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- PDB-8as2: Structure of arrestin2 in complex with 4P CCR5 phosphopeptide and... -

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Basic information

Entry
Database: PDB / ID: 8as2
TitleStructure of arrestin2 in complex with 4P CCR5 phosphopeptide and Fab30
Components
  • Beta-arrestin-1
  • C-C chemokine receptor type 5
  • Fab30 heavy chain
  • Fab30 light chain
KeywordsSIGNALING PROTEIN / arrestin / GPCR
Function / homology
Function and homology information


angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / G protein-coupled receptor internalization / arrestin family protein binding / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of cardiac muscle hypertrophy / stress fiber assembly ...angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / G protein-coupled receptor internalization / arrestin family protein binding / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / pseudopodium / negative regulation of interleukin-6 production / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / enzyme inhibitor activity / insulin-like growth factor receptor binding / clathrin-coated pit / negative regulation of protein ubiquitination / GTPase activator activity / cytoplasmic vesicle membrane / Activated NOTCH1 Transmits Signal to the Nucleus / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein phosphorylation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / Cargo recognition for clathrin-mediated endocytosis / protein transport / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / Ub-specific processing proteases / protein ubiquitination / nuclear body / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Phage display vector pTDisp (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsIsaikina, P. / Jakob, R.P. / Maier, T. / Grzesiek, S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31-201270 Switzerland
CitationJournal: Mol.Cell / Year: 2023
Title: A key GPCR phosphorylation motif discovered in arrestin2⋅CCR5 phosphopeptide complexes.
Authors: Isaikina, P. / Petrovic, I. / Jakob, R.P. / Sarma, P. / Ranjan, A. / Baruah, M. / Panwalkar, V. / Maier, T. / Shukla, A.K. / Grzesiek, S.
History
DepositionAug 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Beta-arrestin-1
B: C-C chemokine receptor type 5
H: Fab30 heavy chain
L: Fab30 light chain


Theoretical massNumber of molelcules
Total (without water)92,0254
Polymers92,0254
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.638, 122.178, 145.559
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

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


Mass: 40319.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARRB1, ARR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49407
#2: Protein/peptide C-C chemokine receptor type 5


Mass: 2659.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Antibody Fab30 heavy chain


Mass: 25053.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage display vector pTDisp (others) / Production host: Escherichia coli (E. coli)
#4: Antibody Fab30 light chain


Mass: 23992.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage display vector pTDisp (others) / 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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1% tryptone (w/v), 0.05M HEPES, 12 % PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3.2→49.49 Å / Num. obs: 17440 / % possible obs: 98.8 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.313 / Rpim(I) all: 0.128 / Net I/σ(I): 5.8
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 7 % / Rmerge(I) obs: 1.866 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1676 / CC1/2: 0.673 / Rpim(I) all: 0.761 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTERrefinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jqi

4jqi


Resolution: 3.2→49.49 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3163 827 4.74 %
Rwork0.2797 --
obs0.2814 17440 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 519.22 Å2 / Biso mean: 197.406 Å2 / Biso min: 98.09 Å2
Refinement stepCycle: final / Resolution: 3.2→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6096 0 32 0 6128
Biso mean--222.69 --
Num. residues----784
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)
13.65991.8998-1.53934.7301-0.10382.28860.1551-0.07630.0259-1.0589-0.3292-0.3704-1.5541-0.8622-0.16911.40250.90591.03722.81730.64340.567615.422820.52-1.8178
20.27231.38490.35496.6732-0.61323.9164-0.5246-0.29660.8736-2.15191.29830.4612-1.0593-1.1433-0.09671.38950.30720.38871.79550.4291.526314.867615.97092.3385
34.8331.4235-1.93696.3276-1.04913.027-1.924-2.2635-0.972.0383-3.0828-1.15542.14091.65660.98161.78650.3144-0.04432.74670.32331.399811.8349-19.108435.4726
42.04721.7674-2.74286.2508-3.97695.39330.30680.1776-0.2250.263-0.4564-0.2442-0.1109-0.62190.16360.5980.05390.08642.3410.22220.86276.5067-5.709921.1036
56.592.5063-3.2063.1195-2.75085.0982-1.87492.1646-0.848-3.1332.1231-1.52951.3470.04430.03782.4629-1.0776-0.04041.9065-0.06791.54337.576214.4063-16.4893
63.63692.1533.06315.32531.8143.3859-0.24560.178-0.3219-0.16430.108-0.21530.0531-0.19110.13041.0164-0.0020.20282.98030.06371.0176-13.7052-9.0921-5.0083
73.60361.056-0.79845.91111.74782.98870.14811.1208-1.7742-0.4526-0.8524-0.71923.4663.585-0.11462.5610.9891-0.22593.2551-0.43681.0645-24.6788-31.5257-28.8639
86.9991.37221.34376.1439-2.91451.9871-1.08641.8809-1.0288-1.7690.084-0.8707-0.46031.2196-0.16281.8025-0.2361-0.14083.0024-0.41660.5425-4.1234-3.262-28.7441
92.25440.6919-2.82893.77710.23634.878-0.35370.2665-0.145-0.50230.36060.0924-0.5505-1.3577-1.22751.23770.33190.66993.25510.31620.6259-1.88630.1918-21.5617
102.3077-0.1520.57623.78591.08031.069-0.52030.97750.1465-1.08850.115-0.3460.9476-0.7952-0.35491.74340.36120.85693.2570.08620.97480.4689-6.3125-20.472
113.8201-0.823-0.86313.0483-0.70431.8215-2.0656-0.6403-1.6233-1.56020.27381.17911.0429-1.0101-0.1591.4746-0.6650.80033.0919-1.23531.8004-21.2509-24.3419-38.9432
123.18070.7662-1.89832.1119-2.12062.5734-0.55370.60650.3636-0.43780.7684-0.7115-1.40130.6248-0.75172.2716-0.07880.63571.7008-0.27281.5476-24.9283-15.6541-44.9873
136.36352.34280.45815.29280.97671.5663-1.3303-0.0921.0309-1.08320.1991.895-0.045-1.1194-0.24991.5759-0.64670.37362.1615-0.34371.2374-25.5693-21.7138-42.3872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 150 )A6 - 150
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 182 )A151 - 182
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 203 )A183 - 203
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 357 )A204 - 357
5X-RAY DIFFRACTION5chain 'B' and (resid 335 through 338 )B335 - 338
6X-RAY DIFFRACTION6chain 'H' and (resid 17 through 131 )H17 - 131
7X-RAY DIFFRACTION7chain 'H' and (resid 132 through 236 )H132 - 236
8X-RAY DIFFRACTION8chain 'L' and (resid 13 through 31 )L13 - 31
9X-RAY DIFFRACTION9chain 'L' and (resid 32 through 51 )L32 - 51
10X-RAY DIFFRACTION10chain 'L' and (resid 52 through 113 )L52 - 113
11X-RAY DIFFRACTION11chain 'L' and (resid 114 through 152 )L114 - 152
12X-RAY DIFFRACTION12chain 'L' and (resid 153 through 168 )L153 - 168
13X-RAY DIFFRACTION13chain 'L' and (resid 169 through 224 )L169 - 224

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