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- PDB-4edn: Crystal structure of beta-parvin CH2 domain in complex with paxil... -

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Basic information

Entry
Database: PDB / ID: 4edn
TitleCrystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif
Components
  • Beta-parvin
  • Paxillin
KeywordsSIGNALING PROTEIN/CELL ADHESION / calponin homology domain / protein-protein interaction / LD motif / integrin signaling / focal adhesion / Adaptor protein / Paxillin / Integrin linked kinase / SIGNALING PROTEIN-CELL ADHESION complex
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 / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / neuropilin binding / vinculin binding / Cell-extracellular matrix interactions / cell projection assembly / signal complex assembly / lamellipodium assembly ...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 / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / neuropilin binding / vinculin binding / Cell-extracellular matrix interactions / cell projection assembly / signal complex assembly / lamellipodium assembly / microtubule associated complex / growth hormone receptor signaling pathway / Smooth Muscle Contraction / GAB1 signalosome / endothelial cell migration / 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 / cellular response to reactive oxygen species / beta-catenin binding / VEGFA-VEGFR2 Pathway / Z disc / cell-cell junction / cell migration / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / cell cortex / protein phosphatase binding / cell adhesion / focal adhesion / signal transduction / metal ion binding / plasma membrane / cytoplasm / cytosol
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
Paxillin / Beta-parvin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
G: Beta-parvin
H: Beta-parvin
I: Beta-parvin
J: Beta-parvin
K: Paxillin
L: Paxillin
M: Paxillin
N: Paxillin
O: Paxillin
P: Paxillin
Q: Paxillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,22218
Polymers169,12617
Non-polymers961
Water68538
1
A: Beta-parvin
K: Paxillin


Theoretical massNumber of molelcules
Total (without water)17,5732
Polymers17,5732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-parvin
L: Paxillin


Theoretical massNumber of molelcules
Total (without water)17,5732
Polymers17,5732
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-parvin
M: Paxillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6693
Polymers17,5732
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-parvin
N: Paxillin


Theoretical massNumber of molelcules
Total (without water)17,5732
Polymers17,5732
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Beta-parvin
O: Paxillin


Theoretical massNumber of molelcules
Total (without water)17,5732
Polymers17,5732
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Beta-parvin
P: Paxillin


Theoretical massNumber of molelcules
Total (without water)17,5732
Polymers17,5732
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Beta-parvin
Q: Paxillin


Theoretical massNumber of molelcules
Total (without water)17,5732
Polymers17,5732
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Beta-parvin


Theoretical massNumber of molelcules
Total (without water)15,3721
Polymers15,3721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Beta-parvin


Theoretical massNumber of molelcules
Total (without water)15,3721
Polymers15,3721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Beta-parvin


Theoretical massNumber of molelcules
Total (without water)15,3721
Polymers15,3721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)330.741, 55.842, 95.550
Angle α, β, γ (deg.)90.000, 97.440, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A238 - 264
2116B238 - 264
3116C238 - 264
4116D238 - 264
5116E238 - 264
6116F238 - 264
7116G238 - 264
8116H238 - 264
9116I238 - 264
10116J238 - 264

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Components

#1: Protein
Beta-parvin / Affixin


Mass: 15371.638 Da / Num. of mol.: 10 / 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: Protein/peptide
Paxillin


Mass: 2201.434 Da / Num. of mol.: 7 / Fragment: LD1 motif / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49023
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.1M Ammonium sulfate, 0.01M Tris, pH 8.5, 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: Jul 22, 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: 2.9→50 Å / Num. obs: 38837 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 85.2 Å2 / Rsym value: 0.078 / Net I/σ(I): 19.829
Reflection shellResolution: 2.9→3 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.132 / Rsym value: 0.742 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 42.983 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 1948 5 %RANDOM
Rwork0.2283 ---
all0.2301 38837 --
obs0.2301 38837 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 195.65 Å2 / Biso mean: 92.6497 Å2 / Biso min: 45.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å2-0.33 Å2
2--0.82 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10968 0 5 38 11011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0211206
X-RAY DIFFRACTIONr_angle_refined_deg0.7881.98715181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5451329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20425.311531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.688152015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5941524
X-RAY DIFFRACTIONr_chiral_restr0.0510.21769
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0218306
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 190 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.375
BLOOSE POSITIONAL0.985
CLOOSE POSITIONAL0.295
DLOOSE POSITIONAL0.515
ELOOSE POSITIONAL0.395
FLOOSE POSITIONAL0.345
GLOOSE POSITIONAL0.385
HLOOSE POSITIONAL0.495
ILOOSE POSITIONAL0.415
JLOOSE POSITIONAL0.515
ALOOSE THERMAL4.7310
BLOOSE THERMAL4.4610
CLOOSE THERMAL2.2810
DLOOSE THERMAL3.8410
ELOOSE THERMAL2.3310
FLOOSE THERMAL2.1510
GLOOSE THERMAL2.0710
HLOOSE THERMAL2.810
ILOOSE THERMAL0.7510
JLOOSE THERMAL4.2710
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 154 -
Rwork0.309 2462 -
all-2616 -
obs-2616 97.47 %
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)
14.15962.93820.20537.76731.69632.2611-0.02520.131-0.00750.41990.05110.30440.32990.1134-0.0260.40690.05160.03210.0172-0.00390.11716.24214.033-26.119
22.14851.80164.57268.5616-1.366515.4081-0.2630.08750.6011-0.66480.64161.6760.0583-0.6795-0.37860.4012-0.0641-0.14480.16610.33210.75530.49514.951-31.027
318.21720.1857-2.565.4602-0.33563.53130.2360.39380.3368-0.6295-0.1269-0.4217-0.1958-0.0506-0.10920.38240.02050.03720.01230.00460.31441.84538.242-26.511
45.1926-0.7084-1.25059.9161-1.69544.6302-0.0761-0.6755-0.13460.56340.2564-0.0309-0.1682-0.1874-0.18020.32070.01370.05140.11810.01620.2136-5.44145.684-16.472
52.9425-1.78651.77224.2769-1.18255.85390.0014-0.10480.245-0.14480.0408-0.0348-0.0661-0.337-0.04230.2811-0.08440.00280.4434-0.10280.437238.75242.115-38.861
64.739-1.4656-0.45054.3836-2.86725.0431-0.0671-0.412-0.18550.05410.15710.654-0.2451-1.2261-0.090.34690.0408-0.09350.6872-0.08090.462131.42743.507-39.929
79.7648-1.12355.36265.9179-0.955911.19380.0371-1.7475-0.27710.8395-0.4915-0.3690.62430.42150.45440.4236-0.12070.06531.0005-0.03110.219321.47622.1054.641
83.9993-1.89080.04473.293-1.12986.89720.1335-0.81890.30220.3787-0.2869-0.3197-0.2170.72580.15330.2085-0.0841-0.03080.5918-0.07660.34126.92322.939-8.632
97.33812.8775-1.51233.1101-0.20644.72440.13250.27870.0025-0.1385-0.17220.0317-0.05810.34780.03980.23990.1001-0.09460.6315-0.1680.330967.4124.455-5.339
103.22611.508-2.46634.15580.39246.08150.0584-0.5716-0.14940.0083-0.0949-0.8547-0.07851.5890.03650.21980.0308-0.08460.9558-0.10280.479774.6623.338-2.954
1118.3953-4.31694.44164.9519-1.23614.3568-0.1254-0.467-1.08630.2943-0.133-0.28060.54950.02340.25840.7882-0.11710.11830.47110.19580.433986.1118.342.935
126.4355-1.15040.12655.4955-1.67556.481-0.1479-0.85310.46990.7513-0.1669-0.1932-0.481-0.15060.31470.5142-0.1176-0.07990.4025-0.03560.37784.94721.64738.32
139.5803-4.7612-0.26112.96660.08294.0958-0.11470.4666-0.5181-0.21090.0913-0.34430.73770.52840.02340.85910.01520.03450.4433-0.15291.037763.60317.432-34.132
148.0178-1.1578-0.0037.8785-0.0063.3629-0.0433-0.6889-0.70580.48220.1503-0.22780.57450.0772-0.1070.5326-0.0076-0.08860.4377-0.05440.550960.42828.846-26.608
1511.0545-2.39420.0593.468-0.32413.32650.0287-0.7633-0.38440.57010.49841.1935-0.4647-1.0363-0.52720.4116-0.03960.07320.82720.28860.742233.497-0.5081.089
167.3791-1.8339-1.95266.6259-2.00258.74820.29490.2581-0.9695-0.4990.29310.66970.906-0.6487-0.58810.3656-0.1168-0.28660.52660.02040.534941.35-5.057-10.029
175.09323.64498.13666.11763.324715.3858-0.56460.11730.2246-0.6202-0.0625-0.0695-0.4997-0.29740.62710.53610.0583-0.02880.8298-0.17450.528367.32925.3779.089
183.3431.34160.19654.8559-1.56159.7231-0.1347-0.33820.63710.4653-0.18850.8027-0.6183-1.21110.32330.37730.00990.01160.8-0.25870.553661.98621.19421.615
193.4603-0.45610.5545.20211.59075.1396-0.1329-0.39390.813-0.15430.06830.5936-0.6773-0.66230.06470.41130.18340.07090.663-0.03940.5704-29.75150.782-27.81
204.5996-0.7682-0.45259.24232.80465.5036-0.3832-0.530.39060.20270.19711.6427-0.4455-1.54070.18620.35410.2578-0.04671.0123-0.04590.8562-37.65448.062-29.687
2140.405315.4881-4.084928.0834-10.111416.4349-0.66112.4604-0.6656-1.70240.95070.82950.8041-1.0196-0.28970.8558-0.06680.02370.3965-0.07910.11091.9315.183-43.831
2229.844-8.3451-11.851411.08073.56184.75190.365-0.17060.3582-0.7883-0.3397-0.4997-0.18170.1635-0.02530.3516-0.11520.06210.5380.23540.528121.30831.013-24.639
230.1249-0.794-0.386112.3842-2.292617.1342-0.16030.0199-0.0012-0.5790.01990.1785-0.8491-1.43820.14040.96290.2351-0.09170.8773-0.19950.895128.85459.026-42.026
245.1009-4.311814.122214.225-13.619939.36710.1380.72430.54391.1653-1.6837-0.67670.21132.14421.54581.0405-0.21380.05871.6083-0.08890.67527.84430.29612.919
2525.88486.28316.000524.53538.705910.9395-0.07420.85470.0798-1.11150.2144-1.2014-0.38620.5437-0.14030.5835-0.06450.18131.16550.09210.637885.96410.837-12.353
2681.8958-43.94919.900123.9268-5.33461.2654-1.2251-3.881-1.04270.24251.51370.2397-0.1231-0.4296-0.28861.2980.19660.33631.36720.58830.694892.3927.39454.581
270.9958-3.18980.003110.537-1.00173.28890.106-0.0409-0.0068-0.31260.24820.0016-0.1441-0.5286-0.35421.12930.1968-0.15140.6764-0.06711.156570.5838.445-28.227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 326
2X-RAY DIFFRACTION2A327 - 364
3X-RAY DIFFRACTION3B239 - 279
4X-RAY DIFFRACTION4B280 - 364
5X-RAY DIFFRACTION5C238 - 325
6X-RAY DIFFRACTION6C326 - 364
7X-RAY DIFFRACTION7D240 - 279
8X-RAY DIFFRACTION8D280 - 364
9X-RAY DIFFRACTION9E238 - 325
10X-RAY DIFFRACTION10E326 - 364
11X-RAY DIFFRACTION11F240 - 279
12X-RAY DIFFRACTION12F280 - 364
13X-RAY DIFFRACTION13G240 - 276
14X-RAY DIFFRACTION14G277 - 364
15X-RAY DIFFRACTION15H240 - 280
16X-RAY DIFFRACTION16H281 - 364
17X-RAY DIFFRACTION17I241 - 279
18X-RAY DIFFRACTION18I280 - 364
19X-RAY DIFFRACTION19J240 - 322
20X-RAY DIFFRACTION20J323 - 364
21X-RAY DIFFRACTION21K2 - 13
22X-RAY DIFFRACTION22L0 - 19
23X-RAY DIFFRACTION23M3 - 12
24X-RAY DIFFRACTION24N2 - 13
25X-RAY DIFFRACTION25O1 - 12
26X-RAY DIFFRACTION26P2 - 12
27X-RAY DIFFRACTION27Q1 - 14

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