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- PDB-2pav: Ternary complex of Profilin-Actin with the Last Poly-Pro of Human VASP -

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Basic information

Entry
Database: PDB / ID: 2pav
TitleTernary complex of Profilin-Actin with the Last Poly-Pro of Human VASP
Components
  • Actin, alpha skeletal muscle
  • Profilin-1
  • Vasodilator-stimulated phosphoprotein
KeywordsSTRUCTURAL PROTEIN / Ternary complex / Profilin / Actin / VASP / Poly-Proline / Loading Poly-Pro Site
Function / homology
Function and homology information


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 / regulation of actin filament polymerization / Signaling by ROBO receptors / Cell-extracellular matrix interactions ...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 / regulation of actin filament polymerization / Signaling by ROBO receptors / Cell-extracellular matrix interactions / actin polymerization or depolymerization / positive regulation of ATP-dependent activity / proline-rich region binding / positive regulation of ruffle assembly / PCP/CE pathway / filopodium membrane / negative regulation of stress fiber assembly / cytoskeletal motor activator activity / positive regulation of actin filament polymerization / myosin heavy chain binding / tropomyosin binding / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / lamellipodium membrane / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / Generation of second messenger molecules / skeletal muscle thin filament assembly / positive regulation of epithelial cell migration / actin monomer binding / bicellular tight junction / stress fiber / skeletal muscle fiber development / titin binding / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / phosphotyrosine residue binding / axon guidance / filopodium / actin filament / neural tube closure / RHO GTPases Activate Formins / modulation of chemical synaptic transmission / small GTPase binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / SH3 domain binding / calcium-dependent protein binding / Platelet degranulation / lamellipodium / actin cytoskeleton / actin binding / cell body / actin cytoskeleton organization / cell cortex / protein homotetramerization / blood microparticle / cytoskeleton / hydrolase activity / postsynapse / protein stabilization / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / glutamatergic synapse / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / 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 / Beta-Lactamase / 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 / Nucleotidyltransferase; domain 5 / PH-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Profilin-1 / Vasodilator-stimulated phosphoprotein / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFerron, F. / Rebowski, G. / Dominguez, R.
CitationJournal: Embo J. / Year: 2007
Title: Structural basis for the recruitment of profilin-actin complexes during filament elongation by Ena/VASP.
Authors: Ferron, F. / Rebowski, G. / Lee, S.H. / Dominguez, R.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 6, 2013Group: Advisory / Other
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_conn_type / struct_ref_seq_dif / struct_sheet / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_type.id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _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

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
P: Profilin-1
V: Vasodilator-stimulated phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7175
Polymers58,1703
Non-polymers5472
Water9,764542
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.467, 75.460, 180.741
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 AP

#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: alpha skeletal muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 / VASP


Mass: 1354.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P50552

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Non-polymers , 3 types, 544 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


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


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200 mM sodium formate, 20% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2005
RadiationMonochromator: Bent conical Si-mirror (Rh coated) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 47947 / Num. obs: 47947 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 28.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 5.7 / Num. unique all: 4691 / Rsym value: 0.345 / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BTF

2btf


Resolution: 1.8→47.09 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.503 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2401 5 %RANDOM
Rwork0.158 ---
all0.16 45338 --
obs0.16 47739 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.002 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3968 0 32 542 4542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224351
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9825969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53224.153183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16915761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.341527
X-RAY DIFFRACTIONr_chiral_restr0.1870.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023321
X-RAY DIFFRACTIONr_nbd_refined0.210.22262
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23016
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2458
X-RAY DIFFRACTIONr_metal_ion_refined0.0360.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.231
X-RAY DIFFRACTIONr_mcbond_it1.0961.52784
X-RAY DIFFRACTIONr_mcangle_it1.6124413
X-RAY DIFFRACTIONr_scbond_it2.7331798
X-RAY DIFFRACTIONr_scangle_it4.094.51520
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 170 -
Rwork0.189 3273 -
obs-3443 97.51 %
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)
10.2876-0.0216-0.10050.54430.04850.8485-0.03230.027-0.02580.02060.01560.05220.1288-0.04970.0167-0.1012-0.00870.0025-0.04190.0021-0.0514.2318.43966.404
21.13490.22460.33512.5944-0.43571.70960.0657-0.03920.02470.3214-0.0577-0.0437-0.29220.0758-0.0081-0.0411-0.0240.0106-0.0771-0.0165-0.090216.09649.0477.82
38.7444-3.10235.067711.5629-6.90285.4278-0.30690.24190.76670.2084-0.4350.5532-0.99420.11930.74180.0002-0.0021-0.0004-0.00050.0020.000620.36263.03369.215
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 325 - 32
21AA33 - 7033 - 70
31AA71 - 13071 - 130
41AA131 - 148131 - 148
51AA149 - 181149 - 181
61AA182 - 262182 - 262
71AA263 - 274263 - 274
81AA275 - 336275 - 336
91AA337 - 375337 - 375
102PB1 - 151 - 15
112PB16 - 3816 - 38
122PB39 - 9239 - 92
132PB93 - 11693 - 116
142PB117 - 139117 - 139
153VC201 - 2064 - 9
163VC207 - 21310 - 16

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