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- PDB-4uwx: Structure of liprin-alpha3 in complex with mDia1 Diaphanous- inhi... -

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Basic information

Entry
Database: PDB / ID: 4uwx
TitleStructure of liprin-alpha3 in complex with mDia1 Diaphanous- inhibitory domain
Components
  • LIPRIN-ALPHA-3
  • PROTEIN DIAPHANOUS HOMOLOG 1
KeywordsPEPTIDE BINDING PROTEIN / PEPTIDE-BINDING PROTEIN / ACTIN POLYMERISATION / RHOGNBPS / SYNAPE MATURATION / CELL MOTILITY / FH1 / FH2 DOMAIN / ACTIN-NUCLEATION FACTOR - DIAPHANOUS-RELATED FORMIN
Function / homology
Function and homology information


epididymosome / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / negative regulation of neuron projection regeneration / multicellular organismal locomotion / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / RHOF GTPase cycle / RHOB GTPase cycle ...epididymosome / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / negative regulation of neuron projection regeneration / multicellular organismal locomotion / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / Receptor-type tyrosine-protein phosphatases / RHOD GTPase cycle / RHOA GTPase cycle / actin nucleation / neuron projection retraction / synaptic vesicle docking / RHO GTPases Activate Formins / protein localization to microtubule / profilin binding / cellular response to histamine / presynaptic active zone cytoplasmic component / neurotransmitter secretion / regulation of short-term neuronal synaptic plasticity / regulation of microtubule-based process / regulation of release of sequestered calcium ion into cytosol / axon midline choice point recognition / regulation of cytoskeleton organization / presynaptic active zone / synaptic vesicle exocytosis / brush border / synaptic vesicle endocytosis / ephrin receptor signaling pathway / cytoskeleton organization / actin filament polymerization / Neutrophil degranulation / acrosomal vesicle / actin filament / sensory perception of sound / synapse organization / brain development / protein localization / small GTPase binding / mitotic spindle / ruffle membrane / neuron projection development / presynapse / gene expression / actin binding / regulation of cell shape / actin cytoskeleton organization / transmembrane transporter binding / neuron projection / positive regulation of cell migration / centrosome / glutamatergic synapse / synapse / nucleus / identical protein binding / cytoplasm
Similarity search - Function
Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / Formin Homology Region 1 / LAR-interacting protein, Liprin / Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain ...Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / Formin Homology Region 1 / LAR-interacting protein, Liprin / Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / 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 / SAM domain (Sterile alpha motif) / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / NICKEL (II) ION / Protein diaphanous homolog 1 / Liprin-alpha-3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBrenig, J. / de Boor, S. / Knyphausen, P. / Kuhlmann, N. / Wroblowski, S. / Baldus, L. / Scislowski, L. / Artz, O. / Trauschies, P. / Baumann, U. ...Brenig, J. / de Boor, S. / Knyphausen, P. / Kuhlmann, N. / Wroblowski, S. / Baldus, L. / Scislowski, L. / Artz, O. / Trauschies, P. / Baumann, U. / Neundorf, I. / Lammers, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Biochemical Basis for the Inhibitory Effect of Liprin-Alpha3 on Mouse Diaphanous 1 (Mdia1) Function.
Authors: Brenig, J. / De Boor, S. / Knyphausen, P. / Kuhlmann, N. / Wroblowski, S. / Baldus, L. / Scislowski, L. / Artz, O. / Trauschies, P. / Baumann, U. / Neundorf, I. / Lammers, M.
History
DepositionAug 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN DIAPHANOUS HOMOLOG 1
B: PROTEIN DIAPHANOUS HOMOLOG 1
C: LIPRIN-ALPHA-3
D: LIPRIN-ALPHA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2158
Polymers58,8544
Non-polymers3624
Water7,080393
1
A: PROTEIN DIAPHANOUS HOMOLOG 1
C: LIPRIN-ALPHA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6084
Polymers29,4272
Non-polymers1812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-13.3 kcal/mol
Surface area12390 Å2
MethodPISA
2
B: PROTEIN DIAPHANOUS HOMOLOG 1
D: LIPRIN-ALPHA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6084
Polymers29,4272
Non-polymers1812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-13.2 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.090, 49.381, 106.370
Angle α, β, γ (deg.)90.00, 97.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN DIAPHANOUS HOMOLOG 1 / DIAPHANOUS-RELATED FORMIN-1 / DRF1 / P140MDIA / MDIA1 / MDIA1


Mass: 27199.328 Da / Num. of mol.: 2 / Fragment: DIAPHANOUS-INHIBITORY DOMAIN, RESIDUES 135-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O08808
#2: Protein/peptide LIPRIN-ALPHA-3 / PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE F POLYPEPTIDE-IN TERACTING PROTEIN ALPHA-3 / PTPRF- ...PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE F POLYPEPTIDE-IN TERACTING PROTEIN ALPHA-3 / PTPRF-INTERACTING PROTEIN ALPHA-3 / LIPR IN-ALPHA3


Mass: 2227.567 Da / Num. of mol.: 2 / Fragment: COILED-COIL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60469
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 8 / Details: 0.2 M NACL, 0.1 M TRIS/HCL PH 8.0, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 20, 2013 / Details: MIRRORS TOROIDAL FOCUSSING
RadiationMonochromator: BARTELS SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→105.37 Å / Num. obs: 75030 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.13 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.37
Reflection shellResolution: 1.65→1.66 Å / Redundancy: 3.24 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.33 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z2C
Resolution: 1.65→32.317 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.093 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.084 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 3777 5 %RANDOM
Rwork0.1755 ---
obs0.177 75028 99.667 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 26.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.064 Å20 Å2-0.136 Å2
2--2.16 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 18 393 4337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193985
X-RAY DIFFRACTIONr_bond_other_d0.0070.023965
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.9975354
X-RAY DIFFRACTIONr_angle_other_deg1.31639117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.225489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10924.74192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74915782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4441534
X-RAY DIFFRACTIONr_chiral_restr0.1110.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024428
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02850
X-RAY DIFFRACTIONr_nbd_refined0.3080.21439
X-RAY DIFFRACTIONr_nbd_other0.2950.261
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22037
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.259
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_it2.9671.8913985
X-RAY DIFFRACTIONr_mcbond_other0.7511.9753965
X-RAY DIFFRACTIONr_mcangle_it4.5052.7595354
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.8716.067516
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.45818.6923395
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 275 -
Rwork0.321 5223 -
obs--99.927 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3261-0.0494-0.32660.1150.18580.50680.0035-0.03590.0021-0.00070.0098-0.01540.00130.0249-0.01330.07390.0165-0.0030.05030.00210.096119.4759-2.1112136.3159
20.3282-0.01780.37390.02170.00340.5409-0.0008-0.0234-0.0192-0.00220.00870.0080.01570.0076-0.0080.07440.01210.00440.0427-0.00110.098486.38143.8452127.5499
32.9638-1.0686-4.06124.68361.35295.74230.1839-0.29950.0995-0.02140.1066-0.001-0.36030.4948-0.29040.0794-0.06350.0440.111-0.05040.1457124.817311.656148.5679
44.82970.22482.42641.0115-0.0013.47350.09060.1354-0.03390.0649-0.0471-0.02980.24190.1019-0.04340.12970.0209-0.00140.01070.00720.126981.3074-9.8234116.0037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A131 - 368
2X-RAY DIFFRACTION2B135 - 369
3X-RAY DIFFRACTION3C567 - 581
4X-RAY DIFFRACTION4D567 - 581

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