[English] 日本語
Yorodumi
- PDB-3su8: Crystal structure of a truncated intracellular domain of Plexin-B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3su8
TitleCrystal structure of a truncated intracellular domain of Plexin-B1 in complex with Rac1
Components
  • Plexin-B1
  • Ras-related C3 botulinum toxin substrate 1
KeywordsAPOPTOSIS/SIGNALING PROTEIN / Axon guidance / signal transduction / APOPTOSIS-SIGNALING PROTEIN complex
Function / homology
Function and homology information


semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis / semaphorin receptor binding / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / negative regulation of osteoblast proliferation / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / localization within membrane / Activated NTRK2 signals through CDK5 ...semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis / semaphorin receptor binding / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / negative regulation of osteoblast proliferation / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / regulation of hydrogen peroxide metabolic process / negative regulation of receptor-mediated endocytosis / inhibitory synapse assembly / engulfment of apoptotic cell / ruffle assembly / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate CIT / cell projection assembly / RHO GTPases activate KTN1 / semaphorin receptor activity / ruffle organization / RHOD GTPase cycle / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / ossification involved in bone maturation / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / thioesterase binding / negative regulation of fibroblast migration / negative regulation of cell adhesion / Azathioprine ADME / Wnt signaling pathway, planar cell polarity pathway / regulation of stress fiber assembly / motor neuron axon guidance / sphingosine-1-phosphate receptor signaling pathway / regulation of lamellipodium assembly / Nef and signal transduction / Sema4D mediated inhibition of cell attachment and migration / Activation of RAC1 / positive regulation of Rho protein signal transduction / positive regulation of cell-substrate adhesion / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / lamellipodium assembly / GTPase activating protein binding / Activation of RAC1 downstream of NMDARs / semaphorin-plexin signaling pathway / NRAGE signals death through JNK / regulation of cytoskeleton organization / regulation of cell size / Rac protein signal transduction / positive regulation of axonogenesis / DSCAM interactions / small GTPase mediated signal transduction / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / Rho GDP-dissociation inhibitor binding / ficolin-1-rich granule membrane / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / RHO GTPases activate IQGAPs / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / regulation of GTPase activity / neuron projection morphogenesis / regulation of actin cytoskeleton organization / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / G protein activity / regulation of cell migration / RAC1 GTPase cycle / small monomeric GTPase / GTPase activator activity / actin filament polymerization / cell motility / cell-matrix adhesion / substrate adhesion-dependent cell spreading / actin filament organization / secretory granule membrane / VEGFR2 mediated vascular permeability / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / G alpha (12/13) signalling events
Similarity search - Function
GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, TIG domain 2 / TIG domain found in plexin / TIG domain / Plexin, TIG domain 1 / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat ...GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, TIG domain 2 / TIG domain found in plexin / TIG domain / Plexin, TIG domain 1 / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain profile. / Sema domain superfamily / Sema domain / small GTPase Rho family profile. / Small GTPase Rho / IPT/TIG domain / Rho GTPase activation protein / ig-like, plexins, transcription factors / domain found in Plexins, Semaphorins and Integrins / PSI domain / IPT domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulin-like fold / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Plexin-B1 / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBell, C.H. / Aricescu, A.R. / Jones, E.Y. / Siebold, C.
CitationJournal: Plos Biol. / Year: 2011
Title: A Dual Binding Mode for RhoGTPases in Plexin Signalling.
Authors: Bell, C.H. / Aricescu, A.R. / Jones, E.Y. / Siebold, C.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 1
X: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0764
Polymers90,5302
Non-polymers5472
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-26 kcal/mol
Surface area36310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.450, 63.810, 84.550
Angle α, β, γ (deg.)90.00, 107.53, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 20668.826 Da / Num. of mol.: 1 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000
#2: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 69860.766 Da / Num. of mol.: 1 / Fragment: UNP residues 1533-2135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43157
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
Sequence detailsS1625T CONFLICT IN UNP ENTRY O43157

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.81 %

-
Data collection

Diffraction
IDCrystal-ID
RCSB0666571
11
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15655 / Biso Wilson estimate: 72.26 Å2

-
Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→45.89 Å / Cor.coef. Fo:Fc: 0.9043 / Cor.coef. Fo:Fc free: 0.8542 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 786 5.02 %RANDOM
Rwork0.2066 ---
all0.2082 16434 --
obs0.2082 15648 --
Displacement parametersBiso mean: 66.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.707 Å20 Å210.6322 Å2
2---2.312 Å20 Å2
3---1.605 Å2
Refine analyzeLuzzati coordinate error obs: 0.678 Å
Refinement stepCycle: LAST / Resolution: 3.2→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5729 0 33 0 5762
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085885HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.937997HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2069SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes139HARMONIC2
X-RAY DIFFRACTIONt_gen_planes837HARMONIC5
X-RAY DIFFRACTIONt_it5885HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.6
X-RAY DIFFRACTIONt_other_torsion18.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion760SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6397SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2956 123 4.38 %
Rwork0.2528 2684 -
all0.2547 2807 -
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.63450.295-0.11041.64040.51443.3850.17530.0027-0.20150.3594-0.01680.2888-0.0877-0.4187-0.1585-0.00090.03170.1005-0.12070.0395-0.073422.4945-18.842631.646
21.99181.32670.90472.5341.03582.50950.0474-0.0902-0.3226-0.31240.00920.32090.0419-0.4128-0.0566-0.1318-0.068-0.07870.06380.062-0.11418.1161-35.0871-6.5955
32.3308-2.3222-4.26524.2102-3.51443.64570.00650.27610.1682-0.1570.07990.0653-0.153-0.0743-0.08640.17040.08820.0811-0.01490.12550.114242.9258-54.84115.6567
41.7625-0.1447-0.56992.61731.31333.53660.0983-0.07070.08740.08330.0985-0.3179-0.32150.058-0.1968-0.01630.01750.0908-0.1167-0.0084-0.136238.7754-19.882114.5173
52.39260.6145-1.05542.5630.68814.25210.2215-0.1683-0.01240.29660.0559-0.0036-0.08650.0262-0.2774-0.15290.0962-0.0279-0.26540.0791-0.189430.0475-18.897126.5785
66.68663.6071.3456.73270.89284.091-0.1325-0.1743-0.0456-0.3893-0.11960.137-0.08390.06680.2521-0.3039-0.1633-0.1876-0.181-0.036-0.0549-4.6276-50.4964-29.858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ X|1560 - X|1699 }X1560 - 1699
2X-RAY DIFFRACTION2{ X|1700 - X|1890 }X1700 - 1890
3X-RAY DIFFRACTION3{ X|1891 - X|1908 }X1891 - 1908
4X-RAY DIFFRACTION4{ X|1909 - X|1999 }X1909 - 1999
5X-RAY DIFFRACTION5{ X|2000 - X|2129 }X2000 - 2129
6X-RAY DIFFRACTION6{ A|1 - A|178 }A1 - 178

+
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