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- PDB-6iui: Crystal structure of GIT1 PBD domain in complex with Paxillin LD4... -

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Basic information

Entry
Database: PDB / ID: 6iui
TitleCrystal structure of GIT1 PBD domain in complex with Paxillin LD4 motif
Components
  • ARF GTPase-activating protein GIT1
  • Paxillin
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


negative regulation of ARF protein signal transduction / structural constituent of postsynaptic specialization / RAC2 GTPase cycle / : / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle / motor learning ...negative regulation of ARF protein signal transduction / structural constituent of postsynaptic specialization / RAC2 GTPase cycle / : / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle / motor learning / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / synaptic vesicle recycling / regulation of ARF protein signal transduction / negative regulation of inflammatory response to wounding / inhibitory synapse / intramembranous ossification / immunological synapse formation / vinculin binding / positive regulation of microtubule nucleation / dendritic spine development / neuropilin binding / regulation of G protein-coupled receptor signaling pathway / signal complex assembly / gamma-tubulin binding / negative regulation of glycolytic process / neurotransmitter receptor localization to postsynaptic specialization membrane / microtubule associated complex / negative regulation of interleukin-1 beta production / growth hormone receptor signaling pathway / regulation of synaptic vesicle exocytosis / positive regulation of receptor catabolic process / mitotic spindle pole / calyx of Held / excitatory synapse / GABA-ergic synapse / neuron development / endothelial cell migration / Smooth Muscle Contraction / ephrin receptor signaling pathway / GAB1 signalosome / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of stress fiber assembly / cellular response to epidermal growth factor stimulus / protein tyrosine kinase binding / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / substrate adhesion-dependent cell spreading / cell-matrix adhesion / cell redox homeostasis / transforming growth factor beta receptor signaling pathway / locomotory behavior / regulation of cytokinesis / brain development / small GTPase binding / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / cell-cell junction / cell migration / presynapse / lamellipodium / cell cortex / growth cone / postsynapse / scaffold protein binding / protein phosphatase binding / cellular response to lipopolysaccharide / postsynaptic density / cytoskeleton / cell adhesion / endosome / neuron projection / focal adhesion / centrosome / dendrite / glutamatergic synapse / synapse / protein-containing complex binding / signal transduction / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
: / Leupaxin/Paxillin/TGFB1I1 / Arf GTPase-activating protein GIT1/2, coiled-coil domain / GIT coiled-coil Rho guanine nucleotide exchange factor / ARF GTPase-activating protein GIT1, C-terminal / G protein-coupled receptor kinase-interacting protein 1 C term / GIT, Spa2 homology (SHD) domain / Spa2 homology domain (SHD) of GIT / Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins / Paxillin ...: / Leupaxin/Paxillin/TGFB1I1 / Arf GTPase-activating protein GIT1/2, coiled-coil domain / GIT coiled-coil Rho guanine nucleotide exchange factor / ARF GTPase-activating protein GIT1, C-terminal / G protein-coupled receptor kinase-interacting protein 1 C term / GIT, Spa2 homology (SHD) domain / Spa2 homology domain (SHD) of GIT / Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins / Paxillin / : / : / Paxillin family / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / Nucleotidyltransferases domain 2 / ARFGAP/RecO-like zinc finger / 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) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Paxillin / Paxillin / ARF GTPase-activating protein GIT1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiang, M. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770791 China
National Natural Science Foundation of China31570741 China
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structural basis of the target-binding mode of the G protein-coupled receptor kinase-interacting protein in the regulation of focal adhesion dynamics.
Authors: Liang, M. / Xie, X. / Pan, J. / Jin, G. / Yu, C. / Wei, Z.
History
DepositionNov 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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: ARF GTPase-activating protein GIT1
B: ARF GTPase-activating protein GIT1
C: Paxillin
D: Paxillin


Theoretical massNumber of molelcules
Total (without water)35,4344
Polymers35,4344
Non-polymers00
Water0
1
A: ARF GTPase-activating protein GIT1
D: Paxillin


Theoretical massNumber of molelcules
Total (without water)17,7172
Polymers17,7172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-15 kcal/mol
Surface area7890 Å2
MethodPISA
2
B: ARF GTPase-activating protein GIT1
C: Paxillin


Theoretical massNumber of molelcules
Total (without water)17,7172
Polymers17,7172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-15 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.803, 128.803, 47.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein ARF GTPase-activating protein GIT1 / ARF GAP GIT1 / Cool-associated and tyrosine-phosphorylated protein 1 / CAT1 / G protein-coupled ...ARF GAP GIT1 / Cool-associated and tyrosine-phosphorylated protein 1 / CAT1 / G protein-coupled receptor kinase-interactor 1 / GRK-interacting protein 1


Mass: 14692.856 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Git1 / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z272
#2: Protein/peptide Paxillin /


Mass: 3024.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4DRY6, UniProt: P49023*PLUS

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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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 30% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12341 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Χ2: 0.732 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6470.9866210.7510.4011.0650.426100
2.64-2.6970.7966090.7970.3240.860.444100
2.69-2.7470.645830.8480.2610.6910.464100
2.74-2.86.90.5366200.8820.220.580.458100
2.8-2.866.90.396160.9330.160.4220.452100
2.86-2.936.90.2826210.9690.1160.3050.487100
2.93-36.80.2435950.9770.1010.2640.49899.8
3-3.086.80.1886110.9830.0780.2040.50299.8
3.08-3.176.50.1416240.9890.060.1530.517100
3.17-3.285.80.1136130.990.0510.1240.57499.8
3.28-3.396.90.0926180.9940.0380.0990.652100
3.39-3.537.10.0786080.9950.0320.0850.747100
3.53-3.697.10.0726060.9960.0290.0770.868100
3.69-3.886.90.0626290.9970.0250.0670.93100
3.88-4.136.90.0546220.9970.0220.0580.96499.8
4.13-4.456.60.056170.9970.0210.0541.048100
4.45-4.895.90.0486140.9980.0220.0541.12599.7
4.89-5.66.90.0496270.9980.020.0531.09499.8
5.6-7.056.80.0476320.9970.020.0511.014100
7.05-5060.0426550.9970.0190.0471.45398.3

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IUH

6iuh


Resolution: 2.6→32.201 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.99
RfactorNum. reflection% reflection
Rfree0.2256 611 5 %
Rwork0.1941 --
obs0.1957 12229 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 303.07 Å2 / Biso mean: 130.9752 Å2 / Biso min: 58.89 Å2
Refinement stepCycle: final / Resolution: 2.6→32.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 0 0 2070
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022097
X-RAY DIFFRACTIONf_angle_d0.5212842
X-RAY DIFFRACTIONf_chiral_restr0.017353
X-RAY DIFFRACTIONf_plane_restr0.003361
X-RAY DIFFRACTIONf_dihedral_angle_d10.099772
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6004-2.86190.30141520.258328853037100
2.8619-3.27570.29831450.26328803025100
3.2757-4.12570.27051560.223729033059100
4.1257-32.20320.18851580.16352950310899
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)
13.1731.9842-1.10474.2369-5.51188.69320.3723-1.26930.87011.3877-0.39241.1078-0.0104-0.60630.09370.72010.10310.08060.8967-0.02310.8812-41.4502-20.801511.5655
210.00311.37972.73982.90991.10597.1218-0.1736-0.55410.29420.7461-0.0349-1.5272-0.7104-0.04330.27130.74520.0043-0.02790.62730.04930.6393-31.3987-17.33610.9861
33.61640.7579-3.29342.63140.81994.0032-0.2847-0.1233-3.5414-2.38450.8126-1.00871.29850.5441-0.65741.0793-0.07020.0511.0189-0.29861.5085-38.2586-37.66581.2035
48.7102-1.12891.1637.81392.40367.97-1.67531.22670.1635-2.30591.313-0.6419-1.02130.40290.3280.9408-0.1270.04580.61440.03430.5984-34.1812-19.4131.1012
54.47390.6420.77924.1752-3.40743.0845-0.3032-3.22.45834.33931.3751-0.3441-2.6972.5834-0.96751.8277-0.27340.19731.1442-0.41391.2705-47.1677-22.5952-12.4741
69.71432.68180.51175.46491.75575.5086-0.4597-1.62742.42742.24350.8271-0.0778-0.9129-1.2073-0.26691.00880.24230.45281.22540.1431.1478-56.0494-25.929-14.3729
75.1254-2.38062.83854.3653.0087.1093-1.1507-1.1943-0.13480.40091.38090.8703-1.2908-1.0673-0.29740.79630.07840.07681.15170.36961.5343-59.0762-25.6162-22.1333
88.1376-2.3272-1.30032.5604-1.10379.30430.3102-0.12360.1039-0.5320.84411.46460.335-1.336-0.92480.6014-0.1085-0.03430.77490.15970.8514-51.445-29.7117-22.9246
95.1087-0.53230.58914.9636-5.61527.39580.3519-0.8022.01410.4656-0.2382-1.8605-0.51341.1635-0.36580.8072-0.12620.04460.848-0.01361.1899-41.1884-27.6391-23.7629
103.50510.86995.11643.72162.58898.9992-1.3461-0.75271.0229-1.43091.39472.9619-1.38650.1406-0.75541.21940.1364-0.24030.7390.19551.7909-43.9241-10.49312.9495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 647 through 673 )A647 - 673
2X-RAY DIFFRACTION2chain 'A' and (resid 674 through 697 )A674 - 697
3X-RAY DIFFRACTION3chain 'A' and (resid 698 through 704 )A698 - 704
4X-RAY DIFFRACTION4chain 'A' and (resid 705 through 768 )A705 - 768
5X-RAY DIFFRACTION5chain 'B' and (resid 650 through 673 )B650 - 673
6X-RAY DIFFRACTION6chain 'B' and (resid 674 through 704 )B674 - 704
7X-RAY DIFFRACTION7chain 'B' and (resid 705 through 728 )B705 - 728
8X-RAY DIFFRACTION8chain 'B' and (resid 729 through 765 )B729 - 765
9X-RAY DIFFRACTION9chain 'C' and (resid 262 through 282 )C262 - 282
10X-RAY DIFFRACTION10chain 'D' and (resid 262 through 281 )D262 - 281

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