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- PDB-2d1k: Ternary complex of the WH2 domain of mim with actin-dnase I -

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Basic information

Entry
Database: PDB / ID: 2d1k
TitleTernary complex of the WH2 domain of mim with actin-dnase I
Components
  • Actin, alpha skeletal muscle
  • Deoxyribonuclease-1
  • Metastasis suppressor protein 1
KeywordsSTRUCTURAL PROTEIN / WASP / WIP / WH2 / ACTIN / DNASE I
Function / homology
Function and homology information


nephron tubule epithelial cell differentiation / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / regulation of neutrophil mediated cytotoxicity / regulation of acute inflammatory response / zymogen granule / renal tubule morphogenesis / deoxyribonuclease I / plasma membrane organization / deoxyribonuclease I activity ...nephron tubule epithelial cell differentiation / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / regulation of neutrophil mediated cytotoxicity / regulation of acute inflammatory response / zymogen granule / renal tubule morphogenesis / deoxyribonuclease I / plasma membrane organization / deoxyribonuclease I activity / neutrophil activation involved in immune response / microspike assembly / cellular response to fluid shear stress / DNA catabolic process / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / endocytic vesicle / skeletal muscle fiber development / stress fiber / titin binding / ruffle / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of epithelial cell proliferation / actin cytoskeleton / lamellipodium / nuclear envelope / actin binding / cell body / actin cytoskeleton organization / hydrolase activity / cell adhesion / protein domain specific binding / signaling receptor binding / apoptotic process / calcium ion binding / positive regulation of gene expression / magnesium ion binding / DNA binding / extracellular region / ATP binding / nucleus / identical protein binding / cytoplasm
Similarity search - Function
I-BAR domain containing protein MTSS1 / I-BAR domain containing protein MTSS1/MTSS2 / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / IMD/I-BAR domain / IRSp53/MIM homology domain ...I-BAR domain containing protein MTSS1 / I-BAR domain containing protein MTSS1/MTSS2 / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / WH2 motif / WH2 domain / WH2 domain profile. / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / AH/BAR domain superfamily / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / 4-Layer Sandwich / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Protein MTSS 1 / Deoxyribonuclease-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChereau, D. / Kerff, F. / Dominguez, R.
CitationJournal: Structure / Year: 2007
Title: Structural basis for the actin-binding function of missing-in-metastasis
Authors: Lee, S.H. / Kerff, F. / Chereau, D. / Ferron, F. / Klug, A. / Dominguez, R.
History
DepositionAug 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
A: Actin, alpha skeletal muscle
B: Deoxyribonuclease-1
C: Metastasis suppressor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7778
Polymers74,5793
Non-polymers1,1985
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-49 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.093, 75.487, 228.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Actin, alpha skeletal muscle / / Alpha-actin 1


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P68135
#2: Protein Deoxyribonuclease-1 / / Deoxyribonuclease I / DNase I


Mass: 29092.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: pancreas / References: UniProt: P00639, deoxyribonuclease I

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Protein/peptide / Sugars , 2 types, 2 molecules C

#3: Protein/peptide Metastasis suppressor protein 1 / MIM / Missing in metastasis protein / Metastasis suppressor YGL-1


Mass: 3611.075 Da / Num. of mol.: 1 / Fragment: WH2 Domain (residues 724-755) / Source method: obtained synthetically
Details: synthetic peptide. This sequence occurs naturally in homo sapiens (humans)
References: UniProt: O43312
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 107 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.43 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→41.4 Å / Num. all: 23598 / Num. obs: 23598 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 25.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 7.2 / Num. unique all: 2069 / % possible all: 80.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2a41
Resolution: 2.5→41.4 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / SU B: 26.973 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 1.383 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28412 1165 5 %RANDOM
Rwork0.21712 ---
obs0.22047 22339 89.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.805 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---1.31 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5171 0 73 103 5347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9757296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1223.898236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.47215896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.941535
X-RAY DIFFRACTIONr_chiral_restr0.0920.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024017
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.22489
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23634
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2560.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.13223357
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.17235333
X-RAY DIFFRACTIONr_scbond_it2.09922263
X-RAY DIFFRACTIONr_scangle_it2.83631962
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 91 -
Rwork0.274 1567 -
obs-1658 87.68 %
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)
13.55280.3360.79257.2027-0.46813.9303-0.09810.1878-0.4053-0.41540.18590.38170.4764-0.0811-0.08790.0866-0.1131-0.0728-0.1732-0.16-0.1243-9.9456.346881.026
22.63430.69521.523.16252.77142.7629-0.01380.5119-0.40390.24450.2942-0.3050.3006-0.1682-0.2803-0.0456-0.08310.0064-0.0559-0.17050.03496.401621.142993.0696
32.6516-0.7170.29623.4349-0.17834.37740.26640.5272-0.0088-0.3319-0.20340.4308-0.0104-0.1248-0.0630.3366-0.0496-0.1575-0.0003-0.0443-0.3343-12.239218.83259.7197
43.89990.89670.63576.31560.92290.94560.2550.14370.3602-0.0454-0.322-0.6203-0.08760.24650.0670.5035-0.0585-0.06130.00740.0958-0.4080.416438.151867.7813
51.7736-0.1348-0.15512.03870.75972.0562-0.01880.0924-0.12810.02010.0876-0.0580.09810.0499-0.0687-0.214-0.0075-0.0307-0.1051-0.0915-0.023212.797638.6182108.6423
617.1877-1.4614-2.7972.128-3.00355.69840.88870.3521.87650.8954-1.32372.05880.6906-0.06120.4351-0.0286-0.0829-0.0669-0.0395-0.0707-0.0268-21.090414.782875.6569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 334 - 33
2X-RAY DIFFRACTION1AA70 - 13770 - 137
3X-RAY DIFFRACTION1AA339 - 374339 - 374
4X-RAY DIFFRACTION2AA34 - 6934 - 69
5X-RAY DIFFRACTION3AA138 - 181138 - 181
6X-RAY DIFFRACTION3AA274 - 338274 - 338
8X-RAY DIFFRACTION4AA182 - 273182 - 273
9X-RAY DIFFRACTION5BB1 - 2601 - 260
10X-RAY DIFFRACTION6CC725 - 7532 - 30

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