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- PDB-4wci: Crystal structure of the 1st SH3 domain from human CD2AP (CMS) in... -

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Basic information

Entry
Database: PDB / ID: 4wci
TitleCrystal structure of the 1st SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 378-393) from human RIN3
Components
  • CD2-associated protein
  • Ras and Rab interactor 3
KeywordsSIGNALING PROTEIN / Endocytosis Adaptor protein Protein-peptide binary complex Kidney / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of mast cell chemotaxis / 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 ...negative regulation of mast cell chemotaxis / 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 / regulation of vesicle size / endothelium development / immunological synapse formation / 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 / RAB GEFs exchange GTP for GDP on RABs / cell-cell junction organization / filopodium assembly / negative regulation of receptor internalization / podosome / Nephrin family interactions / clathrin binding / maintenance of blood-brain barrier / nuclear envelope lumen / glucose import / cell leading edge / filamentous actin / neurotrophin TRK receptor signaling pathway / centriolar satellite / protein secretion / endocytic vesicle / lymph node development / adipose tissue development / stress-activated MAPK cascade / ruffle / ERK1 and ERK2 cascade / actin filament polymerization / GTPase activator activity / guanyl-nucleotide exchange factor activity / trans-Golgi network membrane / liver development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / actin filament organization / positive regulation of protein secretion / regulation of actin cytoskeleton organization / synapse organization / response to virus / regulation of synaptic plasticity / protein catabolic process / response to insulin / neuromuscular junction / lipid metabolic process / structural constituent of cytoskeleton / fibrillar center / small GTPase binding / SH3 domain binding / response to wounding / endocytosis / positive regulation of protein localization to nucleus / male gonad development / actin filament binding / cell migration / actin cytoskeleton / late endosome / T cell receptor signaling pathway / growth cone / cytoplasmic vesicle / protein-containing complex assembly / response to oxidative stress / vesicle / negative regulation of neuron apoptotic process / cell population proliferation / early endosome / cadherin binding / inflammatory response / cell cycle / axon / cell division / neuronal cell body / apoptotic process / dendrite / signal transduction / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ras and Rab interactor 3, SH2 domain / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 ...Ras and Rab interactor 3, SH2 domain / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Variant SH3 domain / SH3 Domains / SH3 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Ras and Rab interactor 3 / CD2-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRouka, E. / Simister, P.C. / Janning, M. / Kirsch, K.H. / Krojer, T. / Knapp, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Rouka, E. / Simister, P.C. / Janning, M. / Kirsch, K.H. / Krojer, T. / Knapp, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Feller, S.M. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Differential Recognition Preferences of the Three Src Homology 3 (SH3) Domains from the Adaptor CD2-associated Protein (CD2AP) and Direct Association with Ras and Rab Interactor 3 (RIN3).
Authors: Rouka, E. / Simister, P.C. / Janning, M. / Kumbrink, J. / Konstantinou, T. / Muniz, J.R. / Joshi, D. / O'Reilly, N. / Volkmer, R. / Ritter, B. / Knapp, S. / von Delft, F. / Kirsch, K.H. / Feller, S.M.
History
DepositionSep 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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: CD2-associated protein
B: Ras and Rab interactor 3
C: CD2-associated protein
D: Ras and Rab interactor 3
E: CD2-associated protein
F: Ras and Rab interactor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4488
Polymers28,2566
Non-polymers1922
Water5,026279
1
A: CD2-associated protein
B: Ras and Rab interactor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5153
Polymers9,4192
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-8 kcal/mol
Surface area4780 Å2
MethodPISA
2
C: CD2-associated protein
D: Ras and Rab interactor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5153
Polymers9,4192
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-9 kcal/mol
Surface area4990 Å2
MethodPISA
3
E: CD2-associated protein
F: Ras and Rab interactor 3


Theoretical massNumber of molelcules
Total (without water)9,4192
Polymers9,4192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-3 kcal/mol
Surface area5110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.526, 55.362, 64.557
Angle α, β, γ (deg.)90.00, 131.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-235-

HOH

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Components

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


Mass: 7593.522 Da / Num. of mol.: 3 / Fragment: UNP residues 1-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD2AP / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y5K6
#2: Protein/peptide Ras and Rab interactor 3 / Ras interaction/interference protein 3


Mass: 1825.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8TB24
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ca(ac) pH 4.2, 0.2 M Li2SO4 and 25% PEG 10 000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.65→48.19 Å / Num. all: 29731 / Num. obs: 29622 / % possible obs: 97.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 6.6
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.4 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J6F

2j6f


Resolution: 1.65→48.186 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1505 5.08 %Random selection
Rwork0.1924 ---
obs0.1938 29619 97.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→48.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 10 279 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071868
X-RAY DIFFRACTIONf_angle_d1.012535
X-RAY DIFFRACTIONf_dihedral_angle_d12.054749
X-RAY DIFFRACTIONf_chiral_restr0.044267
X-RAY DIFFRACTIONf_plane_restr0.005336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70330.32121390.27772351X-RAY DIFFRACTION91
1.7033-1.76410.29551450.24452497X-RAY DIFFRACTION97
1.7641-1.83480.26791350.21982583X-RAY DIFFRACTION98
1.8348-1.91830.21961330.19382575X-RAY DIFFRACTION99
1.9183-2.01940.19731140.192505X-RAY DIFFRACTION96
2.0194-2.14590.19441370.17952615X-RAY DIFFRACTION99
2.1459-2.31160.23621550.1842585X-RAY DIFFRACTION99
2.3116-2.54420.22111430.18522575X-RAY DIFFRACTION99
2.5442-2.91240.19741180.18672572X-RAY DIFFRACTION97
2.9124-3.66910.17571350.172629X-RAY DIFFRACTION99
3.6691-48.20630.22581510.1972627X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.28930.0943-0.33032.49780.36351.37480.00650.13-0.0449-0.1093-0.01850.0698-0.0032-0.0220.00640.1150.005-0.00480.0740.00210.0841-9.28414.0042-10.9796
28.07162.40981.08385.95020.29232.40670.0943-0.04410.4604-0.0018-0.10260.1266-0.3165-0.17250.00950.13720.0284-0.00570.0774-0.03410.1274-11.940815.9392-8.63
32.20330.6683-0.55670.5804-0.68831.1299-0.03720.1099-0.1077-0.06930.0158-0.07420.1069-0.01280.01360.11510.00360.00530.0576-0.02070.0833-3.5861-18.8426-11.79
45.1459-0.48320.98756.9862-1.37595.82190.16740.1543-0.1941-0.4296-0.05680.44480.2846-0.1095-0.11450.1159-0.0382-0.00350.07190.00050.1713-14.0624-25.7125-9.3881
52.4839-0.99791.07691.7153-0.00832.00870.02820.18170.1696-0.1035-0.0402-0.0301-0.09160.13170.01890.1091-0.00290.02360.09520.01890.099113.0624-2.4457-11.9963
64.5903-1.0701-0.3718.21241.10163.8979-0.00750.213-0.0581-0.14330.1483-0.34570.07140.1489-0.14370.09490.0108-0.00640.10630.01510.107524.2386-8.1031-9.4071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 58)
2X-RAY DIFFRACTION2(chain 'B' and resid 380 through 389)
3X-RAY DIFFRACTION3(chain 'C' and resid -4 through 58)
4X-RAY DIFFRACTION4(chain 'D' and resid 379 through 388)
5X-RAY DIFFRACTION5(chain 'E' and resid -4 through 58)
6X-RAY DIFFRACTION6(chain 'F' and resid 379 through 389)

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