[English] 日本語
Yorodumi
- PDB-3l4f: Crystal Structure of betaPIX Coiled-Coil Domain and Shank PDZ Complex -

+
Open data


ID or keywords:

Loading...

-
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


somatostatin receptor binding / determination of affect / negative regulation of microtubule nucleation / presynaptic actin cytoskeleton organization / Ephrin signaling / NRAGE signals death through JNK / EGFR downregulation / RHOU GTPase cycle / RHOV GTPase cycle / G alpha (12/13) signalling events ...somatostatin receptor binding / determination of affect / negative regulation of microtubule nucleation / presynaptic actin cytoskeleton organization / Ephrin signaling / NRAGE signals death through JNK / EGFR downregulation / RHOU GTPase cycle / RHOV GTPase cycle / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / synaptic receptor adaptor activity / olfactory behavior / RHOA GTPase cycle / synapse maturation / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / storage vacuole / astrocyte cell migration / structural constituent of postsynaptic density / positive regulation of growth hormone secretion / 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 / lamellipodium assembly / small GTPase-mediated signal transduction / positive regulation of dendritic spine development / adult behavior / mitotic spindle pole / Golgi organization / associative learning / social behavior / Rho protein signal transduction / neuromuscular process controlling balance / positive regulation of excitatory postsynaptic potential / excitatory synapse / hematopoietic progenitor cell differentiation / long-term memory / GABA-ergic synapse / 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 / protein-containing complex assembly / postsynaptic membrane / postsynapse / dendritic spine / postsynaptic density / neuron projection / positive regulation of apoptotic process / focal adhesion / neuronal cell body / centrosome / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / protein-containing complex / identical protein binding / membrane / 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 ...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 / PDZ superfamily / Ankyrin repeats (3 copies) / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more