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- PDB-7ajk: Crystal structure of CRYI-B Rac1 complex -

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Basic information

Entry
Database: PDB / ID: 7ajk
TitleCrystal structure of CRYI-B Rac1 complex
Components
  • CYFIP-related Rac1 interactor B
  • Ras-related C3 botulinum toxin substrate 1
KeywordsCYTOSOLIC PROTEIN / Actin / cytoskeleton / Rac1 / GTPase / Inhibitor
Function / homology
Function and homology information


MHC class Ib protein binding, via antigen binding groove / negative regulation of small GTPase mediated signal transduction / regulation of respiratory burst / regulation of neutrophil migration / cellular response to molecule of bacterial origin / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of hydrogen peroxide metabolic process / negative regulation of receptor-mediated endocytosis ...MHC class Ib protein binding, via antigen binding groove / negative regulation of small GTPase mediated signal transduction / regulation of respiratory burst / regulation of neutrophil migration / cellular response to molecule of bacterial origin / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of hydrogen peroxide metabolic process / negative regulation of receptor-mediated endocytosis / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / negative regulation of actin filament polymerization / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of chemotaxis / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / positive regulation of bicellular tight junction assembly / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / motor neuron axon guidance / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / Activation of RAC1 / RHO GTPases activate KTN1 / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / Azathioprine ADME / positive regulation of cell-substrate adhesion / positive regulation of neutrophil chemotaxis / Sema4D mediated inhibition of cell attachment and migration / Ephrin signaling / CD28 dependent Vav1 pathway / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / regulation of establishment of cell polarity / positive regulation of memory T cell activation / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / NRAGE signals death through JNK / regulation of cell size / positive regulation of Rho protein signal transduction / Rho GDP-dissociation inhibitor binding / establishment or maintenance of cell polarity / regulation of mitochondrial fission / Rac protein signal transduction / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / positive regulation of focal adhesion assembly / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / positive regulation of microtubule polymerization / actin filament polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / regulation of cell migration / secretory granule membrane / platelet alpha granule lumen / small monomeric GTPase / actin filament organization / cell-matrix adhesion / Signal transduction by L1 / VEGFR2 mediated vascular permeability / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell chemotaxis / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / cell motility / RHO GTPases Activate Formins / trans-Golgi network / Signaling by SCF-KIT / MAPK6/MAPK4 signaling / small GTPase binding
Similarity search - Function
CYFIP-related Rac1 interactor / CYRIA/CYRIB, Rac1 binding domain / CYRIA/CYRIB Rac1 binding domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases ...CYFIP-related Rac1 interactor / CYRIA/CYRIB, Rac1 binding domain / CYRIA/CYRIB Rac1 binding domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related C3 botulinum toxin substrate 1 / CYFIP-related Rac1 interactor B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYelland, T. / Anh, L. / Insall, R. / Machesky, L. / Ismail, S.
Funding support1items
OrganizationGrant numberCountry
Cancer Research UK
CitationJournal: Structure / Year: 2021
Title: Structural Basis of CYRI-B Direct Competition with Scar/WAVE Complex for Rac1.
Authors: Yelland, T. / Le, A.H. / Nikolaou, S. / Insall, R. / Machesky, L. / Ismail, S.
History
DepositionSep 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
BBB: Ras-related C3 botulinum toxin substrate 1
CCC: CYFIP-related Rac1 interactor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2324
Polymers56,6862
Non-polymers5472
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, 30uM Kd
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-26 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.870, 81.870, 355.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 19836.857 Da / Num. of mol.: 1
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, small monomeric GTPase
#2: Protein CYFIP-related Rac1 interactor B / L1


Mass: 36848.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYRIB, CYRI, FAM49B, BM-009 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NUQ9
#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


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop
Details: 8% v/v PEG4,000 0.1M Tris pH 8.5 0.2M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 3.1→59.382 Å / Num. obs: 13493 / % possible obs: 97.92 % / Redundancy: 10.6 % / CC1/2: 0.99 / Net I/σ(I): 18.7
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 2398 / CC1/2: 0.917

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GZL

4gzl


Resolution: 3.1→59.382 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.891 / SU B: 23.055 / SU ML: 0.397 / Cross valid method: FREE R-VALUE / ESU R Free: 0.475
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2818 672 4.98 %
Rwork0.2486 12821 -
all0.25 --
obs-13493 97.839 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 79.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.897 Å20.449 Å20 Å2
2--0.897 Å20 Å2
3----2.91 Å2
Refinement stepCycle: LAST / Resolution: 3.1→59.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3567 0 33 12 3612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133663
X-RAY DIFFRACTIONr_bond_other_d00.0173451
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.654965
X-RAY DIFFRACTIONr_angle_other_deg1.1281.5768002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2735450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.65922.472178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26515642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7051522
X-RAY DIFFRACTIONr_chiral_restr0.0420.2490
X-RAY DIFFRACTIONr_chiral_restr_other0.3950.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
X-RAY DIFFRACTIONr_nbd_refined0.2090.2876
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2280.23200
X-RAY DIFFRACTIONr_nbtor_refined0.160.21833
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4990.217
X-RAY DIFFRACTIONr_nbd_other0.2750.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2770.23
X-RAY DIFFRACTIONr_mcbond_it7.3988.4261818
X-RAY DIFFRACTIONr_mcbond_other7.3998.4211816
X-RAY DIFFRACTIONr_mcangle_it10.79412.6542264
X-RAY DIFFRACTIONr_mcangle_other10.79512.6542264
X-RAY DIFFRACTIONr_scbond_it7.448.8611844
X-RAY DIFFRACTIONr_scbond_other7.4388.8631845
X-RAY DIFFRACTIONr_scangle_it11.18813.0932701
X-RAY DIFFRACTIONr_scangle_other11.18613.0952702
X-RAY DIFFRACTIONr_lrange_it14.802101.7354193
X-RAY DIFFRACTIONr_lrange_other14.801101.7554194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.1810.315420.287937X-RAY DIFFRACTION99.5931
3.181-3.2680.374500.314906X-RAY DIFFRACTION99.4797
3.268-3.3620.408560.317862X-RAY DIFFRACTION99.5662
3.362-3.4660.404430.308849X-RAY DIFFRACTION98.1298
3.466-3.5790.302390.285844X-RAY DIFFRACTION99.1021
3.579-3.7050.33420.279813X-RAY DIFFRACTION99.073
3.705-3.8440.327380.272767X-RAY DIFFRACTION98.2906
3.844-4.0010.227400.267751X-RAY DIFFRACTION98.875
4.001-4.1790.311460.248713X-RAY DIFFRACTION97.6834
4.179-4.3830.207410.208686X-RAY DIFFRACTION98.6432
4.383-4.6190.216330.207668X-RAY DIFFRACTION97.2261
4.619-4.8990.296220.216633X-RAY DIFFRACTION97.6155
4.899-5.2370.248320.242596X-RAY DIFFRACTION97.6672
5.237-5.6550.376320.276543X-RAY DIFFRACTION96.9646
5.655-6.1940.314270.274521X-RAY DIFFRACTION96.8198
6.194-6.9220.28230.265476X-RAY DIFFRACTION96.7054
6.922-7.9890.212280.232410X-RAY DIFFRACTION93.9914
7.989-9.7730.173160.179362X-RAY DIFFRACTION95.2141
9.773-13.7750.156120.177304X-RAY DIFFRACTION92.9412
13.775-59.3820.532100.346180X-RAY DIFFRACTION87.963

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