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

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Basic information

Entry
Database: PDB / ID: 2vzd
TitleCrystal structure of the C-terminal calponin homology domain of alpha parvin in complex with paxillin LD1 motif
Components
  • ALPHA-PARVIN
  • PAXILLIN
KeywordsCELL ADHESION / CALPONIN HOMOLOGY DOMAIN / CELL MEMBRANE / METAL-BINDING / CYTOSKELETON / CELL JUNCTION / ACTIN-BINDING / PHOSPHOPROTEIN / MEMBRANE / LD1 MOTIF / LIM DOMAIN
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: 2.1 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Dec 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: ALPHA-PARVIN
B: ALPHA-PARVIN
C: PAXILLIN
D: PAXILLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,06518
Polymers34,6664
Non-polymers1,40014
Water1,53185
1
A: ALPHA-PARVIN
C: PAXILLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1369
Polymers17,3332
Non-polymers8037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-9.6 kcal/mol
Surface area9610 Å2
MethodPQS
2
B: ALPHA-PARVIN
D: PAXILLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9299
Polymers17,3332
Non-polymers5977
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-13.4 kcal/mol
Surface area9170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)133.123, 37.503, 70.244
Angle α, β, γ (deg.)90.00, 90.33, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLUGLUBB315 - 37274 - 131
21LEULEUGLUGLUAA315 - 37274 - 131
12ARGARGLEULEUBB247 - 3036 - 62
22ARGARGLEULEUAA247 - 3036 - 62

NCS oper: (Code: given
Matrix: (-0.2002, 0.867, -0.4563), (0.867, -0.0602, -0.4947), (-0.4564, -0.4946, -0.7397)
Vector: -25.9179, 45.6576, 41.5894)

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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
#2: Protein/peptide PAXILLIN /


Mass: 2177.388 Da / Num. of mol.: 2 / Fragment: PAXILLIN LD1 MOTIF, RESIDUES 1-20 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P49023

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Non-polymers , 5 types, 99 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: 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
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.6 Å3/Da / Density % sol: 52.36 % / Description: NONE
Crystal growpH: 7.5 / Details: 20% (W/V) PEG 10000, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.969
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 5, 2006 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.1→30.03 Å / Num. obs: 20260 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4

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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: 2.1→28.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.368 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1039 5.1 %RANDOM
Rwork0.217 ---
obs0.219 19208 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-0.86 Å2
2--1.36 Å20 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 92 85 2439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222931
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.132.0283991
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9645377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88525.203123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90815557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1061511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022227
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21513
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22005
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0890.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2041.51811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.36122902
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.32431237
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.4844.51089
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 1074 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.290.5
medium thermal0.122
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.315 65
Rwork0.306 1398
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)
12.8527-0.52370.11273.58872.29015.5678-0.07280.064-0.06660.27240.2757-0.41190.17660.2352-0.203-0.19690.0359-0.0253-0.2055-0.0396-0.2064-20.8211.9847.623
24.0503-1.4974-1.73273.72171.23164.16510.0810.1242-0.0470.0748-0.23560.2204-0.2154-0.54330.1545-0.179-0.0143-0.0238-0.1139-0.1087-0.1592-14.89623.08939.516
314.066-5.49033.243914.2173.78940.4222-0.474-0.38270.29110.4295-0.0592-2.14081.5141.4210.5333-0.03530.0644-0.00840.0481-0.17160.2653-12.978-0.456-4.027
412.11754.6880.320434.85310.970818.61040.33471.44950.6232-0.1876-0.49110.1073-0.01920.35430.15640.05830.1210.18690.0961-0.05920.0033-21.2836.4751.327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A247 - 372
2X-RAY DIFFRACTION2B247 - 372
3X-RAY DIFFRACTION3C2 - 13
4X-RAY DIFFRACTION4D1 - 13

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