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- PDB-4x1v: Crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in... -

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Basic information

Entry
Database: PDB / ID: 4x1v
TitleCrystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 76-91) from human ARAP1
Components
  • Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1
  • CD2-associated protein
KeywordsSIGNALING PROTEIN / Endocytosis adaptor protein / Protein-peptide binary complex / kidney / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / : / response to glial cell derived neurotrophic factor / : / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / slit diaphragm ...: / : / response to glial cell derived neurotrophic factor / : / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / slit diaphragm / response to transforming growth factor beta / podocyte differentiation / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / cell-cell adhesion mediated by cadherin / collateral sprouting / protein heterooligomerization / renal albumin absorption / substrate-dependent cell migration, cell extension / membrane organization / phosphatidylinositol 3-kinase regulatory subunit binding / cell-cell junction organization / filopodium assembly / type 1 angiotensin receptor binding / podosome / Nephrin family interactions / regulation of small GTPase mediated signal transduction / positive regulation of filopodium assembly / negative regulation of stress fiber assembly / positive regulation of epidermal growth factor receptor signaling pathway / Golgi cisterna membrane / clathrin binding / maintenance of blood-brain barrier / positive regulation of receptor recycling / nuclear envelope lumen / cell leading edge / glucose import / filamentous actin / phosphatidylinositol-3,4,5-trisphosphate binding / neurotrophin TRK receptor signaling pathway / centriolar satellite / protein secretion / lymph node development / adipose tissue development / stress-activated MAPK cascade / ruffle / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ERK1 and ERK2 cascade / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / positive regulation of GTPase activity / trans-Golgi network membrane / liver development / positive regulation of protein secretion / regulation of actin cytoskeleton organization / actin filament organization / synapse organization / protein catabolic process / response to virus / regulation of synaptic plasticity / response to insulin / neuromuscular junction / trans-Golgi network / lipid metabolic process / structural constituent of cytoskeleton / fibrillar center / response to wounding / SH3 domain binding / positive regulation of protein localization to nucleus / male gonad development / actin filament binding / cell migration / actin cytoskeleton / late endosome / T cell receptor signaling pathway / regulation of cell shape / growth cone / cytoplasmic vesicle / protein-containing complex assembly / vesicle / response to oxidative stress / negative regulation of neuron apoptotic process / cell population proliferation / cadherin binding / inflammatory response / cell cycle / cell division / axon / intracellular membrane-bounded organelle / apoptotic process / dendrite / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
ARAP, RhoGAP domain / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 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 ...ARAP, RhoGAP domain / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 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-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / 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. / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 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
Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 / CD2-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.58 Å
AuthorsRouka, E. / Krojer, T. / von Delft, F. / Knapp, S. / Kirsch, K.H. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Feller, S.M. / Simister, P.C.
CitationJournal: to be published
Title: Crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 76-91) from human ARAP1
Authors: Rouka, E. / Feller, S.M. / Simister, P.C.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD2-associated protein
B: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)9,4262
Polymers9,4262
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-5 kcal/mol
Surface area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.590, 44.590, 32.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein CD2-associated protein / Adapter protein CMS / Cas ligand with multiple SH3 domains


Mass: 7444.361 Da / Num. of mol.: 1 / Fragment: UNP residues 109-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD2AP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y5K6
#2: Protein/peptide Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 / Centaurin-delta-2 / Cnt-d2


Mass: 1981.416 Da / Num. of mol.: 1 / Fragment: UNP residues 76-91 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96P48
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.4 M tri-sodium citrate dehydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.58→44.59 Å / Num. obs: 8587 / % possible obs: 99.9 % / Redundancy: 7.2 % / Net I/σ(I): 2.24

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementResolution: 1.58→44.59 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.667 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19993 432 4.8 %RANDOM
Rwork0.15966 ---
obs0.16154 8587 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.58→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms578 0 0 68 646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019632
X-RAY DIFFRACTIONr_bond_other_d0.0010.02591
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.97864
X-RAY DIFFRACTIONr_angle_other_deg0.93531373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.201583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18125.15233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21415113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.369154
X-RAY DIFFRACTIONr_chiral_restr0.1230.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02144
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5312.04302
X-RAY DIFFRACTIONr_mcbond_other2.5282.05303
X-RAY DIFFRACTIONr_mcangle_it4.0573.02379
X-RAY DIFFRACTIONr_mcangle_other4.0583.033380
X-RAY DIFFRACTIONr_scbond_it3.3322.265330
X-RAY DIFFRACTIONr_scbond_other3.3272.266331
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8333.288481
X-RAY DIFFRACTIONr_long_range_B_refined7.03316.59705
X-RAY DIFFRACTIONr_long_range_B_other6.94316.08687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.578→1.619 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 31 -
Rwork0.175 621 -
obs--100 %

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