function / homology
Function and homology information


VxPx cargo-targeting to cilium / hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / positive regulation of membrane tubulation / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / negative regulation of dendritic spine development / NAD(P)H oxidase H2O2-forming activity ...VxPx cargo-targeting to cilium / hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / positive regulation of membrane tubulation / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / negative regulation of dendritic spine development / NAD(P)H oxidase H2O2-forming activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / protein localization to cilium / actin filament depolymerization / podosome / intermediate filament / regulation of postsynapse organization / intercellular bridge / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / actin filament bundle assembly / cilium assembly / cytoskeleton organization / phosphatidylinositol-4,5-bisphosphate binding / FAD binding / GTPase activator activity / trans-Golgi network membrane / negative regulation of protein phosphorylation / actin filament / monooxygenase activity / small GTPase binding / SH3 domain binding / actin filament binding / actin cytoskeleton / actin binding / Factors involved in megakaryocyte development and platelet production / midbody / dendritic spine / endosome membrane / Golgi membrane / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding / signal transduction / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / BAR domain of APPL family / Arf GTPase activating protein ...ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / 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 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / FAD-binding domain / FAD binding domain / AH/BAR domain superfamily / Variant SH3 domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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 / FAD/NAD(P)-binding domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
[F-actin]-monooxygenase MICAL1 / 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: 1.168 Å
AuthorsNiu, F. / Wei, Z. / Yu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170697 China
Citation
Journal: Int J Mol Sci / Year: 2023
Title: Crystal Structure of the SH3 Domain of ASAP1 in Complex with the Proline Rich Motif (PRM) of MICAL1 Reveals a Unique SH3/PRM Interaction Mode.
Authors: Jia, X. / Lin, L. / Xu, S. / Li, L. / Wei, Z. / Yu, C. / Niu, F.
#1: Journal: Int J Mol Sci / Year: 2023
Title: Crystal Structure of the SH3 Domain of ASAP1 in Complex with the Proline Rich Motif (PRM) of MICAL1 Reveals a Unique SH3/PRM Interaction Mode.
Authors: Jia, X. / Lin, L. / Xu, S. / Li, L. / Wei, Z. / Yu, C. / Niu, F.
History
DepositionNov 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: 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 1
C: Proline rich motif from MICAL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0423
Polymers8,9462
Non-polymers961
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.181, 45.181, 59.391
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-1325-

HOH

21A-1330-

HOH

31A-1365-

HOH

41A-1394-

HOH

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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: 7641.383 Da / Num. of mol.: 1 / Fragment: SH3 domain
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 Proline rich motif from MICAL1 / Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin ...Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin homology and LIM domains


Mass: 1304.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICAL1, MICAL, NICAL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDZ2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.96 Å3/Da / Density % sol: 37.12 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M HEPES, pH 7.5, 1.4M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.168→39.128 Å / Num. obs: 21440 / % possible obs: 91.74 % / Redundancy: 4.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.32
Reflection shellResolution: 1.17→1.21 Å / Num. unique obs: 1130 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIXv1.9refinement
Cootmodel building
HKL-3000data scaling
PHASESphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.168→39.128 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / Phase error: 14.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1424 1989 9.28 %
Rwork0.1114 --
obs0.1143 21440 91.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.168→39.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 5 114 751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008683
X-RAY DIFFRACTIONf_angle_d1.317935
X-RAY DIFFRACTIONf_dihedral_angle_d14.607267
X-RAY DIFFRACTIONf_chiral_restr0.07195
X-RAY DIFFRACTIONf_plane_restr0.008128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.168-1.19690.2163630.1576665X-RAY DIFFRACTION44
1.1969-1.22930.1568980.1379994X-RAY DIFFRACTION66
1.2293-1.26550.17621280.13051244X-RAY DIFFRACTION82
1.2655-1.30630.16411430.12131416X-RAY DIFFRACTION93
1.3063-1.3530.16461490.11591490X-RAY DIFFRACTION99
1.353-1.40720.13571560.10671524X-RAY DIFFRACTION100
1.4072-1.47120.14681540.10611480X-RAY DIFFRACTION100
1.4712-1.54880.1541580.10481516X-RAY DIFFRACTION100
1.5488-1.64580.13581560.10651508X-RAY DIFFRACTION100
1.6458-1.77290.14921530.11071523X-RAY DIFFRACTION100
1.7729-1.95130.14071530.10571515X-RAY DIFFRACTION100
1.9513-2.23370.12681610.09831512X-RAY DIFFRACTION100
2.2337-2.81410.13141630.11941514X-RAY DIFFRACTION100
2.8141-39.1280.14631540.11241550X-RAY DIFFRACTION100

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