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- PDB-4edl: Crystal structure of beta-parvin CH2 domain -

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Basic information

Entry
Database: PDB / ID: 4edl
TitleCrystal structure of beta-parvin CH2 domain
ComponentsBeta-parvin
KeywordsSIGNALING PROTEIN / calponin homology domain / protein-protein interaction / LD motif / integrin signaling / focal adhesion / Adaptor protein / Paxillin and integrin-linked kinase
Function / homology
Function and homology information


establishment or maintenance of cell polarity regulating cell shape / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Cell-extracellular matrix interactions / cell projection assembly / lamellipodium assembly / substrate adhesion-dependent cell spreading / Z disc / lamellipodium / actin cytoskeleton / actin binding ...establishment or maintenance of cell polarity regulating cell shape / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Cell-extracellular matrix interactions / cell projection assembly / lamellipodium assembly / substrate adhesion-dependent cell spreading / Z disc / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / 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 / molecular replacement / Resolution: 2.1 Å
AuthorsStiegler, A.L. / Draheim, K.M. / Li, X. / Chayen, N.E. / Calderwood, D.A. / Boggon, T.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for paxillin binding and focal adhesion targeting of beta-parvin.
Authors: Stiegler, A.L. / Draheim, K.M. / Li, X. / Chayen, N.E. / Calderwood, D.A. / Boggon, T.J.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Beta-parvin
B: Beta-parvin
C: Beta-parvin
D: Beta-parvin
E: Beta-parvin
F: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,28523
Polymers92,2306
Non-polymers1,05517
Water4,216234
1
A: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6205
Polymers15,3721
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4342
Polymers15,3721
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4963
Polymers15,3721
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7447
Polymers15,3721
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4342
Polymers15,3721
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5584
Polymers15,3721
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.893, 52.584, 82.331
Angle α, β, γ (deg.)90.000, 101.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-parvin / Affixin


Mass: 15371.638 Da / Num. of mol.: 6 / Fragment: C-terminal calponin homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARVB, CGI-56 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HBI1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1.86 Å3/Da / Density % sol: 33.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 4000, 0.1M sodium citrate, 3% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2011
RadiationMonochromator: Si-111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 39650 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 32.1 Å2 / Rsym value: 0.067 / Net I/σ(I): 14.011
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.155 / Rsym value: 0.509 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0 / SU B: 14.425 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1990 5 %RANDOM
Rwork0.215 ---
all0.2176 39650 --
obs0.2176 39650 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.15 Å2 / Biso mean: 50.0852 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å22.2 Å2
2---1.11 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 68 234 6593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026483
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9848743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51724.822309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.819151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3311519
X-RAY DIFFRACTIONr_chiral_restr0.0850.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214797
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 135 -
Rwork0.283 2604 -
all-2739 -
obs-2739 97.23 %
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)
12.22093.8437-2.286810.80983.992217.6017-0.37590.1693-0.0179-0.76120.5283-0.14580.38070.1295-0.15240.1628-0.13290.05660.1666-0.03210.096-20.6879-6.14658.6527
217.99828.52223.17394.4394-0.491711.7630.13850.2429-0.03740.02830.16060.0334-0.4078-0.5753-0.29910.27420.16790.05410.2102-0.02470.133913.841233.993838.8998
316.22564.2682-4.95785.69993.42899.14930.0762-0.53280.0150.2690.0479-0.32360.37870.0805-0.12410.1275-0.06090.07770.1569-0.06980.1863-34.778137.032619.693
410.65038.63981.542711.842.721924.836-0.09980.1756-1.027-0.85770.2361-1.51391.75130.683-0.13640.399-0.01440.13780.341-0.0770.283921.0208-6.137610.8598
512.77955.78960.62096.65671.16826.29290.2398-0.04010.15370.2394-0.16910.960.2054-0.9731-0.07080.1447-0.00350.02520.51110.0720.3334-25.368134.660137.7782
631.2357-9.9644-2.223417.4845-5.99317.93571.2218-1.60771.62841.66920.1731-0.5408-1.91842.7055-1.39490.9983-0.36780.38820.7722-0.38830.5986.967236.224820.9111
74.97132.5898-0.69613.14550.61566.59380.0875-0.00050.34860.132-0.02350.2624-0.31140.0062-0.0640.0554-0.0298-0.01360.0562-0.00280.0769-25.96726.437728.3723
86.23731.9213-1.63196.21961.85316.3867-0.19280.214-0.4407-0.18250.0542-0.24650.13420.11530.13860.0339-0.03230.00240.05750.0090.050735.065835.361828.1872
93.41970.4554-2.87057.3225-2.83067.4575-0.07550.101-0.1995-0.6316-0.0277-0.25310.40580.29170.10320.07960.04210.0030.12330.00380.1045-26.711525.73650.5913
109.01211.2473-2.30082.46670.1926.04750.3002-0.22280.4450.1623-0.238-0.0195-0.2426-0.0835-0.06220.0636-0.0391-0.03060.11460.00860.06413.55446.600729.5729
116.22311.3725-0.52893.65721.34436.9461-0.23880.49330.0708-0.82640.2175-0.46960.00370.02050.02130.2615-0.10160.11730.1056-0.01160.0904-4.05934.713528.963
125.1528-0.3127-5.223711.5399-4.516313.02820.012-0.2793-0.0214-0.6535-0.0696-0.0750.22720.31190.05760.11280.05440.0540.10480.00030.054412.932725.19631.5052
132.27190.4919-2.4145.0391-0.39315.2313-0.0990.30620.1492-0.71290.1250.255-0.2069-0.3205-0.02610.1394-0.0058-0.06750.104-0.01450.0727-29.19395.622418.4612
146.25321.1232-0.93784.87441.61384.8805-0.1231-0.2188-0.88750.2267-0.16770.09310.5562-0.37380.29080.0876-0.06140.04180.06150.02260.194128.727628.337532.2633
154.90530.7439-2.30055.9537-0.98478.63540.31390.04850.1183-0.2268-0.0260.7811-0.2519-0.5646-0.28790.03590.0193-0.02660.1011-0.00140.1073-34.765632.07753.1202
163.0183-1.3124-2.96925.0104-0.59985.6630.16660.41530.0409-0.5515-0.15360.0113-0.2688-0.3689-0.01310.11660.0158-0.02030.10320.00710.028410.45615.601719.4981
176.13731.3701-0.64824.0612-0.14283.8571-0.32940.1597-0.6036-0.37380.23090.03830.5914-0.44950.09850.1437-0.07540.04150.0885-0.01280.1387-11.088427.79532.2247
186.4461.6538-5.73617.6694-4.611211.37510.444-0.10490.71580.08420.42651.0987-0.6872-0.5723-0.87050.07920.04930.02320.1578-0.01160.22175.431231.8654.3793
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 254
2X-RAY DIFFRACTION2B237 - 254
3X-RAY DIFFRACTION3C238 - 254
4X-RAY DIFFRACTION4D238 - 254
5X-RAY DIFFRACTION5E237 - 254
6X-RAY DIFFRACTION6F238 - 254
7X-RAY DIFFRACTION7A255 - 311
8X-RAY DIFFRACTION8B255 - 311
9X-RAY DIFFRACTION9C255 - 311
10X-RAY DIFFRACTION10D255 - 311
11X-RAY DIFFRACTION11E255 - 311
12X-RAY DIFFRACTION12F255 - 311
13X-RAY DIFFRACTION13A312 - 364
14X-RAY DIFFRACTION14B312 - 364
15X-RAY DIFFRACTION15C312 - 364
16X-RAY DIFFRACTION16D312 - 364
17X-RAY DIFFRACTION17E312 - 364
18X-RAY DIFFRACTION18F312 - 364

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