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- PDB-3u23: Atomic resolution crystal structure of the 2nd SH3 domain from hu... -

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Basic information

Entry
Database: PDB / ID: 3u23
TitleAtomic resolution crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide from human RIN3
Components
  • CD2-associated protein
  • Ras and Rab interactor 3
KeywordsPROTEIN BINDING / Structural Genomics / Structural Genomics Consortium / SGC / Beta-barrel / Adaptor protein
Function / homology
Function and homology information


negative regulation of mast cell chemotaxis / response to glial cell derived neurotrophic factor / transforming growth factor beta1 production / localization of cell / negative regulation of small GTPase mediated signal transduction / slit diaphragm / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / podocyte differentiation ...negative regulation of mast cell chemotaxis / response to glial cell derived neurotrophic factor / transforming growth factor beta1 production / localization of cell / negative regulation of small GTPase mediated signal transduction / slit diaphragm / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / podocyte differentiation / regulation of vesicle size / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / protein heterooligomerization / collateral sprouting / renal albumin absorption / substrate-dependent cell migration, cell extension / cell-cell adhesion mediated by cadherin / phosphatidylinositol 3-kinase regulatory subunit binding / filopodium assembly / membrane organization / RAB GEFs exchange GTP for GDP on RABs / negative regulation of receptor internalization / cell-cell junction organization / Nephrin family interactions / podosome / clathrin binding / maintenance of blood-brain barrier / nuclear envelope lumen / neurotrophin TRK receptor signaling pathway / D-glucose import / filamentous actin / cell leading edge / protein secretion / endocytic vesicle / adipose tissue development / lymph node development / stress-activated MAPK cascade / ruffle / ERK1 and ERK2 cascade / actin filament polymerization / GTPase activator activity / actin filament organization / guanyl-nucleotide exchange factor activity / trans-Golgi network membrane / positive regulation of protein secretion / regulation of actin cytoskeleton organization / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein catabolic process / liver development / response to insulin / synapse organization / regulation of synaptic plasticity / SH3 domain binding / structural constituent of cytoskeleton / response to wounding / small GTPase binding / lipid metabolic process / positive regulation of protein localization to nucleus / response to virus / centriolar satellite / male gonad development / fibrillar center / endocytosis / actin filament binding / late endosome / cell migration / T cell receptor signaling pathway / actin cytoskeleton / growth cone / response to oxidative stress / protein-containing complex assembly / cytoplasmic vesicle / vesicle / negative regulation of neuron apoptotic process / early endosome / cell population proliferation / cadherin binding / inflammatory response / axon / cell division / neuronal cell body / apoptotic process / dendrite / signal transduction / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ras and Rab interactor 3, SH2 domain / RIN1-like 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. ...Ras and Rab interactor 3, SH2 domain / RIN1-like 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: 1.11 Å
AuthorsSimister, P.C. / Rouka, E. / Janning, M. / Muniz, J.R.C. / Kirsch, K.H. / Knapp, S. / von Delft, F. / Filippakopoulos, P. / Arrowsmith, C.H. / Krojer, T. ...Simister, P.C. / Rouka, E. / Janning, M. / Muniz, J.R.C. / Kirsch, K.H. / Knapp, S. / von Delft, F. / Filippakopoulos, P. / Arrowsmith, C.H. / Krojer, T. / Edwards, A.M. / Weigelt, J. / 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 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Other
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3103
Polymers9,2482
Non-polymers621
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-2 kcal/mol
Surface area4690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.130, 32.040, 39.180
Angle α, β, γ (deg.)90.00, 92.56, 90.00
Int Tables number5
Space group name H-MC121

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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 (E. coli) / References: UniProt: Q9Y5K6
#2: Protein/peptide Ras and Rab interactor 3 / Ras interaction/interference protein 3


Mass: 1803.201 Da / Num. of mol.: 1 / Fragment: unp residues 452-467 / Source method: obtained synthetically / Details: Synthesised peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8TB24
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 31.7 %
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 dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2011
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.11→27.43 Å / Num. all: 26161 / Num. obs: 24275 / % possible obs: 92.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 13.68 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.98
Reflection shellResolution: 1.11→1.14 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.24 / % possible all: 59.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2G6F, 1OEB, 2AK5, 2FEI, 3IQL

2g6f

1oeb

2ak5

2fei

3iql


Resolution: 1.11→27.43 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.332 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16663 1217 5 %RANDOM
Rwork0.15071 ---
obs0.15151 23056 92.79 %-
all-26161 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.91 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å2-0 Å2-0.17 Å2
2---0.91 Å2-0 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.11→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms562 0 4 86 652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022622
X-RAY DIFFRACTIONr_bond_other_d0.0010.02454
X-RAY DIFFRACTIONr_angle_refined_deg2.2712.015852
X-RAY DIFFRACTIONr_angle_other_deg1.58631130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.383579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62125.86229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37915122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.098154
X-RAY DIFFRACTIONr_chiral_restr0.1360.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02108
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_it2.5191.5369
X-RAY DIFFRACTIONr_mcbond_other0.7941.5140
X-RAY DIFFRACTIONr_mcangle_it3.852612
X-RAY DIFFRACTIONr_scbond_it5.2233253
X-RAY DIFFRACTIONr_scangle_it8.1984.5233
X-RAY DIFFRACTIONr_rigid_bond_restr2.11231076
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.11→1.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 57 -
Rwork0.337 1075 -
obs--59.36 %
Refinement TLS params.Method: refined / Origin x: 6.401 Å / Origin y: 5.769 Å / Origin z: 2.544 Å
111213212223313233
T0.2759 Å20.0174 Å2-0.0457 Å2-0.1028 Å2-0.0153 Å2--0.1118 Å2
L0.5881 °20.1086 °2-0.6112 °2-1.8449 °2-0.9909 °2--1.062 °2
S0.1267 Å °0.0452 Å °0.0037 Å °-0.1484 Å °-0.0572 Å °0.1937 Å °-0.0333 Å °-0.0027 Å °-0.0694 Å °

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