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- PDB-5e6p: PlexinB2 cytoplasmic region/PDZ-RhoGEF PDZ domain complex -

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Basic information

Entry
Database: PDB / ID: 5e6p
TitlePlexinB2 cytoplasmic region/PDZ-RhoGEF PDZ domain complex
Components
  • Plexin-B2
  • Rho guanine nucleotide exchange factor 11
KeywordsSIGNALING PROTEIN / Plexin / PDZ / PDZ-RhoGEF / Complex
Function / homology
Function and homology information


tRNA stabilization / excitatory synapse assembly / negative regulation of translation in response to stress / semaphorin receptor complex / semaphorin receptor activity / regulation of neuron migration / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / regulation of GTPase activity ...tRNA stabilization / excitatory synapse assembly / negative regulation of translation in response to stress / semaphorin receptor complex / semaphorin receptor activity / regulation of neuron migration / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / regulation of GTPase activity / positive regulation of axonogenesis / RHOB GTPase cycle / NRAGE signals death through JNK / cellular response to stress / RHOC GTPase cycle / establishment of cell polarity / regulation of protein phosphorylation / homophilic cell-cell adhesion / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / neuroblast proliferation / RHOA GTPase cycle / striated muscle contraction / Rho protein signal transduction / synapse assembly / RAC1 GTPase cycle / receptor-mediated endocytosis / regulation of cell migration / GTPase activator activity / guanyl-nucleotide exchange factor activity / positive regulation of translation / regulation of cell growth / neural tube closure / positive regulation of neuron projection development / G protein-coupled receptor binding / brain development / extracellular matrix / transmembrane signaling receptor activity / regulation of cell shape / G alpha (12/13) signalling events / signaling receptor activity / actin cytoskeleton organization / cytoplasmic translation / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin-B, PSI domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Plexin, TIG domain 1 / TIG domain ...: / Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin-B, PSI domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / ARHGEF1-like, PH domain / PH domain / Plexin family / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / Plexin repeat / Plexin repeat / RGS, subdomain 2 / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / RGS domain superfamily / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / 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. / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / PDZ domain / Pdz3 Domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / PDZ domain / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like (UB roll) / PH-like domain superfamily / Immunoglobulin E-set / Roll / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Plexin-B2 / Rho guanine nucleotide exchange factor 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.215 Å
AuthorsPascoe, H.G. / Zhang, X.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088197 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM031954 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008203 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ-RhoGEF.
Authors: Pascoe, H.G. / Gutowski, S. / Chen, H. / Brautigam, C.A. / Chen, Z. / Sternweis, P.C. / Zhang, X.
History
DepositionOct 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: Plexin-B2
B: Rho guanine nucleotide exchange factor 11


Theoretical massNumber of molelcules
Total (without water)81,0962
Polymers81,0962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-6 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.152, 126.152, 211.465
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Plexin-B2


Mass: 71868.688 Da / Num. of mol.: 1 / Fragment: UNP residues 1226-1842
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxnb2 / Plasmid: pskb2 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express / References: UniProt: B2RXS4
#2: Protein Rho guanine nucleotide exchange factor 11 / PDZ-RhoGEF


Mass: 9227.785 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 42-125)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF11, KIAA0380 / Plasmid: pskb2 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: O15085

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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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.2 M K/Na tartrate, 0.1 M Na citrate pH 5.3, 1.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979237 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979237 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 16847 / % possible obs: 99.9 % / Redundancy: 30.1 % / Biso Wilson estimate: 130.9 Å2 / Rsym value: 0.099 / Net I/σ(I): 56
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 27.4 % / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
Cootmodel building
HKL-3000data collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IG3

3ig3


Resolution: 3.215→48.53 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 38.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 731 5.03 %Random selection
Rwork0.2542 ---
obs0.2562 14538 86.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.215→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 0 0 4478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044563
X-RAY DIFFRACTIONf_angle_d0.7546206
X-RAY DIFFRACTIONf_dihedral_angle_d12.5481610
X-RAY DIFFRACTIONf_chiral_restr0.052744
X-RAY DIFFRACTIONf_plane_restr0.003776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.215-3.46320.45791280.39872266X-RAY DIFFRACTION73
3.4632-3.81160.42631210.35632346X-RAY DIFFRACTION75
3.8116-4.36290.33071570.27382696X-RAY DIFFRACTION86
4.3629-5.49550.3041470.26623113X-RAY DIFFRACTION97
5.4955-48.53670.25781780.22373386X-RAY DIFFRACTION100
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)
13.6882-1.2270.13520.78270.21662.74140.59590.6178-0.37740.0893-0.4276-0.34050.3168-0.2526-0.2311.1488-0.2824-0.30870.92260.21581.276695.1313-16.0781-0.6129
23.3888-0.2037-2.25442.9574-0.92136.171-0.4244-0.256-1.04010.0682-0.0598-0.19820.3410.74150.43490.53850.0430.04810.65260.18981.1529109.4092-30.993632.2008
34.7837-0.1079-0.0843.84080.65693.3247-0.01930.6692-1.2952-0.2162-1.09730.5083-0.2025-0.60880.31771.0589-0.02980.71211.45470.45722.144773.5984-48.605452.0995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1461:1598 )A1461 - 1598
2X-RAY DIFFRACTION2( CHAIN A AND ( RESID 1275:1459 OR RESID 1622:1836 ) )A1275 - 1459
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 1275:1459 OR RESID 1622:1836 ) )A1622 - 1836
4X-RAY DIFFRACTION3( CHAIN A AND RESID 1837:1842 ) OR ( CHAIN B AND RESID 45:121 )A1837 - 1842
5X-RAY DIFFRACTION3( CHAIN A AND RESID 1837:1842 ) OR ( CHAIN B AND RESID 45:121 )B45 - 121

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