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- PDB-7dfb: Crystal of Arrestin2-V2Rpp-6-7-Fab30 complex -

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Basic information

Entry
Database: PDB / ID: 7dfb
TitleCrystal of Arrestin2-V2Rpp-6-7-Fab30 complex
Components
  • Beta-arrestin-1
  • FAB30 HEAVY CHAIN
  • FAB30 LIGHT CHAIN
  • V2Rpp-6-7
KeywordsSIGNALING PROTEIN / Arrestin / G-protein-coupled receptor / Phosphopeptide / Antibody fragment
Function / homology
Function and homology information


TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / clathrin heavy chain binding / Cargo recognition for clathrin-mediated endocytosis ...TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / clathrin heavy chain binding / Cargo recognition for clathrin-mediated endocytosis / desensitization of G protein-coupled receptor signaling pathway / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / acetylcholine receptor binding / G protein-coupled receptor internalization / inositol hexakisphosphate binding / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / small molecule binding / pseudopodium / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / G protein-coupled receptor binding / receptor internalization / positive regulation of protein phosphorylation / protein transport / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / signal transduction / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal ...Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
Mus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsSun, J.P. / Yu, X. / Xiao, P. / He, Q.T. / Lin, J.Y. / Zhu, Z.L.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Nat Commun / Year: 2021
Title: Structural studies of phosphorylation-dependent interactions between the V2R receptor and arrestin-2.
Authors: He, Q.T. / Xiao, P. / Huang, S.M. / Jia, Y.L. / Zhu, Z.L. / Lin, J.Y. / Yang, F. / Tao, X.N. / Zhao, R.J. / Gao, F.Y. / Niu, X.G. / Xiao, K.H. / Wang, J. / Jin, C. / Sun, J.P. / Yu, X.
History
DepositionNov 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-arrestin-1
V: V2Rpp-6-7
L: FAB30 LIGHT CHAIN
H: FAB30 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)102,7704
Polymers102,7704
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.480, 116.881, 143.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Beta-arrestin-1 / Arrestin beta-1 / Arrestin-2


Mass: 48272.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARRB1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P17870
#2: Protein/peptide V2Rpp-6-7


Mass: 2916.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Antibody FAB30 LIGHT CHAIN


Mass: 24751.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#4: Antibody FAB30 HEAVY CHAIN


Mass: 26828.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Has ligand of interestY
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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0% PEG 3350, 0.1M Succinic acid, pH 6.5-7.5, 0.2mM DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 3.28→45.36 Å / Num. obs: 30318 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 111.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.04 / Net I/σ(I): 14
Reflection shellResolution: 3.28→3.54 Å / Rmerge(I) obs: 0.929 / Num. unique obs: 3074 / CC1/2: 0.891 / Rpim(I) all: 0.376

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JQI

4jqi


Resolution: 3.28→45.36 Å / SU ML: 0.6236 / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 36.8775 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2905 1416 4.99 %
Rwork0.2314 26966 -
obs0.2344 28382 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.16 Å2
Refinement stepCycle: LAST / Resolution: 3.28→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5913 0 0 0 5913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00966044
X-RAY DIFFRACTIONf_angle_d1.25468257
X-RAY DIFFRACTIONf_chiral_restr0.0631964
X-RAY DIFFRACTIONf_plane_restr0.00771052
X-RAY DIFFRACTIONf_dihedral_angle_d18.68342134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.40.47631530.4042668X-RAY DIFFRACTION97.65
3.4-3.540.40541580.32722680X-RAY DIFFRACTION98.58
3.54-3.70.36611240.30642710X-RAY DIFFRACTION98.64
3.7-3.890.3541530.2962737X-RAY DIFFRACTION99.07
3.89-4.130.39881430.26152650X-RAY DIFFRACTION98.55
4.13-4.450.28351230.22042715X-RAY DIFFRACTION98.3
4.45-4.90.23221050.20222723X-RAY DIFFRACTION98.61
4.9-5.610.23491820.20532701X-RAY DIFFRACTION99.48
5.61-7.060.3141300.24492717X-RAY DIFFRACTION99.1
7.06-45.360.24351450.18172665X-RAY DIFFRACTION97.27

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