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- PDB-2vzc: Crystal structure of the C-terminal calponin homology domain of a... -

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Basic information

Entry
Database: PDB / ID: 2vzc
TitleCrystal structure of the C-terminal calponin homology domain of alpha parvin
ComponentsALPHA-PARVIN
KeywordsCELL ADHESION / MEMBRANE / CYTOPLASM / CYTOSKELETON / CELL JUNCTION / ALTERNATIVE SPLICING / CALPONIN HOMOLOGY DOMAIN / ACTIN-BINDING / CELL MEMBRANE
Function / homology
Function and homology information


actin-mediated cell contraction / smooth muscle cell chemotaxis / establishment or maintenance of cell polarity regulating cell shape / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Cell-extracellular matrix interactions / outflow tract septum morphogenesis / sprouting angiogenesis / heterotypic cell-cell adhesion / establishment or maintenance of cell polarity ...actin-mediated cell contraction / smooth muscle cell chemotaxis / establishment or maintenance of cell polarity regulating cell shape / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Cell-extracellular matrix interactions / outflow tract septum morphogenesis / sprouting angiogenesis / heterotypic cell-cell adhesion / establishment or maintenance of cell polarity / protein kinase inhibitor activity / cilium assembly / substrate adhesion-dependent cell spreading / Z disc / actin cytoskeleton / actin binding / actin cytoskeleton organization / protein stabilization / cadherin binding / focal adhesion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Parvin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsLorenz, S. / Vakonakis, I. / Lowe, E.D. / Campbell, I.D. / Noble, M.E.M. / Hoellerer, M.K.
CitationJournal: Structure / Year: 2008
Title: Structural Analysis of the Interactions between Paxillin Ld Motifs and Alpha-Parvin
Authors: Lorenz, S. / Vakonakis, I. / Lowe, E.D. / Campbell, I.D. / Noble, M.E.M. / Hoellerer, M.K.
History
DepositionJul 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ALPHA-PARVIN
B: ALPHA-PARVIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7616
Polymers30,3112
Non-polymers4514
Water5,026279
1
A: ALPHA-PARVIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3703
Polymers15,1551
Non-polymers2142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-PARVIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3923
Polymers15,1551
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.144, 71.197, 47.146
Angle α, β, γ (deg.)90.00, 99.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALPHA-PARVIN / CALPONIN-LIKE INTEGRIN-LINKED KINASE-BINDING PROTEIN / CH-ILKBP / MATRIX-REMODELING-ASSOCIATED ...CALPONIN-LIKE INTEGRIN-LINKED KINASE-BINDING PROTEIN / CH-ILKBP / MATRIX-REMODELING-ASSOCIATED PROTEIN 2 / ACTOPAXIN


Mass: 15155.380 Da / Num. of mol.: 2
Fragment: C-TERMINAL CALPONIN HOMOLOGY DOMAIN, RESIDUES 242-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NVD7

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Non-polymers , 5 types, 283 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 50.36 %
Description: MOLECULAR REPLACEMENT WITH ENSEMBLE OF CH1 DOMAINS FROM PDB ENTRIES 1WKU, 1TJT, 2EYI AND 1MB8
Crystal growpH: 7.5
Details: 12% (W/V) PEG 8000, 35% (V/V) MPD, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 16, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.05→23.74 Å / Num. obs: 124910 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.5
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.4 / % possible all: 77.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1WKU, 1TJT, 2EYI, 1MB8

1wku

1tjt

2eyi

1mb8


Resolution: 1.05→46.42 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.805 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.159 6274 5 %RANDOM
Rwork0.143 ---
obs0.144 118544 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20.43 Å2
2---0.87 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.05→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 30 279 2378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222927
X-RAY DIFFRACTIONr_bond_other_d0.0030.022038
X-RAY DIFFRACTIONr_angle_refined_deg1.692.0094047
X-RAY DIFFRACTIONr_angle_other_deg1.04135050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3195393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60824.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36315562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9081514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023442
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02604
X-RAY DIFFRACTIONr_nbd_refined0.2610.2754
X-RAY DIFFRACTIONr_nbd_other0.1950.22155
X-RAY DIFFRACTIONr_nbtor_refined0.190.21530
X-RAY DIFFRACTIONr_nbtor_other0.090.21365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6551.52310
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05822944
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.94631359
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6054.51101
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.05→1.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 320
Rwork0.28 6271

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