[English] 日本語
Yorodumi
- PDB-3eg5: Crystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eg5
TitleCrystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP
Components
  • Cell division control protein 42 homolog
  • Protein diaphanous homolog 1
KeywordsSIGNALING PROTEIN / PROTEIN-PROTEIN COMPLEX / RHO PROTEINS / DIAPHANOUS / FORMINS / ARMADILLO REPEAT / G-PROTEIN / GTPASE / Alternative splicing / Cell membrane / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation / Actin-binding / Cell projection / Coiled coil / Cytoplasm / Cytoskeleton / Phosphoprotein / Ubl conjugation
Function / homology
Function and homology information


DCC mediated attractive signaling / RHO GTPases activate KTN1 / RHOV GTPase cycle / negative regulation of neuron projection regeneration / CD28 dependent Vav1 pathway / multicellular organismal locomotion / RHOQ GTPase cycle / ERBB2 Regulates Cell Motility / RHOF GTPase cycle / RHOU GTPase cycle ...DCC mediated attractive signaling / RHO GTPases activate KTN1 / RHOV GTPase cycle / negative regulation of neuron projection regeneration / CD28 dependent Vav1 pathway / multicellular organismal locomotion / RHOQ GTPase cycle / ERBB2 Regulates Cell Motility / RHOF GTPase cycle / RHOU GTPase cycle / RAC3 GTPase cycle / RHOC GTPase cycle / RHO GTPases activate PAKs / CDC42 GTPase cycle / RAC2 GTPase cycle / G beta:gamma signalling through CDC42 / GPVI-mediated activation cascade / establishment or maintenance of apical/basal cell polarity / RHOD GTPase cycle / EPHB-mediated forward signaling / nucleus localization / GBD domain binding / EGFR downregulation / RHO GTPases Activate WASPs and WAVEs / Golgi transport complex / positive regulation of pinocytosis / actin nucleation / neuron projection retraction / RAC1 GTPase cycle / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / RHOB GTPase cycle / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / RHO GTPases activate IQGAPs / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / RHO GTPases Activate Formins / neuron fate determination / RHOA GTPase cycle / regulation of attachment of spindle microtubules to kinetochore / RHOG GTPase cycle / MAPK6/MAPK4 signaling / positive regulation of pseudopodium assembly / profilin binding / Regulation of actin dynamics for phagocytic cup formation / Factors involved in megakaryocyte development and platelet production / cardiac conduction system development / host-mediated perturbation of viral process / heart process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / Myogenesis / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / VEGFA-VEGFR2 Pathway / regulation of microtubule-based process / thioesterase binding / embryonic heart tube development / regulation of postsynapse organization / axon midline choice point recognition / positive regulation of filopodium assembly / endosomal transport / phagocytosis, engulfment / nuclear migration / regulation of mitotic nuclear division / heart contraction / Rho GDP-dissociation inhibitor binding / positive regulation of cytokinesis / spindle midzone / establishment or maintenance of cell polarity / cell leading edge / brush border / lamellipodium membrane / synaptic vesicle endocytosis / ephrin receptor signaling pathway / negative regulation of protein-containing complex assembly / Rho protein signal transduction / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of stress fiber assembly / actin filament polymerization / Neutrophil degranulation / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / actin filament organization / small monomeric GTPase / integrin-mediated signaling pathway / cell periphery / cell projection / filopodium / establishment of localization in cell / sensory perception of sound / cell-cell adhesion / brain development
Similarity search - Function
Formin, diaphanous GTPase-binding domain / Formin, FH3 diaphanous domain / DRF autoregulatory / DRF Autoregulatory Domain / Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / : / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Cdc42 ...Formin, diaphanous GTPase-binding domain / Formin, FH3 diaphanous domain / DRF autoregulatory / DRF Autoregulatory Domain / Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / : / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Cdc42 / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Small GTPase Rho / Small GTPase Rho domain profile. / Histone, subunit A / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Recoverin; domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Alpha Horseshoe / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Protein diaphanous homolog 1 / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLammers, M. / Meyer, S. / Kuehlmann, D. / Wittinghofer, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Specificity of Interactions between mDia Isoforms and Rho Proteins
Authors: Lammers, M. / Meyer, S. / Kuhlmann, D. / Wittinghofer, A.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division control protein 42 homolog
B: Protein diaphanous homolog 1
C: Cell division control protein 42 homolog
D: Protein diaphanous homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1008
Polymers128,0074
Non-polymers1,0934
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.269, 71.269, 244.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUAA1 - 1781 - 178
21METMETGLUGLUCC1 - 1781 - 178
12VALVALHISHISBB83 - 43515 - 367
22VALVALHISHISDD83 - 43515 - 367

NCS ensembles :
ID
1
2

-
Components

#1: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 19802.719 Da / Num. of mol.: 2 / Fragment: UNP residues 1-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: MUS MUSCULUS / Gene: Cdc42 / Plasmid: CDC42-1-178-PGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60766
#2: Protein Protein diaphanous homolog 1 / Diaphanous-related formin-1 / DRF1 / p140mDIA / mDIA1


Mass: 44200.680 Da / Num. of mol.: 2 / Fragment: MDIAN-TSH, UNP residues 69-451 / Mutation: N164T, N165S, N166H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: MUS MUSCULUS / Gene: Diaph1 / Plasmid: MDIAN-TSH-PGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08808
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: Bis-Tris-Propane (PH 8.8 adjusted with citric acid), 26% (w/v) PEG 3350, 250mM Na-Tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9763 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2007 / Details: MIRRORS
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→43.478 Å / Num. all: 38241 / Num. obs: 38038 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Rsym value: 0.084 / Net I/σ(I): 13.52
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.69 / Rsym value: 0.333 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z2C

1z2c


Resolution: 2.7→43.47 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.101 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.986 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24333 1908 5 %RANDOM
Rwork0.20629 ---
obs0.20816 36130 99.49 %-
all-38038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20 Å2
2--0.19 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8228 0 66 47 8341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228428
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.99811400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02351022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53624.922386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.867151592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0341552
X-RAY DIFFRACTIONr_chiral_restr0.0720.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026180
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.23859
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25858
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.2116
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3471.55298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.59828360
X-RAY DIFFRACTIONr_scbond_it0.82833467
X-RAY DIFFRACTIONr_scangle_it1.4114.53040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1391tight positional0.010.05
2B2723tight positional0.010.05
1A1391tight thermal0.020.5
2B2723tight thermal0.020.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 125 -
Rwork0.287 2693 -
obs--99.86 %

+
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