[English] 日本語
Yorodumi
- PDB-2wkq: Structure of a photoactivatable Rac1 containing the Lov2 C450A Mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wkq
TitleStructure of a photoactivatable Rac1 containing the Lov2 C450A Mutant
ComponentsNPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsTRANSFERASE / CELL ADHESION / NUCLEOTIDE-BINDING / PROTEIN ENGINEERING / RAS SUPERFAMILY LOV2 / PHOTOTROPIN1 / PROTEIN DESIGN / SMALL G-PROTEIN / LIGHT- INDUCED SIGNAL TRANSDUCTION / LOV2 / GTPASE / RHO FAMILY / ATP-BINDING / CHIMERA / NUCLEOTIDE-BINDING PROTEIN ENGINEERING / LIGHT-INDUCED SIGNAL TRANSDUCTION / ALTERNATIVE SPLICING / CELL MEMBRANE / ADP-RIBOSYLATION / LIPOPROTEIN / GTP-BINDING
Function / homology
Function and homology information


regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / blue light photoreceptor activity / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process ...regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / blue light photoreceptor activity / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Rho GDP-dissociation inhibitor binding / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / cell projection assembly / RHO GTPases activate CIT / RHO GTPases activate KTN1 / cortical cytoskeleton organization / ruffle organization / hepatocyte growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / Azathioprine ADME / regulation of stress fiber assembly / negative regulation of fibroblast migration / sphingosine-1-phosphate receptor signaling pathway / thioesterase binding / Wnt signaling pathway, planar cell polarity pathway / regulation of lamellipodium assembly / Nef and signal transduction / motor neuron axon guidance / 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 / Activation of RAC1 downstream of NMDARs / semaphorin-plexin signaling pathway / NRAGE signals death through JNK / regulation of cell size / Rac protein signal transduction / DSCAM interactions / positive regulation of lamellipodium assembly / establishment or maintenance of cell polarity / small GTPase mediated signal transduction / RHO GTPases activate PAKs / ficolin-1-rich granule membrane / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases / RHO GTPases activate PKNs / localization / regulation of actin cytoskeleton organization / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of microtubule polymerization / G protein activity / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / RAC1 GTPase cycle / neuron migration / actin filament polymerization / small monomeric GTPase / cell-matrix adhesion / substrate adhesion-dependent cell spreading / cell motility / actin filament organization / secretory granule membrane / RHO GTPases Activate Formins / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of endothelial cell migration / Signal transduction by L1 / cell projection / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / FCGR3A-mediated phagocytosis / Signaling by SCF-KIT / trans-Golgi network / extrinsic component of cytoplasmic side of plasma membrane / cytoplasmic ribonucleoprotein granule / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / ruffle membrane / actin cytoskeleton organization / response to wounding
Similarity search - Function
small GTPase Rho family profile. / Small GTPase Rho / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain ...small GTPase Rho family profile. / Small GTPase Rho / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / Rho (Ras homology) subfamily of Ras-like small GTPases / PAS repeat profile. / Small GTPase / Ras family / PAS domain / PAS domain superfamily / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / GUANOSINE-5'-TRIPHOSPHATE / NPH1-1 / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesAVENA SATIVA (oats)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWu, Y.I. / Frey, D. / Lungu, O.I. / Jaehrig, A. / Schlichting, I. / Kuhlman, B. / Hahn, K.M.
CitationJournal: Nature / Year: 2009
Title: A Genetically Encoded Photoactivatable Rac Controls the Motility of Living Cells.
Authors: Wu, Y.I. / Frey, D. / Lungu, O.I. / Jaehrig, A. / Schlichting, I. / Kuhlman, B. / Hahn, K.M.
History
DepositionJun 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8059
Polymers37,5711
Non-polymers1,2348
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)112.638, 112.638, 69.306
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein NPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 / P21-RAC1 / RAS-LIKE PROTEIN TC25 / CELL MIGRATION-INDUCING GENE 5 PROTEIN


Mass: 37570.918 Da / Num. of mol.: 1
Fragment: NPH1-1 RESIDUES 404-546 AND P21-RAC1, RESIDUES 4-180
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVENA SATIVA (oats), (gene. exp.) HOMO SAPIENS (human)
Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL10 GOLD / References: UniProt: O49003, UniProt: P63000

-
Non-polymers , 6 types, 405 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 450 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 61 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, CYS 450 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 61 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLU 91 TO HIS ENGINEERED RESIDUE IN CHAIN A, ASN 92 TO HIS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.5 % / Description: NONE
Crystal growDetails: 100 MM POTASSIUM CHLORIDE, 5% (W/V) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001
DetectorType: MARRESEARCH MX-225 / Detector: CCD / Date: Sep 26, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 66895 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 15.4 % / Biso Wilson estimate: 18.79 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.5
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.8 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASER1.3.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1MH1, 2VOU
Resolution: 1.6→39.887 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 16.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 3310 4.9 %
Rwork0.1686 --
obs0.1695 66891 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.895 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.9567 Å20 Å2-0 Å2
2--1.9567 Å20 Å2
3----3.9133 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 75 397 2989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092746
X-RAY DIFFRACTIONf_angle_d1.3113755
X-RAY DIFFRACTIONf_dihedral_angle_d19.2171049
X-RAY DIFFRACTIONf_chiral_restr0.085425
X-RAY DIFFRACTIONf_plane_restr0.006473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62290.20441380.19232636X-RAY DIFFRACTION99
1.6229-1.64710.20761380.18082612X-RAY DIFFRACTION100
1.6471-1.67280.21921380.17832623X-RAY DIFFRACTION100
1.6728-1.70030.20071370.18172614X-RAY DIFFRACTION99
1.7003-1.72960.20111400.17142652X-RAY DIFFRACTION100
1.7296-1.7610.21951350.17712597X-RAY DIFFRACTION100
1.761-1.79490.21861340.16912612X-RAY DIFFRACTION100
1.7949-1.83150.181340.16922632X-RAY DIFFRACTION100
1.8315-1.87140.20061350.16862634X-RAY DIFFRACTION100
1.8714-1.91490.21311360.17672665X-RAY DIFFRACTION100
1.9149-1.96280.18851350.16682603X-RAY DIFFRACTION100
1.9628-2.01580.19211360.16332640X-RAY DIFFRACTION100
2.0158-2.07520.1771370.16322646X-RAY DIFFRACTION100
2.0752-2.14210.19781360.16542632X-RAY DIFFRACTION100
2.1421-2.21870.24061370.16492644X-RAY DIFFRACTION100
2.2187-2.30750.18991380.16482655X-RAY DIFFRACTION100
2.3075-2.41250.16791390.16562660X-RAY DIFFRACTION100
2.4125-2.53970.20321380.16442642X-RAY DIFFRACTION100
2.5397-2.69880.19951380.17192662X-RAY DIFFRACTION100
2.6988-2.90710.18641390.17492652X-RAY DIFFRACTION100
2.9071-3.19950.17641410.172681X-RAY DIFFRACTION100
3.1995-3.66220.15831410.15642679X-RAY DIFFRACTION100
3.6622-4.6130.15191430.14772713X-RAY DIFFRACTION100
4.613-39.89910.17791470.16862795X-RAY DIFFRACTION100

+
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