[English] 日本語
Yorodumi
- PDB-5n6o: Wild type human Rac1-GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n6o
TitleWild type human Rac1-GDP
ComponentsRas-related C3 botulinum toxin substrate 1
KeywordsPROTEIN BINDING / Rac / GTPase / GDP / guanine exchange factor / GEF
Function / homology
Function and homology information


embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / positive regulation of ovarian follicle development / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation ...embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / positive regulation of ovarian follicle development / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / kinocilium / interneuron migration / regulation of cell adhesion involved in heart morphogenesis / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / cochlea morphogenesis / regulation of hydrogen peroxide metabolic process / regulation of neuron maturation / respiratory burst / WNT5:FZD7-mediated leishmania damping / ruffle organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / positive regulation of skeletal muscle acetylcholine-gated channel clustering / midbrain dopaminergic neuron differentiation / epithelial cell morphogenesis / cell projection assembly / GTP-dependent protein binding / positive regulation of bicellular tight junction assembly / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / regulation of neuron migration / negative regulation of fibroblast migration / RHO GTPases activate CIT / cell-cell junction organization / quinolinate biosynthetic process / Nef and signal transduction / motor neuron axon guidance / PCP/CE pathway / sphingosine-1-phosphate receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / Activation of RAC1 / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / Ephrin signaling / CD28 dependent Vav1 pathway / hyperosmotic response / positive regulation of neutrophil chemotaxis / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / regulation of receptor signaling pathway via JAK-STAT / lamellipodium assembly / positive regulation of ruffle assembly / NRAGE signals death through JNK / dendrite morphogenesis / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / positive regulation of dendritic spine development / positive regulation of Rho protein signal transduction / pericentriolar material / positive regulation of actin filament polymerization / Rac protein signal transduction / establishment or maintenance of cell polarity / synaptic transmission, GABAergic / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / positive regulation of insulin secretion involved in cellular response to glucose stimulus / RHO GTPases Activate NADPH Oxidases / regulation of neuronal synaptic plasticity / positive regulation of focal adhesion assembly / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / regulation of synaptic vesicle endocytosis / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / phagocytic cup / GPVI-mediated activation cascade / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization
Similarity search - Function
Small GTPase Rho / Small GTPase Rho domain 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 nucleotide triphosphate hydrolases / Rossmann fold ...Small GTPase Rho / Small GTPase Rho domain 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsCherfils, J. / Ferrandez, Y.
Funding support France, 1items
OrganizationGrant numberCountry
Labex lermit France
CitationJournal: Sci Rep / Year: 2017
Title: Allosteric inhibition of the guanine nucleotide exchange factor DOCK5 by a small molecule.
Authors: Ferrandez, Y. / Zhang, W. / Peurois, F. / Akendengue, L. / Blangy, A. / Zeghouf, M. / Cherfils, J.
History
DepositionFeb 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / struct / Item: _audit_author.name / _struct.pdbx_descriptor
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Nov 18, 2020Group: Derived calculations / Structure summary / Category: pdbx_struct_conn_angle / struct / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 1
B: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0946
Polymers39,1592
Non-polymers9354
Water95553
1
A: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0473
Polymers19,5801
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0473
Polymers19,5801
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.641, 82.656, 105.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 19579.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P63000
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0,1 mM MES ph 6.5 PEG 3350 20%

-
Data collection

DiffractionMean temperature: 291.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.586→65.158 Å / Num. obs: 11873 / % possible obs: 99.5 % / Redundancy: 6 % / Net I/σ(I): 8.4
Reflection scaleGroup code: 1

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→44.59 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.821 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.392 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.592 / SU Rfree Blow DPI: 0.319 / SU Rfree Cruickshank DPI: 0.319
RfactorNum. reflection% reflectionSelection details
Rfree0.252 637 5.37 %RANDOM
Rwork0.193 ---
obs0.196 11858 99.5 %-
Displacement parametersBiso max: 120.3 Å2 / Biso mean: 40.4 Å2 / Biso min: 8.25 Å2
Baniso -1Baniso -2Baniso -3
1-15.003 Å20 Å20 Å2
2---32.0673 Å20 Å2
3---17.0643 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: final / Resolution: 2.59→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 82 53 2885
Biso mean--28.76 25.96 -
Num. residues----352
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d986SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes440HARMONIC5
X-RAY DIFFRACTIONt_it2894HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion384SEMIHARMONIC5
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_contact3368SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2894HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3970HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion18.6
LS refinement shellResolution: 2.59→2.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 163 6.03 %
Rwork0.226 2541 -
all0.229 2704 -
obs--97.94 %

+
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