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- PDB-5xhz: Crystal Structure Analysis of CIN85-SH3B in complex with ARAP1-P2 -

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Basic information

Entry
Database: PDB / ID: 5xhz
TitleCrystal Structure Analysis of CIN85-SH3B in complex with ARAP1-P2
Components
  • Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1
  • SH3 domain-containing kinase-binding protein 1
KeywordsPROTEIN BINDING / protein-protein complex
Function / homology
Function and homology information


Reelin signalling pathway / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / CDC42 GTPase cycle / Negative regulation of MET activity / EGFR downregulation / RAC1 GTPase cycle / RHOA GTPase cycle / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation / Cargo recognition for clathrin-mediated endocytosis ...Reelin signalling pathway / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / CDC42 GTPase cycle / Negative regulation of MET activity / EGFR downregulation / RAC1 GTPase cycle / RHOA GTPase cycle / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / type 1 angiotensin receptor binding / negative regulation of stress fiber assembly / positive regulation of filopodium assembly / Golgi cisterna membrane / ubiquitin-dependent endocytosis / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor recycling / R-SMAD binding / endocytic vesicle / cytoskeleton organization / transforming growth factor beta receptor signaling pathway / GTPase activator activity / actin filament organization / cytoplasmic vesicle membrane / trans-Golgi network / SH3 domain binding / GABA-ergic synapse / cell-cell junction / cell migration / regulation of cell shape / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton / neuron projection / transcription cis-regulatory region binding / postsynaptic density / DNA-binding transcription factor activity / focal adhesion / apoptotic process / ubiquitin protein ligase binding / synapse / positive regulation of DNA-templated transcription / glutamatergic synapse / nucleoplasm / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third SH3 domain / ARAP, RhoGAP 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 ...SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third SH3 domain / ARAP, RhoGAP 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 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Variant SH3 domain / SAM domain (Sterile alpha motif) / Rho GTPase activation protein / SH3 Domains / SAM domain profile. / PH domain / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 / SH3 domain-containing kinase-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.319 Å
AuthorsLiu, W. / Yang, W.
CitationJournal: Biochemistry / Year: 2018
Title: Biochemical and Structural Studies of the Interaction between ARAP1 and CIN85.
Authors: Li, Q. / Yang, W. / Wang, Y. / Liu, W.
History
DepositionApr 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SH3 domain-containing kinase-binding protein 1
B: SH3 domain-containing kinase-binding protein 1
C: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1
D: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9055
Polymers17,8464
Non-polymers591
Water4,792266
1
A: SH3 domain-containing kinase-binding protein 1
C: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)8,9232
Polymers8,9232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-3 kcal/mol
Surface area5120 Å2
MethodPISA
2
B: SH3 domain-containing kinase-binding protein 1
D: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9823
Polymers8,9232
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-5 kcal/mol
Surface area5060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.162, 66.162, 34.935
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein SH3 domain-containing kinase-binding protein 1 / Regulator of ubiquitous kinase / Ruk / SH3-containing / expressed in tumorigenic astrocytes


Mass: 7481.354 Da / Num. of mol.: 2 / Fragment: SH3B (UNP RESIDUES 98-157)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sh3kbp1, Ruk, Seta / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R550
#2: Protein/peptide Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 / Centaurin-delta-2 / Cnt-d2


Mass: 1441.811 Da / Num. of mol.: 2 / Fragment: P2 (UNP RESIDUES 80-90) / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q4LDD4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5
Details: 0.2M Sodium acetate trihydrate, 0.1M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.319→50 Å / Num. obs: 34450 / % possible obs: 96 % / Redundancy: 9.3 % / Biso Wilson estimate: 13.91 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.027 / Rrim(I) all: 0.085 / Χ2: 0.469 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.32-1.348.70.6980.8570.2480.7410.44997.4
1.34-1.378.30.6240.8810.2260.6650.45599.5
1.37-1.399.40.5760.8990.1970.6090.45797.9
1.39-1.429.50.5180.9260.1770.5470.4699.1
1.42-1.459.40.4230.9420.1440.4470.4697.7
1.45-1.499.30.3650.9590.1260.3860.45899.3
1.49-1.529.10.320.9620.110.3390.45797
1.52-1.578.70.2870.9680.1020.3050.46699.6
1.57-1.618.80.2430.9780.0860.2580.4797.5
1.61-1.669.60.2210.9830.0750.2330.46897.3
1.66-1.729.50.1820.9860.0610.1920.4898.8
1.72-1.799.50.1590.990.0540.1680.48797.9
1.79-1.879.40.1260.9930.0430.1330.48197.2
1.87-1.978.70.1050.9940.0370.1120.47396.9
1.97-2.19.50.0870.9950.0290.0920.45997
2.1-2.269.90.0770.9960.0260.0820.4996.6
2.26-2.489.80.070.9960.0240.0740.45395
2.48-2.848.70.0630.9960.0220.0670.44394.9
2.84-3.58100.0510.9980.0170.0540.47892.2
3.58-509.30.0480.9980.0160.0510.54672.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U23

3u23


Resolution: 1.319→8.27 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.75
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 1766 5.13 %0
Rwork0.1629 ---
obs0.1641 34440 96.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.95 Å2 / Biso mean: 18.761 Å2 / Biso min: 9.92 Å2
Refinement stepCycle: final / Resolution: 1.319→8.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 4 269 1403
Biso mean--25.69 29.4 -
Num. residues----141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051259
X-RAY DIFFRACTIONf_angle_d0.8111719
X-RAY DIFFRACTIONf_chiral_restr0.078179
X-RAY DIFFRACTIONf_plane_restr0.005231
X-RAY DIFFRACTIONf_dihedral_angle_d12.684840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3188-1.35440.30441240.23592536266096
1.3544-1.3940.25381430.22622554269798
1.394-1.43880.22461150.21252592270799
1.4388-1.48990.22071380.19462537267599
1.4899-1.54920.21741560.18832512266898
1.5492-1.61920.20531620.17352517267998
1.6192-1.70390.21661410.17232537267898
1.7039-1.80960.18531420.16962532267497
1.8096-1.94760.17681280.16062564269297
1.9476-2.14050.17131350.15752522265797
2.1405-2.44330.17891280.16092520264896
2.4433-3.05230.22891310.17162479261094
3.0523-8.27040.13591230.13092272239584

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