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- PDB-7df9: Crystal of Arrestin2-V2Rpp-1-Fab30 complex -

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Basic information

Entry
Database: PDB / ID: 7df9
TitleCrystal of Arrestin2-V2Rpp-1-Fab30 complex
Components
  • Beta-arrestin-1
  • FAB30 HEAVY CHAIN
  • FAB30 LIGHT CHAIN
  • VASOPRESSIN V2 RECEPTOR PHOSPHOPEPTIDE
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: 3.17 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 9, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-arrestin-1
V: VASOPRESSIN V2 RECEPTOR PHOSPHOPEPTIDE
L: FAB30 LIGHT CHAIN
H: FAB30 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)102,8504
Polymers102,8504
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-58 kcal/mol
Surface area36260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.174, 121.536, 144.639
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 (E. coli) / References: UniProt: P17870
#2: Protein/peptide VASOPRESSIN V2 RECEPTOR PHOSPHOPEPTIDE


Mass: 2996.489 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 (E. coli)
#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 (E. coli)
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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 10% 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: BL18U1 / Wavelength: 0.97736 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97736 Å / Relative weight: 1
ReflectionResolution: 3.17→46.52 Å / Num. obs: 17687 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 101.63 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.8
Reflection shellResolution: 3.17→3.39 Å / Rmerge(I) obs: 1.459 / Num. unique obs: 3145 / CC1/2: 0.783 / Rpim(I) all: 0.875

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Processing

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

4jqi


Resolution: 3.17→38.25 Å / SU ML: 0.8259 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 37.9638 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2805 1723 5.19 %
Rwork0.2553 31497 -
obs0.2566 17638 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.71 Å2
Refinement stepCycle: LAST / Resolution: 3.17→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5747 0 0 0 5747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01175882
X-RAY DIFFRACTIONf_angle_d1.36838079
X-RAY DIFFRACTIONf_chiral_restr0.073951
X-RAY DIFFRACTIONf_plane_restr0.00961040
X-RAY DIFFRACTIONf_dihedral_angle_d22.25391992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.260.53521470.43962627X-RAY DIFFRACTION99.78
3.26-3.370.37361490.37362672X-RAY DIFFRACTION99.61
3.37-3.490.41631370.38272597X-RAY DIFFRACTION98.88
3.49-3.630.39691500.33892608X-RAY DIFFRACTION98.92
3.63-3.790.42691300.33382636X-RAY DIFFRACTION98.75
3.79-3.990.35371490.30232601X-RAY DIFFRACTION98.6
3.99-4.240.31191440.27042637X-RAY DIFFRACTION99.11
4.24-4.570.27841310.24242610X-RAY DIFFRACTION98.7
4.57-5.030.25041700.23172631X-RAY DIFFRACTION99.26
5.03-5.760.33081310.24182615X-RAY DIFFRACTION98.64
5.76-7.240.27331200.25982669X-RAY DIFFRACTION99.25
7.24-38.250.17841650.17212594X-RAY DIFFRACTION98.25

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