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- PDB-2a40: Ternary complex of the WH2 domain of WAVE with Actin-DNAse I -

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Basic information

Entry
Database: PDB / ID: 2a40
TitleTernary complex of the WH2 domain of WAVE with Actin-DNAse I
Components
  • Actin, alpha skeletal muscle
  • Deoxyribonuclease-1
  • Wiskott-Aldrich syndrome protein family member 2
KeywordsSTRUCTURAL PROTEIN / WAVE / WH2 / WASP / Actin / DNAse I / arp2/3
Function / homology
Function and homology information


SCAR complex / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / lamellipodium morphogenesis / ameboidal-type cell migration / positive regulation of Arp2/3 complex-mediated actin nucleation / deoxyribonuclease I / Arp2/3 complex binding / actin filament-based movement ...SCAR complex / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / lamellipodium morphogenesis / ameboidal-type cell migration / positive regulation of Arp2/3 complex-mediated actin nucleation / deoxyribonuclease I / Arp2/3 complex binding / actin filament-based movement / postsynaptic actin cytoskeleton organization / deoxyribonuclease I activity / neutrophil activation involved in immune response / DNA catabolic process / protein kinase A binding / lamellipodium assembly / negative regulation of stress fiber assembly / cytoskeletal motor activator activity / megakaryocyte development / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / Fc-gamma receptor signaling pathway involved in phagocytosis / Rac protein signal transduction / troponin I binding / actin filament bundle / protein kinase A regulatory subunit binding / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / RHO GTPases Activate WASPs and WAVEs / vascular endothelial growth factor receptor signaling pathway / skeletal muscle fiber development / positive regulation of lamellipodium assembly / stress fiber / titin binding / ruffle / actin filament polymerization / viral process / filopodium / actin filament / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / VEGFA-VEGFR2 Pathway / endocytosis / calcium-dependent protein binding / cell-cell junction / actin cytoskeleton / lamellipodium / nuclear envelope / cell body / actin binding / actin cytoskeleton organization / basolateral plasma membrane / angiogenesis / early endosome / hydrolase activity / cadherin binding / protein domain specific binding / apoptotic process / calcium ion binding / positive regulation of gene expression / magnesium ion binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SCAR/WAVE family / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain ...SCAR/WAVE family / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / WH2 motif / Wiskott Aldrich syndrome homology region 2 / 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 / 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 / : / Deoxyribonuclease-1 / Actin, alpha skeletal muscle / Wiskott-Aldrich syndrome protein family member 2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChereau, D. / Kerff, F. / Dominguez, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Actin-bound structures of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 and the implications for filament assembly
Authors: Chereau, D. / Kerff, F. / Graceffa, P. / Grabarek, Z. / Langsetmo, K. / Dominguez, R.
History
DepositionJun 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.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.conn_type_id / _struct_conn.id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 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: Wiskott-Aldrich syndrome protein family member 2
D: Actin, alpha skeletal muscle
E: Deoxyribonuclease-1
F: Wiskott-Aldrich syndrome protein family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,83718
Polymers149,5816
Non-polymers2,25612
Water16,250902
1
A: Actin, alpha skeletal muscle
B: Deoxyribonuclease-1
C: Wiskott-Aldrich syndrome protein family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,01110
Polymers74,7903
Non-polymers1,2207
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-50 kcal/mol
Surface area26480 Å2
MethodPISA
2
D: Actin, alpha skeletal muscle
E: Deoxyribonuclease-1
F: Wiskott-Aldrich syndrome protein family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8268
Polymers74,7903
Non-polymers1,0365
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-48 kcal/mol
Surface area26830 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12060 Å2
ΔGint-101 kcal/mol
Surface area52290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.719, 41.598, 153.048
Angle α, β, γ (deg.)90.00, 108.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBE

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


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


Mass: 29092.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P00639, deoxyribonuclease I

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Protein/peptide / Sugars , 2 types, 4 molecules CF

#3: Protein/peptide Wiskott-Aldrich syndrome protein family member 2 / WASP-family protein member 2 / WAVE-2 protein / Verprolin homology domain-containing protein 2


Mass: 3822.230 Da / Num. of mol.: 2 / Fragment: WH2 domain, residues 433-464 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (humans)
References: GenBank: 26454860, UniProt: Q9Y6W5*PLUS
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 912 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 902 / 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: 2.4 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: sodium formate, PEG3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / 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: 1.8→47.51 Å / Num. all: 132595 / Num. obs: 106912 / % possible obs: 80.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 4 / Num. unique all: 6309 / % possible all: 69

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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 1ATN

1atn


Resolution: 1.8→47.51 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.497 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.147 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21503 5386 5 %RANDOM
Rwork0.16648 ---
obs0.1689 101526 80.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.74 Å2
2---0.14 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10102 0 136 902 11140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210718
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.97414631
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88751371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17623.979480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.928151815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.781570
X-RAY DIFFRACTIONr_chiral_restr0.1060.21653
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028106
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.34833
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.57490
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.51458
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.515
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.391
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.561
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.87926687
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.637310661
X-RAY DIFFRACTIONr_scbond_it2.31924537
X-RAY DIFFRACTIONr_scangle_it3.28333925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 332 -
Rwork0.202 6309 -
obs-6309 68.96 %
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)
12.12930.4003-0.15612.26190.34011.6301-0.03990.39940.0638-0.2620.04950.16-0.0927-0.1321-0.00950.00090.0046-0.09-0.02830.0234-0.131621.74810.40634.507
26.58441.9946-2.44740.6147-0.75290.9223-0.12440.3679-0.0888-0.05310.1575-0.1741-0.1997-0.1117-0.0331-0.02-0.0579-0.0198-0.039-0.0241-0.05496.813-5.32145.228
30.9719-0.093-0.16380.4799-0.37081.5656-0.0037-0.03150.06620.01830.0134-0.0249-0.11870.1273-0.00970.018-0.016-0.0519-0.0782-0.0132-0.10440.07112.06150.853
40.52140.15840.01551.2883-0.47441.48570.0274-0.05840.01370.00680.05780.0458-0.0035-0.2181-0.08520.00790.0029-0.0748-0.05080.0061-0.110726.6640.77167.724
53.75940.0202-2.11790.6342-0.02981.7148-0.01240.2836-0.14930.0213-0.0520.0028-0.0499-0.16310.0644-0.0666-0.0177-0.0588-0.0772-0.0177-0.1375-13.462-11.80557.01
67.0824-2.02130.15424.36820.9150.24590.2626-0.23620.2979-0.2389-0.18820.124-0.42430.1598-0.07440.10360.0518-0.0611-0.19740.075-0.072229.52226.73640.02
72.5756-0.9119-0.84042.6854-0.00132.7006-0.0201-0.56930.14350.25650.2032-0.211-0.19460.4428-0.1831-0.0143-0.0199-0.05240.0708-0.0731-0.1678-46.61111.18937.891
85.5765-0.9526-0.44420.16270.07590.0354-0.0766-0.3432-0.01440.11540.13590.05-0.209-0.0686-0.05930.01580.10140.03950.064-0.0004-0.0881-31.428-4.23427.212
91.2206-0.0859-0.56820.43660.29972.14510.0520.07610.0557-0.03810.01320.0192-0.217-0.1544-0.06520.03730.0292-0.0229-0.05270.0229-0.1328-64.98512.24921.51
100.5915-0.1235-0.03941.83080.38541.75920.04190.08680.0166-0.01550.0473-0.081-0.00160.2683-0.08920.00360-0.0579-0.0027-0.0077-0.1446-51.3331.1284.733
111.14250.2015-0.59360.7661-0.20291.21250.0309-0.0449-0.02490.0599-0.0220.0158-0.07840.0036-0.0089-0.02120.016-0.0561-0.07070.0025-0.1262-11.138-10.63815.508
120.95590.00941.2023.52920.85781.71430.4719-0.21640.6978-0.2457-0.1091-0.2024-0.6370.7415-0.36290.2396-0.06650.1630.055-0.0870.0159-54.60427.25432.282
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 33
2X-RAY DIFFRACTION1A70 - 137
3X-RAY DIFFRACTION1A339 - 366
4X-RAY DIFFRACTION2A34 - 69
5X-RAY DIFFRACTION3A138 - 181
6X-RAY DIFFRACTION3A274 - 338
7X-RAY DIFFRACTION3A1548 - 1549
8X-RAY DIFFRACTION4A182 - 273
9X-RAY DIFFRACTION5B1 - 260
10X-RAY DIFFRACTION6C433 - 454
11X-RAY DIFFRACTION7D5 - 33
12X-RAY DIFFRACTION7D70 - 137
13X-RAY DIFFRACTION7D339 - 366
14X-RAY DIFFRACTION8D34 - 69
15X-RAY DIFFRACTION9D138 - 181
16X-RAY DIFFRACTION9D274 - 338
17X-RAY DIFFRACTION10D182 - 273
18X-RAY DIFFRACTION11E1 - 260
19X-RAY DIFFRACTION12F433 - 454

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