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

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Basic information

Entry
Database: PDB / ID: 2vzg
TitleCrystal structure of the C-terminal calponin homology domain of alpha- parvin in complex with paxillin LD2 motif
Components
  • Alpha-parvin
  • Paxillin
KeywordsCELL ADHESION / CALPONIN HOMOLOGY DOMAIN / CELL MEMBRANE / METAL-BINDING / CYTOSKELETON / CELL JUNCTION / ACTIN-BINDING / MEMBRANE / LD2 MOTIF / LIM DOMAIN / PHOSPHOPROTEIN
Function / homology
Function and homology information


actin-mediated cell contraction / smooth muscle cell chemotaxis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / Cell-extracellular matrix interactions / neuropilin binding / outflow tract septum morphogenesis / signal complex assembly / heterotypic cell-cell adhesion ...actin-mediated cell contraction / smooth muscle cell chemotaxis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / Cell-extracellular matrix interactions / neuropilin binding / outflow tract septum morphogenesis / signal complex assembly / heterotypic cell-cell adhesion / sprouting angiogenesis / microtubule associated complex / growth hormone receptor signaling pathway / establishment or maintenance of cell polarity / protein kinase inhibitor activity / cilium assembly / endothelial cell migration / Smooth Muscle Contraction / GAB1 signalosome / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / Z disc / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / cell-cell junction / cell migration / actin cytoskeleton / lamellipodium / actin binding / cell cortex / regulation of cell shape / actin cytoskeleton organization / protein phosphatase binding / protein stabilization / cell adhesion / cadherin binding / focal adhesion / signal transduction / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Parvin / Paxillin / : / : / Paxillin family / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. ...Parvin / Paxillin / : / : / Paxillin family / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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
TRIETHYLENE GLYCOL / Paxillin / Alpha-parvin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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. / Hoellerer, M.K.
History
DepositionAug 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Apr 24, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / entity / entity_name_com / entity_src_gen / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / struct_biol / struct_ref / struct_ref_seq
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 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

Downloads & links

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Assembly

Deposited unit
A: Paxillin
B: Alpha-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0989
Polymers17,4432
Non-polymers6557
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-11.2 kcal/mol
Surface area10400 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.008, 94.422, 41.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-2023-

HOH

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Components

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Protein/peptide / Protein , 2 types, 2 molecules AB

#1: Protein/peptide Paxillin /


Mass: 2287.571 Da / Num. of mol.: 1 / Fragment: PAXILLIN LD1 MOTIF, RESIDUES 141-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PXN / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P49023
#2: Protein Alpha-parvin / Actopaxin / CH-ILKBP / Calponin-like integrin-linked kinase-binding protein / Matrix-remodeling- ...Actopaxin / CH-ILKBP / Calponin-like integrin-linked kinase-binding protein / Matrix-remodeling-associated protein 2


Mass: 15155.380 Da / Num. of mol.: 1
Fragment: C-TERMINAL CALPONIN HOMOLOGY DOMAIN, RESIDUES 242-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARVA, MXRA2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9NVD7

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Non-polymers , 4 types, 72 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 40% (W/V) PEG200, 0.1 M CITRATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.968
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 2, 2007 / Details: MIRRORS
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.8→27.71 Å / Num. obs: 13920 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VZC

2vzc


Resolution: 1.8→58.22 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.158 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 690 5 %RANDOM
Rwork0.186 ---
obs0.187 13218 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.84 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→58.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1149 0 43 65 1257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2252.0231983
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4015188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43325.23165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53615278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.915156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021103
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2691
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21017
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5571.5886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9321423
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.563625
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2224.5554
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 53
Rwork0.255 965
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)
12.14380.123-0.16171.3746-0.06593.6838-0.0089-0.0696-0.08010.0197-0.02230.0817-0.0681-0.14920.0311-0.1653-0.0110.0005-0.1499-0.0006-0.1427-12.732-13.627-0.33
242.654-8.42014.247812.0463-2.4449.70810.5851-0.5105-1.48440.8002-0.18310.6299-0.14330.2189-0.4020.0217-0.03790.0143-0.1212-0.0001-0.02-18.942-13.12318.092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B247 - 372
2X-RAY DIFFRACTION2A5 - 15

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