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- PDB-6jmu: Crystal structure of GIT1/Paxillin complex -

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Basic information

Entry
Database: PDB / ID: 6jmu
TitleCrystal structure of GIT1/Paxillin complex
Components
  • ARF GTPase-activating protein GIT1
  • Paxillin
KeywordsCELL ADHESION / GIT1 / Paxillin / Complex
Function / homology
Function and homology information


BH4 domain binding / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / negative regulation of ARF protein signal transduction / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / intramembranous ossification / structural constituent of postsynaptic specialization / RHOV GTPase cycle / Ephrin signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHOQ GTPase cycle ...BH4 domain binding / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / negative regulation of ARF protein signal transduction / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / intramembranous ossification / structural constituent of postsynaptic specialization / RHOV GTPase cycle / Ephrin signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHOQ GTPase cycle / GAB1 signalosome / motor learning / RHOU GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / immunological synapse formation / dendritic spine development / response to peptide / negative regulation of inflammatory response to wounding / synaptic vesicle recycling / Smooth Muscle Contraction / neuropilin binding / focal adhesion assembly / vinculin binding / inhibitory synapse / positive regulation of microtubule nucleation / MAP kinase scaffold activity / VEGFA-VEGFR2 Pathway / regulation of G protein-coupled receptor signaling pathway / regulation of ARF protein signal transduction / gamma-tubulin binding / branching morphogenesis of an epithelial tube / lamellipodium assembly / negative regulation of glycolytic process / growth hormone receptor signaling pathway / positive regulation of receptor catabolic process / negative regulation of interleukin-1 beta production / mitotic spindle pole / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synaptic vesicle exocytosis / positive regulation of protein kinase activity / cell leading edge / neuron development / ephrin receptor signaling pathway / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / cytoskeleton organization / lipopolysaccharide-mediated signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / stress fiber / transforming growth factor beta receptor signaling pathway / presynaptic modulation of chemical synaptic transmission / peptidyl-tyrosine phosphorylation / cell redox homeostasis / integrin-mediated signaling pathway / cellular response to epidermal growth factor stimulus / excitatory synapse / protein tyrosine kinase binding / calyx of Held / locomotory behavior / regulation of cytokinesis / GTPase activator activity / brain development / beta-catenin binding / integrin binding / GABA-ergic synapse / small GTPase binding / positive regulation of angiogenesis / cell-cell junction / regulation of cell shape / cell migration / lamellipodium / cellular response to lipopolysaccharide / presynapse / growth cone / signaling receptor complex adaptor activity / scaffold protein binding / protein phosphatase binding / cell cortex / postsynapse / endosome / postsynaptic density / neuron projection / focal adhesion / centrosome / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / mitochondrion / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Arf GTPase-activating protein GIT1/2, coiled-coil domain / GIT coiled-coil Rho guanine nucleotide exchange factor / : / GIT, Spa2 homology (SHD) domain / ARF GTPase-activating protein GIT1, C-terminal / Spa2 homology domain (SHD) of GIT / G protein-coupled receptor kinase-interacting protein 1 C term / Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins / Paxillin / : ...Arf GTPase-activating protein GIT1/2, coiled-coil domain / GIT coiled-coil Rho guanine nucleotide exchange factor / : / GIT, Spa2 homology (SHD) domain / ARF GTPase-activating protein GIT1, C-terminal / Spa2 homology domain (SHD) of GIT / G protein-coupled receptor kinase-interacting protein 1 C term / 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 repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ARF GTPase-activating protein GIT1 / Paxillin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhu, J. / Lin, L. / Xia, Y. / Zhang, R. / Zhang, M.
CitationJournal: Mol.Cell / Year: 2020
Title: GIT/PIX Condensates Are Modular and Ideal for Distinct Compartmentalized Cell Signaling.
Authors: Zhu, J. / Zhou, Q. / Xia, Y. / Lin, L. / Li, J. / Peng, M. / Zhang, R. / Zhang, M.
History
DepositionMar 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: 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
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

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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)36,8024
Polymers36,8024
Non-polymers00
Water3,855214
1
A: ARF GTPase-activating protein GIT1
C: Paxillin


Theoretical massNumber of molelcules
Total (without water)18,4012
Polymers18,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-17 kcal/mol
Surface area8080 Å2
MethodPISA
2
B: ARF GTPase-activating protein GIT1
D: Paxillin


Theoretical massNumber of molelcules
Total (without water)18,4012
Polymers18,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-15 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.200, 90.954, 52.309
Angle α, β, γ (deg.)90.000, 107.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ARF GTPase-activating protein GIT1 / ARF GAP GIT1 / G protein-coupled receptor kinase-interactor 1 / GRK-interacting protein 1


Mass: 15206.399 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Git1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q68FF6
#2: Protein/peptide Paxillin


Mass: 3194.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pxn / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8VI36
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1.92 Å3/Da / Density % sol: 36.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: (NH4)2SO4, PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.37
ReflectionResolution: 2→50 Å / Num. obs: 18573 / % possible obs: 98.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Χ2: 0.898 / Net I/σ(I): 4.5 / Num. measured all: 126793
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.036.80.7649040.7470.3120.8270.73698.8
2.03-2.076.70.6569530.9550.2760.7140.77498.8
2.07-2.116.60.6129070.8480.2540.6640.79899.5
2.11-2.156.50.5259150.8880.2190.570.80198.2
2.15-2.26.20.4479000.8690.1960.490.7895.9
2.2-2.256.90.3799420.9190.1530.4090.80199.1
2.25-2.317.10.349240.9430.1360.3670.80299.1
2.31-2.3770.2899430.9620.1160.3120.82699.2
2.37-2.4470.2499100.9730.10.2690.83498.7
2.44-2.5270.2189440.9750.0870.2350.90299.6
2.52-2.616.90.2019630.9770.0820.2180.88199.7
2.61-2.716.80.1628920.9870.0670.1760.92299.3
2.71-2.846.30.1499260.9860.0640.1630.90295.6
2.84-2.997.10.1439190.9860.0570.1540.9399.2
2.99-3.177.20.1159330.9930.0450.1230.97199.6
3.17-3.427.10.0979520.9930.0390.1051.10299.5
3.42-3.7670.0819190.9930.0330.0881.12899
3.76-4.316.40.0649220.9960.0270.071.18596.6
4.31-5.437.20.0579480.9980.0230.0611.03499.9
5.43-506.80.04395710.0170.0470.81197.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JX0

2jx0


Resolution: 2→45.477 Å / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 29.55
RfactorNum. reflection% reflection
Rfree0.2087 970 5.23 %
Rwork0.1749 --
obs0.1766 18537 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.48 Å2 / Biso mean: 32.33 Å2 / Biso min: 12.25 Å2
Refinement stepCycle: final / Resolution: 2→45.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 214 2503
Biso mean---39.44 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082323
X-RAY DIFFRACTIONf_angle_d1.073145
X-RAY DIFFRACTIONf_chiral_restr0.038375
X-RAY DIFFRACTIONf_plane_restr0.006409
X-RAY DIFFRACTIONf_dihedral_angle_d15.194897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0022-2.10770.24951580.23872493265193
2.1077-2.23960.26811420.22092444258692
2.2396-2.41230.23171410.20112505264694
2.4123-2.65470.19951270.18532529265695
2.6547-3.0380.21361200.17582498261893
3.038-3.82420.18371330.15152552268594
3.8242-21.87930.19721340.15542517265193
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)
11.8305-0.4010.28642.74890.72945.94140.06860.0338-0.0626-0.1586-0.17310.36190.2239-0.48090.04010.1677-0.007700.1361-0.00380.2217-19.0966-9.7129159.9961
21.23670.7452-0.44981.13150.18846.28290.05520.5418-0.0455-0.1403-0.0944-0.2080.34871.09470.00030.17290.07020.05270.3831-0.03120.2899-8.203-6.4594154.5596
32.4210.23012.33082.3540.55666.89720.18330.082-0.012-0.0191-0.0441-0.04710.24510.1156-0.04220.14270.01130.04070.1243-0.01980.1959-13.0699-2.2463162.0446
41.37020.26740.60681.8723-1.71066.42980.0817-0.03440.01080.1634-0.1887-0.1021-0.42010.2690.11190.2218-0.03590.05460.1278-0.01370.2196-13.2671-25.019175.5343
51.6669-0.6421-1.73971.73021.66012.6036-0.2670.0975-0.11040.0866-0.28240.5650.0011-0.78860.33140.19920.00090.08470.242-0.03170.2821-23.5267-28.5922175.5747
62.31460.77030.1650.47570.75662.52990.3013-0.15070.193-0.459-0.39650.2619-0.6519-0.59090.20430.39360.02050.11870.3-0.03140.2291-28.2926-25.3769199.3084
72.74520.1349-2.1781.8156-0.93442.3989-0.0080.2013-0.1245-0.3306-0.1788-0.0614-0.3068-0.14370.15510.22810.0270.00350.1352-0.01330.206-15.8127-34.2318174.5148
86.6121-0.71313.4063.43280.20486.33950.0048-0.0860.23010.14-0.140.0411-0.1157-0.25720.21010.1521-0.01560.05190.1209-0.00480.3105-23.10493.4625161.4012
97.91980.7106-4.04816.4734-2.56849.169-0.10510.0707-0.30270.12610.12-0.1829-0.26-0.09840.06330.127-0.00010.02770.17340.01710.2602-8.7159-38.4471179.1448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 644 through 697 )A644 - 697
2X-RAY DIFFRACTION2chain 'A' and (resid 698 through 728 )A698 - 728
3X-RAY DIFFRACTION3chain 'A' and (resid 729 through 770 )A729 - 770
4X-RAY DIFFRACTION4chain 'B' and (resid 644 through 704 )B644 - 704
5X-RAY DIFFRACTION5chain 'B' and (resid 705 through 728 )B705 - 728
6X-RAY DIFFRACTION6chain 'B' and (resid 729 through 738 )B729 - 738
7X-RAY DIFFRACTION7chain 'B' and (resid 739 through 770 )B739 - 770
8X-RAY DIFFRACTION8chain 'C' and (resid 259 through 279 )C259 - 279
9X-RAY DIFFRACTION9chain 'D' and (resid 260 through 279 )D260 - 279

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