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- PDB-3chw: Complex of Dictyostelium discoideum Actin with Profilin and the L... -

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Basic information

Entry
Database: PDB / ID: 3chw
TitleComplex of Dictyostelium discoideum Actin with Profilin and the Last Poly-Pro of Human VASP
Components
  • Major actin
  • Profilin-1
  • Vasodilator-stimulated phosphoprotein 16-residue peptide
KeywordsSTRUCTURAL PROTEIN / Ternary complex / Profilin / Actin / Dictyostelium discoideum / VASP / Poly-Proline / Methyl Histidine / ATP-binding / Cytoskeleton / Nucleotide-binding / Phosphoprotein / Actin-binding / Cell junction / Cell projection / Membrane / SH3-binding
Function / homology
Function and homology information


RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / intranuclear rod / Platelet degranulation / Regulation of actin dynamics for phagocytic cup formation / phototaxis / leading edge of lamellipodium / phagolysosome / macropinocytic cup / cell pole ...RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / intranuclear rod / Platelet degranulation / Regulation of actin dynamics for phagocytic cup formation / phototaxis / leading edge of lamellipodium / phagolysosome / macropinocytic cup / cell pole / synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / profilin binding / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Cell-extracellular matrix interactions / Signaling by ROBO receptors / regulation of actin filament polymerization / plasma membrane repair / actin polymerization or depolymerization / early phagosome / hyperosmotic response / filopodium membrane / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / phagocytic cup / myosin binding / cortical actin cytoskeleton / positive regulation of actin filament polymerization / positive regulation of epithelial cell migration / cell leading edge / pseudopodium / lamellipodium membrane / mitotic cytokinesis / Generation of second messenger molecules / endocytic vesicle / actin monomer binding / bicellular tight junction / phagocytic vesicle / phagocytosis / vesicle-mediated transport / response to cAMP / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / lipid droplet / neural tube closure / actin filament / RHO GTPases Activate Formins / axon guidance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / modulation of chemical synaptic transmission / cell morphogenesis / structural constituent of cytoskeleton / small GTPase binding / SH3 domain binding / endocytosis / chemotaxis / cell-cell junction / actin cytoskeleton / Platelet degranulation / lamellipodium / actin binding / cell cortex / actin cytoskeleton organization / protein homotetramerization / blood microparticle / protein stabilization / cytoskeleton / hydrolase activity / cadherin binding / focal adhesion / glutamatergic synapse / regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vasodilator-stimulated phosphoprotein/ENA/VASP-like / Profilin1/2/3, vertebrate / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / : / Profilin conserved site / Profilin signature. / Profilin / Profilin ...Vasodilator-stimulated phosphoprotein/ENA/VASP-like / Profilin1/2/3, vertebrate / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Profilin superfamily / Dynein light chain 2a, cytoplasmic / 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. / Beta-Lactamase / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / PH-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Profilin-1 / Major actin / Vasodilator-stimulated phosphoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBaek, K. / Dominguez, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Modulation of actin structure and function by phosphorylation of Tyr-53 and profilin binding.
Authors: Baek, K. / Liu, X. / Ferron, F. / Shu, S. / Korn, E.D. / Dominguez, R.
History
DepositionMar 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _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: Major actin
P: Profilin-1
V: Vasodilator-stimulated phosphoprotein 16-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5025
Polymers57,9553
Non-polymers5472
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-27.4 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.037, 76.183, 180.822
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AP

#1: Protein Major actin


Mass: 41660.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: P07830
#2: Protein Profilin-1 / / Profilin I


Mass: 14940.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: pfn1 / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07737

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Protein/peptide , 1 types, 1 molecules V

#3: Protein/peptide Vasodilator-stimulated phosphoprotein 16-residue peptide / VASP


Mass: 1354.509 Da / Num. of mol.: 1 / Fragment: Last Poly-Pro Repeat / Source method: obtained synthetically
Details: This sequence occurs naturally in human VASP protein.
References: UniProt: P50552

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Non-polymers , 3 types, 319 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2007 / Details: Rh-coated Si mirror
RadiationMonochromator: Double bounce Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 24210 / Num. obs: 21716 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Χ2: 1.396 / Net I/σ(I): 20.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 15.8 / Num. unique all: 1937 / Rsym value: 0.349 / Χ2: 1.506 / % possible all: 80.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.27 Å
Translation2.5 Å47.27 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PAV

2pav


Resolution: 2.3→38.87 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.493 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.455 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1101 5.1 %RANDOM
Rwork0.157 ---
all0.161 24210 --
obs0.161 21648 89.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.306 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3951 0 32 317 4300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224152
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9815653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26724.07172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74715705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6121524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023136
X-RAY DIFFRACTIONr_nbd_refined0.2050.22023
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2311
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.28
X-RAY DIFFRACTIONr_mcbond_it2.63322651
X-RAY DIFFRACTIONr_mcangle_it3.8334192
X-RAY DIFFRACTIONr_scbond_it6.05141700
X-RAY DIFFRACTIONr_scangle_it8.15861449
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 74 -
Rwork0.151 1358 -
all-1432 -
obs--80.81 %
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)
10.85940.3391-0.33681.8905-0.30110.9816-0.00940.0368-0.114-0.0143-0.04960.08430.0973-0.06340.0591-0.1797-0.0380.0071-0.1095-0.0047-0.18674.596-17.327-24.206
22.90190.7737-0.03612.7549-0.14281.6930.2571-0.22930.24140.253-0.1676-0.0818-0.0609-0.0121-0.0895-0.1764-0.05370.0233-0.0999-0.0687-0.198717.90612.655-12.783
311.222-3.2931-2.548212.7459-3.71882.27220.10980.56621.0343-0.1249-0.18121.2973-1.2987-1.55130.0714-0.0002-0.0023-0.0001-0.0011-0.0007022.02626.649-21.171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 32
2X-RAY DIFFRACTION1A33 - 40
3X-RAY DIFFRACTION1A51 - 70
4X-RAY DIFFRACTION1A71 - 130
5X-RAY DIFFRACTION1A131 - 148
6X-RAY DIFFRACTION1A149 - 181
7X-RAY DIFFRACTION1A182 - 262
8X-RAY DIFFRACTION1A263 - 274
9X-RAY DIFFRACTION1A275 - 336
10X-RAY DIFFRACTION1A337 - 375
11X-RAY DIFFRACTION2P1 - 15
12X-RAY DIFFRACTION2P16 - 38
13X-RAY DIFFRACTION2P39 - 92
14X-RAY DIFFRACTION2P93 - 116
15X-RAY DIFFRACTION2P117 - 139
16X-RAY DIFFRACTION3V201 - 207
17X-RAY DIFFRACTION3V208 - 213

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