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- PDB-6iuh: Crystal structure of GIT1 PBD domain in complex with Liprin-alpha2 -

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Basic information

Entry
Database: PDB / ID: 6iuh
TitleCrystal structure of GIT1 PBD domain in complex with Liprin-alpha2
Components
  • ARF GTPase-activating protein GIT1
  • Liprin-alpha-2
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


negative regulation of ARF protein signal transduction / structural constituent of presynapse / structural constituent of postsynaptic specialization / RAC2 GTPase cycle / : / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle ...negative regulation of ARF protein signal transduction / structural constituent of presynapse / structural constituent of postsynaptic specialization / RAC2 GTPase cycle / : / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle / dense core granule cytoskeletal transport / motor learning / Receptor-type tyrosine-protein phosphatases / synaptic vesicle recycling / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / postsynaptic specialization / regulation of ARF protein signal transduction / negative regulation of inflammatory response to wounding / regulation of dendritic spine development / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / inhibitory synapse / intramembranous ossification / immunological synapse formation / positive regulation of microtubule nucleation / dendritic spine development / Glutamate Neurotransmitter Release Cycle / regulation of dendritic spine morphogenesis / regulation of G protein-coupled receptor signaling pathway / gamma-tubulin binding / negative regulation of glycolytic process / neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of interleukin-1 beta production / regulation of synaptic vesicle exocytosis / presynaptic active zone / positive regulation of receptor catabolic process / mitotic spindle pole / calyx of Held / excitatory synapse / GABA-ergic synapse / neuron development / ephrin receptor signaling pathway / cellular response to epidermal growth factor stimulus / protein tyrosine kinase binding / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / cell-matrix adhesion / cell redox homeostasis / locomotory behavior / regulation of cytokinesis / synapse organization / brain development / small GTPase binding / synaptic vesicle / presynapse / lamellipodium / presynaptic membrane / growth cone / postsynapse / scaffold protein binding / protein phosphatase binding / cellular response to lipopolysaccharide / dendritic spine / postsynaptic density / endosome / neuron projection / axon / focal adhesion / centrosome / dendrite / glutamatergic synapse / synapse / protein-containing complex binding / cell surface / extracellular exosome / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / 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 / Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 ...: / 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 / Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / LAR-interacting protein, Liprin / 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 / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / 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
IODIDE ION / Liprin-alpha-2 / ARF GTPase-activating protein GIT1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.0Feb 20, 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: Liprin-alpha-2
D: Liprin-alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8317
Polymers37,4514
Non-polymers3813
Water2,540141
1
A: ARF GTPase-activating protein GIT1
C: Liprin-alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8523
Polymers18,7252
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-16 kcal/mol
Surface area8810 Å2
MethodPISA
2
B: ARF GTPase-activating protein GIT1
D: Liprin-alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9794
Polymers18,7252
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-15 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.200, 38.617, 99.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 Liprin-alpha-2 / Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 / PTPRF- ...Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 / PTPRF-interacting protein alpha-2


Mass: 4032.511 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPFIA2 / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75334
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Potassium iodide, 0.1M MES pH 6.5, 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 32467 / % possible obs: 99.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 29.38 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.05 / Rrim(I) all: 0.11 / Χ2: 1.549 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.835.60.84216060.8650.390.930.672100
1.83-1.865.50.77715900.8830.3670.8620.658100
1.86-1.95.20.6516230.9210.3140.7230.756100
1.9-1.945.10.59315950.9090.2890.6620.82999.9
1.94-1.985.50.44416010.9560.2080.4920.86699.8
1.98-2.035.70.4216150.9380.1940.4641.00299.9
2.03-2.085.70.32815960.9620.1530.3631.02399.4
2.08-2.135.50.28216170.970.1330.3131.17599.7
2.13-2.25.40.22516030.9810.1080.251.25599.6
2.2-2.275.20.216340.9850.0990.2241.47199.8
2.27-2.3550.1715790.9840.0860.1911.5299.4
2.35-2.445.40.15516250.9890.0750.1731.58899.1
2.44-2.555.50.13716160.9880.0660.1531.70599.4
2.55-2.695.40.12116070.9910.0590.1351.85799.6
2.69-2.865.30.10716370.9910.0530.121.99999
2.86-3.084.90.09416230.9930.0490.1062.26698.9
3.08-3.395.30.08316340.9940.0410.0932.40498.3
3.39-3.884.90.07416330.9950.0380.0832.76897.6
3.88-4.884.50.06516480.9950.0360.0752.95997.2
4.88-504.70.06617850.9940.0360.0762.79398.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JX0

2jx0


Resolution: 1.8→49.567 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 1592 5 %
Rwork0.2266 30249 -
obs0.2285 31841 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.47 Å2 / Biso mean: 39.3705 Å2 / Biso min: 17.11 Å2
Refinement stepCycle: final / Resolution: 1.8→49.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 3 141 2538
Biso mean--35.19 46.52 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032478
X-RAY DIFFRACTIONf_angle_d0.6183357
X-RAY DIFFRACTIONf_chiral_restr0.021400
X-RAY DIFFRACTIONf_plane_restr0.003435
X-RAY DIFFRACTIONf_dihedral_angle_d10.933966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.85810.3341390.32472666280598
1.8581-1.92450.28191450.301827482893100
1.9245-2.00160.2981440.272927162860100
2.0016-2.09270.28651430.25592721286499
2.0927-2.2030.27511440.23162726287099
2.203-2.34110.31121440.23592745288999
2.3411-2.52180.2941440.23742739288399
2.5218-2.77560.29521460.23552761290799
2.7756-3.17710.28421450.22442755290099
3.1771-4.00260.24281450.20292762290798
4.0026-49.58580.2331530.212910306398
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)
12.57471.51021.9616.73273.30734.6925-0.2276-0.04710.30720.014-0.30811.0771-0.138-0.44770.46160.17380.01430.03450.2563-0.03810.31375.7374-2.102-28.6188
21.7080.90341.38914.5812.7912.97720.0486-0.25420.06711.0433-0.36450.45850.4537-0.42080.32640.3789-0.03330.07220.26260.00680.25888.8353-6.7341-21.9146
32.1936-0.01230.92285.26852.15457.20360.0527-0.03740.07820.8064-0.0178-0.2454-0.00730.244800.2534-0.0286-0.02030.17720.03350.178716.8558-10.5499-22.8312
42.42151.1641.71373.45781.60261.58690.0618-0.07270.08660.37670.0011-0.05780.1423-0.08880.00020.17180.02070.04150.17490.00940.179616.8872-2.7831-24.358
53.869-3.4078-3.4896.8052.91725.150.05910.1332-0.3106-0.03-0.67621.4730.0904-1.09260.68820.2444-0.0002-0.06660.4547-0.17090.45175.7045-16.65218.1646
61.5351-1.1011-1.31181.29241.27462.68780.25690.2374-0.147-1.4219-0.81120.9476-0.7848-0.70990.49180.56890.1556-0.20280.3782-0.07820.35599.007-12.61821.216
72.04360.0212-1.10053.17412.62347.27220.30850.2388-0.1009-1.008-0.45020.0768-0.4371-0.17870.00470.43450.1284-0.04930.22210.02310.216716.863-8.82632.4607
82.5341-1.1147-1.51294.31182.94383.9730.1676-0.011-0.0753-0.1699-0.15060.13560.0844-0.2392-0.02490.23310.0159-0.06720.22070.01640.244916.8038-16.05426.6886
98.20613.00322.12872.03643.76217.73780.581-0.1446-0.42550.6843-0.657-0.42440.53080.33750.20140.32140.0168-0.00260.34890.06070.286827.9682-0.7187-25.8209
107.59361.74895.02923.60771.16026.768-0.18130.68680.4633-0.30940.06960.3657-0.30030.22450.02850.30490.0572-0.01680.27930.04840.31612.80453.6592-35.3213
117.3376-3.6997-2.43032.0295.36287.70690.29510.25580.3561-0.8525-0.3308-0.2901-0.54050.05150.150.25490.0241-0.01340.27520.03210.191227.5019-17.95215.9406
126.6917-1.8234-3.35734.01761.51235.6573-0.1667-0.744-0.39750.6495-0.12310.67410.4676-0.01670.13910.3937-0.10910.01790.3415-0.0120.378712.37-22.45915.1563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 646 through 673 )A646 - 673
2X-RAY DIFFRACTION2chain 'A' and (resid 674 through 704 )A674 - 704
3X-RAY DIFFRACTION3chain 'A' and (resid 705 through 728 )A705 - 728
4X-RAY DIFFRACTION4chain 'A' and (resid 729 through 768 )A729 - 768
5X-RAY DIFFRACTION5chain 'B' and (resid 646 through 673 )B646 - 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 768 )B729 - 768
9X-RAY DIFFRACTION9chain 'C' and (resid 637 through 645 )C637 - 645
10X-RAY DIFFRACTION10chain 'C' and (resid 646 through 670 )C646 - 670
11X-RAY DIFFRACTION11chain 'D' and (resid 636 through 645 )D636 - 645
12X-RAY DIFFRACTION12chain 'D' and (resid 646 through 670 )D646 - 670

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