[English] 日本語
Yorodumi
- PDB-5bwm: The complex structure of C3cer exoenzyme and GDP bound RhoA (NADH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bwm
TitleThe complex structure of C3cer exoenzyme and GDP bound RhoA (NADH-bound state)
Components
  • ADP-ribosyltransferase
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN/Transferase / ADP Ribose Transferases / Bacterial Toxins / SIGNALING PROTEIN-Transferase complex
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity ...alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / regulation of systemic arterial blood pressure by endothelin / establishment of epithelial cell apical/basal polarity / beta selection / negative regulation of cell size / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / positive regulation of podosome assembly / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / odontogenesis / motor neuron apoptotic process / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / Rho protein signal transduction / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / endothelial cell migration / RHOA GTPase cycle / mitotic spindle assembly / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / negative regulation of reactive oxygen species biosynthetic process / RHO GTPases activate PKNs / skeletal muscle tissue development / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / regulation of cell migration / substrate adhesion-dependent cell spreading / cell-matrix adhesion / secretory granule membrane / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / neuron migration / cell morphogenesis / positive regulation of protein serine/threonine kinase activity / G protein activity / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / positive regulation of non-canonical NF-kappaB signal transduction / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events
Similarity search - Function
Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 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 ...Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 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 nucleotide triphosphate hydrolases / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Transforming protein RhoA / ADP-ribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Bacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsToda, A. / Tsurumura, T. / Yoshida, T. / Tsuge, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research, MEXT of Japan25121733 Japan
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Rho GTPase Recognition by C3 Exoenzyme Based on C3-RhoA Complex Structure.
Authors: Toda, A. / Tsurumura, T. / Yoshida, T. / Tsumori, Y. / Tsuge, H.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transforming protein RhoA
B: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7817
Polymers45,5242
Non-polymers1,2575
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-20 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.479, 50.479, 136.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20235.180 Da / Num. of mol.: 1 / Fragment: UNP residues 1-179 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pGEX4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61586
#2: Protein ADP-ribosyltransferase


Mass: 25288.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: c3cer / Plasmid: pRham / Production host: Escherichia coli DH10B (bacteria) / Strain (production host): DH10B / References: UniProt: Q8KNY0

-
Non-polymers , 5 types, 60 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES (pH 6.4), 20% PEG1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13477 / % possible obs: 99.6 % / Redundancy: 4.7 % / Net I/σ(I): 17.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.81 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A2B and 3BW8

1a2b

3bw8


Resolution: 2.5→45.56 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 27.71 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24596 665 4.9 %RANDOM
Rwork0.20926 ---
obs0.21103 12780 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 81 55 3210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023216
X-RAY DIFFRACTIONr_bond_other_d0.0050.023073
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9974339
X-RAY DIFFRACTIONr_angle_other_deg1.34237117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.8135380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31724.932148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.40515601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.5681518
X-RAY DIFFRACTIONr_chiral_restr0.1280.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213532
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1254.3141526
X-RAY DIFFRACTIONr_mcbond_other3.1264.3121525
X-RAY DIFFRACTIONr_mcangle_it4.8396.461904
X-RAY DIFFRACTIONr_mcangle_other4.8386.4621905
X-RAY DIFFRACTIONr_scbond_it3.4194.8031690
X-RAY DIFFRACTIONr_scbond_other3.4124.8031690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3467.0582436
X-RAY DIFFRACTIONr_long_range_B_refined9.40441.7613635
X-RAY DIFFRACTIONr_long_range_B_other9.40441.76213636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 41 -
Rwork0.386 987 -
obs--99.81 %
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)
10.4168-0.0968-0.21240.26910.58362.82430.0665-0.0769-0.0316-0.01-0.1435-0.05770.0596-0.09750.07690.1695-0.0218-0.03660.22-0.02540.5522-6.54425.270728.1989
22.9695-1.5612-0.43251.57190.82030.935-0.0207-0.5164-0.12030.32090.05290.120.38690.1315-0.03220.24540.0077-0.06670.31460.04680.45062.935418.59537.6816
31.80581.6421-0.36362.10151.16314.1453-0.0881-0.18620.099-0.1312-0.32950.101-0.1632-0.58580.41760.03250.1037-0.04920.3632-0.06260.5333-24.211927.489312.8633
42.28010.346-0.33640.11750.27762.2382-0.1958-0.22940.0072-0.0015-0.0857-0.01560.4699-0.31580.28150.2745-0.04420.04960.179-0.0320.5207-17.703715.99867.2726
50.6661-1.6517-0.75264.28852.88386.502-0.0772-0.0410.01880.13930.0947-0.01720.02940.0642-0.01740.2582-0.0062-0.01420.30490.03060.4199-8.598825.826611.5246
61.0157-0.25270.61230.76760.83412.3753-0.0665-0.27560.2212-0.2327-0.036-0.0947-0.0304-0.45380.10250.3016-0.0123-0.03620.2855-0.03410.5413-21.140424.80798.2168
75.38730.67782.89550.59330.77563.2045-0.4313-0.13960.132-0.15540.26740.00350.1060.04430.16390.33790.01310.06590.2349-0.02730.3999-5.485321.50850.5912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 114
2X-RAY DIFFRACTION2A115 - 179
3X-RAY DIFFRACTION3B15 - 61
4X-RAY DIFFRACTION4B62 - 146
5X-RAY DIFFRACTION5B147 - 155
6X-RAY DIFFRACTION6B156 - 196
7X-RAY DIFFRACTION7B197 - 219

+
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