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- PDB-2wtr: Full length Arrestin2 -

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Basic information

Entry
Database: PDB / ID: 2wtr
TitleFull length Arrestin2
Components(BETA-ARRESTIN-1Arrestin) x 2
KeywordsSIGNALING PROTEIN / SENSORY TRANSDUCTION / G-PROTEIN-COUPLED RECEPTOR DESENSITIZATION / PHOSPHOPROTEIN
Function / homology
Function and homology information


MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / clathrin heavy chain binding / clathrin coat of coated pit / Ub-specific processing proteases / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis ...MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / clathrin heavy chain binding / clathrin coat of coated pit / Ub-specific processing proteases / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / inositol hexakisphosphate binding / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / G protein-coupled receptor internalization / acetylcholine receptor binding / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / negative regulation of Notch signaling pathway / pseudopodium / phosphatidylinositol-3,4,5-trisphosphate binding / small molecule binding / positive regulation of receptor internalization / visual perception / G protein-coupled receptor binding / receptor internalization / protein transport / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / positive regulation of protein phosphorylation / signal transduction / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / 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 ...Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhou, H.G. / Standfuss, J. / Watson, K.A. / Krasel, C.
CitationJournal: To be Published
Title: A New Dimeric Crystal Form for Arrestin2
Authors: Zhou, H.G. / Standfuss, J. / Watson, K.A. / Krasel, C.
History
DepositionSep 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-ARRESTIN-1
B: BETA-ARRESTIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9396
Polymers94,3892
Non-polymers5494
Water1,71195
1
A: BETA-ARRESTIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4763
Polymers47,2021
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-ARRESTIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4623
Polymers47,1881
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.290, 72.930, 115.360
Angle α, β, γ (deg.)90.00, 98.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-ARRESTIN-1 / Arrestin / ARRESTIN2 / ARRESTIN BETA-1


Mass: 47201.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PTRC-HISB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-LYSS / References: UniProt: P17870
#2: Protein BETA-ARRESTIN-1 / Arrestin / ARRESTIN2 / ARRESTIN BETA-1


Mass: 47187.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PTRC-HISB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-LYSS / References: UniProt: P17870
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.75 Å3/Da / Density % sol: 55.23 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALS WERE GROWN USING THE HANGING-DROP METHOD IN A NEXTAL TRAY (QIAGEN) AT 277 K AGAINST A 1 ML RESERVOIR SOLUTION CONSISTING OF 12% (W/V) PEG 2000, 0.1M BACL2, 0.1 M TRIS-HCL PH7.5. THE ...Details: CRYSTALS WERE GROWN USING THE HANGING-DROP METHOD IN A NEXTAL TRAY (QIAGEN) AT 277 K AGAINST A 1 ML RESERVOIR SOLUTION CONSISTING OF 12% (W/V) PEG 2000, 0.1M BACL2, 0.1 M TRIS-HCL PH7.5. THE HANGING DROP CONTAINED 2 MICROLITRES OF CONCENTRATED ARRESTIN2 PROTEIN (BETWEEN 9-11 MG/ML IN 0.1M TRIS-HCL PH 8.5) AND 2 MICROLITRES OF RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 22285 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 61.25 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 2.5 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G4M

1g4m


Resolution: 2.9→47.074 Å / SU ML: 0.45 / σ(F): 1.38 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2951 1144 5.1 %
Rwork0.2485 --
obs0.2508 22273 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.027 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 73.62 Å2
Baniso -1Baniso -2Baniso -3
1--10.9198 Å20 Å2-7.0202 Å2
2--29.7769 Å20 Å2
3----18.8571 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5727 0 4 95 5826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025840
X-RAY DIFFRACTIONf_angle_d0.5487902
X-RAY DIFFRACTIONf_dihedral_angle_d20.6913635
X-RAY DIFFRACTIONf_chiral_restr0.038906
X-RAY DIFFRACTIONf_plane_restr0.0031018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.0320.39431460.33692611X-RAY DIFFRACTION97
3.032-3.19180.32041480.28862594X-RAY DIFFRACTION97
3.1918-3.39170.32511250.25782637X-RAY DIFFRACTION97
3.3917-3.65350.27271360.24142643X-RAY DIFFRACTION97
3.6535-4.0210.31811530.23022623X-RAY DIFFRACTION97
4.021-4.60240.25861430.19992628X-RAY DIFFRACTION97
4.6024-5.79690.24221340.21732671X-RAY DIFFRACTION97
5.7969-47.08040.27691590.26842722X-RAY DIFFRACTION98

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