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- PDB-2a3z: Ternary complex of the WH2 domain of WASP with Actin-DNAse I -

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Basic information

Entry
Database: PDB / ID: 2a3z
TitleTernary complex of the WH2 domain of WASP with Actin-DNAse I
Components
  • Actin, alpha skeletal muscle
  • Deoxyribonuclease-1
  • Wiskott-Aldrich syndrome protein
KeywordsSTRUCTURAL PROTEIN / WASP / WH2 / actin / DNAse I / arp2/3
Function / homology
Function and homology information


regulation of T cell antigen processing and presentation / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / regulation of actin polymerization or depolymerization / Cdc42 protein signal transduction / GTPase regulator activity / actin filament-based movement / deoxyribonuclease I activity ...regulation of T cell antigen processing and presentation / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / regulation of actin polymerization or depolymerization / Cdc42 protein signal transduction / GTPase regulator activity / actin filament-based movement / deoxyribonuclease I activity / neutrophil activation involved in immune response / negative regulation of cell motility / vesicle membrane / actin polymerization or depolymerization / regulation of stress fiber assembly / DNA catabolic process / regulation of lamellipodium assembly / negative regulation of stress fiber assembly / cytoskeletal motor activator activity / endosomal transport / tropomyosin binding / myosin heavy chain binding / positive regulation of double-strand break repair via homologous recombination / mesenchyme migration / troponin I binding / RHOJ GTPase cycle / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / phospholipase binding / striated muscle thin filament / CDC42 GTPase cycle / Generation of second messenger molecules / skeletal muscle myofibril / actin monomer binding / RHO GTPases Activate WASPs and WAVEs / epidermis development / skeletal muscle fiber development / phagocytic vesicle / stress fiber / titin binding / RAC1 GTPase cycle / actin filament polymerization / T cell activation / filopodium / actin filament / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / defense response / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / SH3 domain binding / cellular response to type II interferon / calcium-dependent protein binding / cell-cell junction / blood coagulation / actin cytoskeleton / lamellipodium / site of double-strand break / nuclear envelope / cell body / actin binding / protein-containing complex assembly / hydrolase activity / immune response / protein domain specific binding / apoptotic process / calcium ion binding / positive regulation of gene expression / protein kinase binding / magnesium ion binding / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / WH2 motif / Wiskott Aldrich syndrome homology region 2 ...Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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 / PH-like domain superfamily / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FORMIC ACID / : / Deoxyribonuclease-1 / Actin nucleation-promoting factor WAS / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.078 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 / 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 / pdbx_struct_special_symmetry / 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 / _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 / _pdbx_struct_special_symmetry.label_asym_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 / _struct_ref_seq_dif.details
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,34612
Polymers73,9883
Non-polymers1,3589
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-47 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.270, 41.798, 119.418
Angle α, β, γ (deg.)90.00, 108.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1569-

HOH

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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 / 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.: 1 / 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, 2 molecules C

#3: Protein/peptide Wiskott-Aldrich syndrome protein / WASp


Mass: 3019.393 Da / Num. of mol.: 1 / Fragment: WH2 domain, residues 430-458 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (humans)
References: GenBank: 15215303, UniProt: P42768*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.: 1
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 , 6 types, 403 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.5 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: sodium formate, PEG2000 MME, pH 7.2, 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: 2.078→40.1 Å / Num. all: 43853 / Num. obs: 42018 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.2
Reflection shellResolution: 2.078→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4189 / % possible all: 97.3

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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: 2.078→40.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.688 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.201 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 4184 10 %RANDOM
Rwork0.15335 ---
obs0.15907 37834 95.8 %-
all-43853 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.191 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å22.28 Å2
2--1.13 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.078→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5003 0 83 395 5481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9757248
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1345676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02224.184239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45515898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.51533
X-RAY DIFFRACTIONr_chiral_restr0.1330.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024009
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.22311
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23664
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2361
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0730.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.121.53319
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65325270
X-RAY DIFFRACTIONr_scbond_it2.98232262
X-RAY DIFFRACTIONr_scangle_it4.3294.51957
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.078→2.132 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 254 -
Rwork0.192 2382 -
obs-2382 83.66 %
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)
12.1842-0.35510.07592.04250.47691.8752-0.08-0.4658-0.13080.12520.1354-0.15790.07540.2361-0.0554-0.04390.0364-0.03950.05540.0472-0.082170.044-11.0524.414
20.2815-0.3576-1.06510.53531.46194.17630.0264-0.31380.0006-0.10820.0397-0.03070.04150.1936-0.0661-0.01590.061-0.0020.1071-0.0151-0.045355.0294.35735.232
31.835-0.3333-0.07380.38390.0140.8830.00380.0615-0.1723-0.0595-0.00250.01240.04850.0339-0.00130.0016-0.0114-0.0221-0.08910.0011-0.018260.507-12.4861.693
41.5459-0.35220.39141.5926-0.11850.4508-0.0545-0.2033-0.05930.02750.02920.0081-0.1067-0.16850.02530.0070.0047-0.0519-0.04480.0035-0.057640.181-1.2919.157
51.79120.1498-0.91950.844-0.40431.09580.0985-0.1529-0.01280.038-0.10620.0532-0.06690.17120.0077-0.0399-0.021-0.0241-0.0256-0.0261-0.099637.46210.63650.816
61.5497-3.16-1.18586.45442.27752.7443-0.267-0.338-0.67310.32780.1440.00491.02790.13250.12290.06940.0301-0.0490.04160.12770.064967.996-27.63513.656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 33
2X-RAY DIFFRACTION1A70 - 137
3X-RAY DIFFRACTION1A339 - 365
4X-RAY DIFFRACTION2A34 - 69
5X-RAY DIFFRACTION3A138 - 181
6X-RAY DIFFRACTION3A274 - 338
7X-RAY DIFFRACTION3A1380 - 1381
8X-RAY DIFFRACTION4A182 - 273
9X-RAY DIFFRACTION5B1 - 260
10X-RAY DIFFRACTION6C431 - 447

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