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- PDB-3l4f: Crystal Structure of betaPIX Coiled-Coil Domain and Shank PDZ Complex -

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Basic information

Entry
Database: PDB / ID: 3l4f
TitleCrystal Structure of betaPIX Coiled-Coil Domain and Shank PDZ Complex
Components
  • Rho guanine nucleotide exchange factor 7
  • SH3 and multiple ankyrin repeat domains protein 1
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / COILED-COIL / PDZ / Guanine-nucleotide releasing factor / Phosphoprotein / SH3 domain / ANK repeat / Cell junction / Cell membrane / Membrane / Postsynaptic cell membrane / Synapse / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


presynaptic actin cytoskeleton organization / somatostatin receptor binding / determination of affect / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events ...presynaptic actin cytoskeleton organization / somatostatin receptor binding / determination of affect / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / synaptic receptor adaptor activity / RHOA GTPase cycle / olfactory behavior / synapse maturation / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / structural constituent of postsynaptic density / righting reflex / postsynaptic actin cytoskeleton organization / protein localization to synapse / vocalization behavior / habituation / regulation of AMPA receptor activity / ankyrin repeat binding / dendritic spine morphogenesis / gamma-tubulin binding / positive regulation of dendritic spine development / lamellipodium assembly / adult behavior / small GTPase-mediated signal transduction / mitotic spindle pole / Golgi organization / social behavior / positive regulation of excitatory postsynaptic potential / associative learning / neuromuscular process controlling balance / Rho protein signal transduction / excitatory synapse / GABA-ergic synapse / long-term memory / hematopoietic progenitor cell differentiation / ruffle / ionotropic glutamate receptor binding / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / SH3 domain binding / signaling receptor complex adaptor activity / lamellipodium / cell cortex / growth cone / scaffold protein binding / postsynaptic membrane / postsynapse / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / positive regulation of apoptotic process / focal adhesion / centrosome / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / protein-containing complex / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
L1 transposable element, trimerization domain / Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PDZ domain 6 / PDZ domain ...L1 transposable element, trimerization domain / Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PDZ domain / Pdz3 Domain / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 7 / SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsIm, Y.J. / Kang, G.B. / Lee, J.H. / Song, H.E. / Park, K.R. / Kim, E. / Song, W.K. / Park, D. / Eom, S.H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural basis for asymmetric association of the betaPIX coiled coil and shank PDZ
Authors: Im, Y.J. / Kang, G.B. / Lee, J.H. / Park, K.R. / Song, H.E. / Kim, E. / Song, W.K. / Park, D. / Eom, S.H.
History
DepositionDec 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Dec 25, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 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: Rho guanine nucleotide exchange factor 7
B: Rho guanine nucleotide exchange factor 7
C: Rho guanine nucleotide exchange factor 7
D: SH3 and multiple ankyrin repeat domains protein 1


Theoretical massNumber of molelcules
Total (without water)36,6194
Polymers36,6194
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-63 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.666, 47.666, 263.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Rho guanine nucleotide exchange factor 7 / PAK-interacting exchange factor beta / Beta-Pix


Mass: 7333.420 Da / Num. of mol.: 3 / Fragment: The C-terminal coiled-coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: beta1PIX / Plasmid: PET-DUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O55043
#2: Protein SH3 and multiple ankyrin repeat domains protein 1 / Shank1 / GKAP/SAPAP-interacting protein / SPANK-1 / Synamon / Somatostatin receptor-interacting ...Shank1 / GKAP/SAPAP-interacting protein / SPANK-1 / Synamon / Somatostatin receptor-interacting protein / SSTR-interacting protein / SSTRIP


Mass: 14618.661 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Shank1 / Plasmid: PET-DUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WV48
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% ETHANOL, 10% ETHYLENE GLYCOL, 0.1M MES-NAOH, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A10.91993
SYNCHROTRONPhoton Factory BL-5A20.97964, 0.97945, 0.96500
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDMay 25, 2006MIRRORS
ADSC QUANTUM 3152CCDNov 10, 2006MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2SI 111 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.919931
20.979641
30.979451
40.9651
ReflectionResolution: 2.8→50 Å / Num. all: 8808 / Num. obs: 8492 / % possible obs: 95.6 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 103.8 Å2 / Rsym value: 0.054 / Net I/σ(I): 36.6
Reflection shellResolution: 2.8→3 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 821 / Rsym value: 0.361 / % possible all: 93.4

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD
Starting model: 1Q3O

1q3o


Resolution: 2.8→41.28 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 730185.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 400 4.7 %RANDOM
Rwork0.272 ---
obs0.272 8492 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 99.98 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 91.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.62 Å216.7 Å20 Å2
2--6.62 Å20 Å2
3----13.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 20 2309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.065 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.492 58 4.3 %
Rwork0.434 1292 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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