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- PDB-8as3: Structure of arrestin2 in complex with 6P CCR5 phosphopeptide and... -

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Basic information

Entry
Database: PDB / ID: 8as3
TitleStructure of arrestin2 in complex with 6P 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 / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / 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 / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / stress fiber assembly / positive regulation of cardiac muscle hypertrophy / negative regulation of NF-kappaB transcription factor activity / pseudopodium / negative regulation of interleukin-6 production / enzyme inhibitor activity / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / clathrin-coated pit / insulin-like growth factor receptor binding / negative regulation of protein ubiquitination / cytoplasmic vesicle membrane / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 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 / Signaling by BRAF and RAF1 fusions / endocytic vesicle membrane / protein transport / Cargo recognition for clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / Clathrin-mediated endocytosis / positive regulation of protein phosphorylation / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / 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 / 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 / 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: 3.5 Å
AuthorsIsaikina, P. / Jakob, R.P. / Maier, T. / Grzesiek, S.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31-201270 Switzerland
Swiss National Science FoundationIZLIZ3-200298 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 1.3Nov 20, 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)92,0724
Polymers92,0724
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-40 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.314, 121.064, 145.285
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: 2706.235 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 interestN
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: 2.78 Å3/Da / Density % sol: 55.72 %
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: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 3.5→49.31 Å / Num. obs: 13152 / % possible obs: 98.2 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1441 / Rpim(I) all: 0.04 / Net I/σ(I): 13.2
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 13.6 % / Rmerge(I) obs: 4.24 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1295 / CC1/2: 0.259 / Rpim(I) all: 1.465 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jqi

4jqi


Resolution: 3.5→49.31 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3326 659 5.07 %
Rwork0.2845 12347 -
obs0.2869 13006 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 443.26 Å2 / Biso mean: 220.1674 Å2 / Biso min: 115.03 Å2
Refinement stepCycle: final / Resolution: 3.5→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6067 0 0 0 6067
Num. residues----783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.780.40881270.42132348247595
3.78-4.160.36721270.36672444257199
4.16-4.760.33291450.27924622607100
4.76-5.990.31971300.31182494262499
5.99-49.310.32361300.24782599272999
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)
15.84117.5683-7.82017.2709-6.6372.13740.0720.10570.8379-0.4994-0.2021-0.675-1.4522-0.31030.022.44840.1093-0.3681.62250.49611.880913.789720.7438-3.1198
24.56132.6409-3.01510.9025-1.89171.56991.0724-0.74071.38191.71270.6485-2.97360.1693-0.65350.36612.8555-0.05-0.48621.84790.89842.816527.76923.9646-6.1626
3-0.52160.3332.60820.77960.71173.2740.32470.2461-0.44430.6953-0.7371-0.5124-0.61010.61730.48712.05680.06840.08582.16810.38661.919614.718419.8083-1.607
42.18140.0254-0.8942-0.5083-0.54124.822-0.0014-0.3631-0.59540.6198-0.4101-0.18450.38050.43410.63472.0082-0.2960.18921.90550.40441.70257.3521-8.698321.9543
51.59841.1115-2.83064.927-1.15997.3457-0.1464-0.8548-0.11041.4343-1.0575-0.3491-0.6610.7510.95851.3201-0.28850.06171.6220.45511.62126.3442-1.902818.8274
64.88136.7855-0.21222.2476-2.85565.1731-1.2891-2.0334-0.8416-1.69241.62861.34680.9914-0.484-2.3911.9921-0.7417-0.33482.16830.17682.22685.482315.8297-13.2516
710.32821.93012.32192.3285-0.53512.60810.54380.3757-0.4998-0.2678-0.1748-0.0567-0.17-1.325-0.29911.5259-0.10910.25921.9044-0.09481.4192-15.7594-9.4668-3.9936
85.1835-0.41283.9961.4603-0.5725-0.2758-0.2848-0.6072-1.2321-0.63080.2616-0.1452-0.8299-0.06880.12951.429-0.10860.38632.0516-0.09861.437-15.1912-15.5702-12.331
99.6342.83574.54034.3369-2.12926.7462-1.64441.2525-2.0633-3.52121.09430.26071.4514-0.4972-0.1791.1180.3748-0.43812.0660.25412.1307-23.2606-34.8507-39.501
1010.37894.15284.85546.2563-1.84477.8417-0.7765-1.3404-0.4701-3.27681.13530.45260.679-0.3741-1.07691.8908-0.0060.0791.59580.01011.6092-22.407-28.6031-26.8118
113.51466.14935.64766.37480.10763.6472-1.34540.0782-0.64650.72220.42050.17043.12762.2397-0.21071.69330.00380.2862.310.37142.2336-24.6488-39.8451-27.7552
124.7185-0.17294.44274.59393.483.0490.43551.5431-0.6903-1.7444-0.0246-1.3555-0.14530.01630.02971.6898-0.10290.68271.8519-0.05561.5854-0.3565-5.4985-21.9527
133.24995.0438-0.35567.60235.32675.7280.8037-0.3456-0.82440.7527-0.4586-0.38650.54750.58470.06571.89190.1924-0.07392.2152-0.33141.541-20.6839-25.36-38.5112
143.8143-2.4909-4.81733.06242.26236.23710.1497-0.96230.1215-0.2131-0.52320.52890.4207-2.03640.29192.0094-0.28650.06291.5453-0.17951.4392-23.6861-20.3712-39.3786
154.1048-6.20190.04973.7615.11826.80710.95310.80240.11561.1426-1.19120.3855-1.0533-2.4090.0022.41460.10950.05611.9533-0.00381.1416-26.7319-23.2336-48.9058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 79 )A6 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 98 )A80 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 159 )A99 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 274 )A160 - 274
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 357 )A275 - 357
6X-RAY DIFFRACTION6chain 'B' and (resid 338 through 345 )B338 - 345
7X-RAY DIFFRACTION7chain 'H' and (resid 17 through 105 )H17 - 105
8X-RAY DIFFRACTION8chain 'H' and (resid 106 through 146 )H106 - 146
9X-RAY DIFFRACTION9chain 'H' and (resid 147 through 165 )H147 - 165
10X-RAY DIFFRACTION10chain 'H' and (resid 166 through 207 )H166 - 207
11X-RAY DIFFRACTION11chain 'H' and (resid 208 through 236 )H208 - 236
12X-RAY DIFFRACTION12chain 'L' and (resid 13 through 113 )L13 - 113
13X-RAY DIFFRACTION13chain 'L' and (resid 114 through 152 )L114 - 152
14X-RAY DIFFRACTION14chain 'L' and (resid 153 through 200 )L153 - 200
15X-RAY DIFFRACTION15chain 'L' and (resid 201 through 224 )L201 - 224

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