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- PDB-5w93: p130Cas complex with paxillin LD1 -

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Basic information

Entry
Database: PDB / ID: 5w93
Titlep130Cas complex with paxillin LD1
Components
  • Breast cancer anti-estrogen resistance protein 1
  • Paxillin
KeywordsCELL ADHESION / p130Cas / BCAR1 / paxillin / Focal Adhesion
Function / homology
Function and homology information


BH4 domain binding / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / antigen receptor-mediated signaling pathway / GAB1 signalosome / cellular response to endothelin / response to peptide / Downstream signal transduction / negative regulation of substrate adhesion-dependent cell spreading ...BH4 domain binding / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / antigen receptor-mediated signaling pathway / GAB1 signalosome / cellular response to endothelin / response to peptide / Downstream signal transduction / negative regulation of substrate adhesion-dependent cell spreading / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / endothelin receptor signaling pathway / : / vinculin binding / hepatocyte growth factor receptor signaling pathway / MAP-kinase scaffold activity / neuropilin binding / focal adhesion assembly / VEGFA-VEGFR2 Pathway / lamellipodium assembly / growth hormone receptor signaling pathway / cellular response to hepatocyte growth factor stimulus / branching morphogenesis of an epithelial tube / cell leading edge / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / endothelial cell migration / cellular response to nitric oxide / positive regulation of protein kinase activity / vascular endothelial growth factor receptor signaling pathway / stress fiber / cytoskeleton organization / positive regulation of stress fiber assembly / ruffle / cell chemotaxis / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / positive regulation of endothelial cell migration / actin filament organization / integrin-mediated signaling pathway / transcription coregulator activity / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / beta-catenin binding / SH3 domain binding / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of angiogenesis / cell-cell junction / cell migration / signaling receptor complex adaptor activity / actin cytoskeleton / integrin binding / lamellipodium / insulin receptor signaling pathway / cell cortex / regulation of cell shape / actin cytoskeleton organization / protein phosphatase binding / cell adhesion / positive regulation of cell migration / G protein-coupled receptor signaling pathway / axon / protein domain specific binding / focal adhesion / protein-containing complex binding / protein kinase binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Breast cancer anti-estrogen resistance protein 1 / BCAR1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / Paxillin / : ...Breast cancer anti-estrogen resistance protein 1 / BCAR1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / Paxillin / : / : / Paxillin family / Alpha-catenin/vinculin-like / 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. / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Breast cancer anti-estrogen resistance protein 1 / Paxillin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsMiller, D.J. / Zheng, J.J.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and functional insights into the interaction between the Cas family scaffolding protein p130Cas and the focal adhesion-associated protein paxillin.
Authors: Zhang, C. / Miller, D.J. / Guibao, C.D. / Donato, D.M. / Hanks, S.K. / Zheng, J.J.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Breast cancer anti-estrogen resistance protein 1
B: Breast cancer anti-estrogen resistance protein 1
C: Breast cancer anti-estrogen resistance protein 1
D: Paxillin
E: Paxillin
F: Paxillin


Theoretical massNumber of molelcules
Total (without water)50,9236
Polymers50,9236
Non-polymers00
Water3,261181
1
A: Breast cancer anti-estrogen resistance protein 1
D: Paxillin


Theoretical massNumber of molelcules
Total (without water)16,9742
Polymers16,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-9 kcal/mol
Surface area7450 Å2
MethodPISA
2
B: Breast cancer anti-estrogen resistance protein 1
E: Paxillin


Theoretical massNumber of molelcules
Total (without water)16,9742
Polymers16,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-10 kcal/mol
Surface area7660 Å2
MethodPISA
3
C: Breast cancer anti-estrogen resistance protein 1
F: Paxillin


Theoretical massNumber of molelcules
Total (without water)16,9742
Polymers16,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-7 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.290, 37.741, 152.502
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-909-

HOH

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Components

#1: Protein Breast cancer anti-estrogen resistance protein 1 / CRK-associated substrate / p130cas


Mass: 14796.829 Da / Num. of mol.: 3 / Fragment: CCHD domain (UNP residues 738-874) / Mutation: C755A, C824S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcar1, Cas, Crkas / Production host: Escherichia coli (E. coli) / References: UniProt: Q61140
#2: Protein/peptide Paxillin /


Mass: 2177.388 Da / Num. of mol.: 3 / Fragment: UNP residues 1-20 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8VI36
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5
Details: The final 5 ul crystallization drop contained 0.5 mM protein and 2 mM peptide. The drop and 500 ul reservoir solution both contained 20 mM HEPES, pH 7.5, and 50 mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2012 / Details: Si 111
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 31426 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rsym value: 0.06 / Net I/σ(I): 30.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2436 / Rsym value: 0.376 / % possible all: 77.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T6G chain B

3t6g


Resolution: 2.001→29.947 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.89
RfactorNum. reflection% reflection
Rfree0.2374 1589 5.06 %
Rwork0.1958 --
obs0.198 31396 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→29.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 0 181 3294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073172
X-RAY DIFFRACTIONf_angle_d0.94319
X-RAY DIFFRACTIONf_dihedral_angle_d13.7211112
X-RAY DIFFRACTIONf_chiral_restr0.038535
X-RAY DIFFRACTIONf_plane_restr0.005555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0008-2.06530.35941010.23652008X-RAY DIFFRACTION73
2.0653-2.13910.25691500.21522619X-RAY DIFFRACTION95
2.1391-2.22470.25781400.20082775X-RAY DIFFRACTION99
2.2247-2.3260.24431480.192753X-RAY DIFFRACTION100
2.326-2.44850.28781440.19112746X-RAY DIFFRACTION100
2.4485-2.60190.24821320.19292797X-RAY DIFFRACTION100
2.6019-2.80260.20571350.19592797X-RAY DIFFRACTION100
2.8026-3.08440.25691730.20942799X-RAY DIFFRACTION100
3.0844-3.53010.221380.19562817X-RAY DIFFRACTION100
3.5301-4.44520.2211500.182797X-RAY DIFFRACTION100
4.4452-29.94980.23291780.19942899X-RAY DIFFRACTION100
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)
10.64530.4199-0.41830.4301-0.26880.6919-0.041-0.1753-0.0010.5209-0.05740.20580.2858-0.1007-0.00030.33580.0118-0.00690.2323-0.0110.29725.1098-9.56452.286
21.37130.245-0.1050.32260.59871.66410.02520.04640.09560.0237-0.05190.0175-0.0125-0.0764-00.2130.0211-0.0050.15320.0080.23529.0123-8.287841.123
31.7737-0.00871.04110.7669-0.08880.95870.1019-0.0563-0.1420.25690.3025-0.34750.44460.61640.00090.27830.0235-0.0290.2599-0.00370.334715.697-13.450944.6793
41.2628-0.33140.34440.7940.68131.4678-0.12390.2263-0.0519-0.5969-0.1454-0.23290.29340.2103-0.0010.2646-0.0129-0.02140.3529-0.10430.325835.2371-9.848247.2227
51.7312-0.54450.04280.51020.33042.5983-0.0719-0.03520.1495-0.03390.1037-0.0647-0.1304-0.1935-00.22730.02580.01250.2851-0.0860.307629.8032-7.035157.5359
60.7065-0.10540.69760.90730.41490.97480.0111-0.0171-0.0735-0.2290.12460.06760.4096-0.5028-0.00010.2432-0.0319-0.02540.4043-0.03870.318923.8867-12.945953.7179
70.9518-0.34611.010.3951-0.45971.9025-0.15111.18320.0587-0.2827-0.0102-0.33030.51220.99370.09590.7507-0.04930.03931.2435-0.14880.514114.3173-21.0611.8558
81.07190.7696-0.07770.59070.18951.2555-0.20891.01250.3846-0.16340.33180.0011-0.2236-0.09140.01160.411-0.07210.05980.88310.0350.437710.1474-13.69118.272
90.2238-0.1184-0.46070.4917-0.16111.4-0.05411.1790.0503-0.44680.19080.1250.8266-0.41750.19930.5043-0.2301-0.04281.053-0.11980.3744.0177-22.04468.3687
100.062-0.02730.05750.1405-0.12960.13520.0640.06570.3675-0.5239-0.15420.4687-0.5676-0.0465-00.38350.0602-0.07640.31630.00830.41783.6671-7.934432.6861
110.19940.1499-0.02190.15240.0320.0577-0.1388-0.10620.01580.5962-0.0976-0.3453-0.50310.116200.57070.0068-0.02540.5295-0.10760.439733.5327-5.376167.1657
120.00760.0062-0.01170.0052-0.01090.02010.16150.08920.553-0.3028-0.03010.3247-0.54370.038200.675-0.09010.00810.6778-0.00140.527314.6081-11.006416.4945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 741 through 774 )
2X-RAY DIFFRACTION2chain 'A' and (resid 775 through 839 )
3X-RAY DIFFRACTION3chain 'A' and (resid 840 through 873 )
4X-RAY DIFFRACTION4chain 'B' and (resid 741 through 774 )
5X-RAY DIFFRACTION5chain 'B' and (resid 775 through 839 )
6X-RAY DIFFRACTION6chain 'B' and (resid 840 through 873 )
7X-RAY DIFFRACTION7chain 'C' and (resid 744 through 778 )
8X-RAY DIFFRACTION8chain 'C' and (resid 779 through 839 )
9X-RAY DIFFRACTION9chain 'C' and (resid 840 through 867 )
10X-RAY DIFFRACTION10chain 'D' and (resid 616 through 627 )
11X-RAY DIFFRACTION11chain 'E' and (resid 616 through 628 )
12X-RAY DIFFRACTION12chain 'F' and (resid 618 through 627 )

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