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- PDB-6kl7: Beta-arrestin 1 mutant S13D/T275D -

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Basic information

Entry
Database: PDB / ID: 6kl7
TitleBeta-arrestin 1 mutant S13D/T275D
ComponentsBeta-arrestin-1
KeywordsSIGNALING PROTEIN / Beta-arrestin-1 / Signaling
Function / homology
Function and homology information


V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / G alpha (s) signalling events / sensory perception of touch / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / protein phosphorylated amino acid binding / Lysosome Vesicle Biogenesis ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / G alpha (s) signalling events / sensory perception of touch / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / protein phosphorylated amino acid binding / Lysosome Vesicle Biogenesis / Ub-specific processing proteases / angiotensin receptor binding / AP-2 adaptor complex binding / MAP2K and MAPK activation / Golgi Associated Vesicle Biogenesis / regulation of inositol trisphosphate biosynthetic process / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / negative regulation of GTPase activity / negative regulation of interleukin-8 production / clathrin-cargo adaptor activity / desensitization of G protein-coupled receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / mitogen-activated protein kinase kinase binding / stress fiber assembly / Thrombin signalling through proteinase activated receptors (PARs) / negative regulation of Notch signaling pathway / sensory perception / response to morphine / negative regulation of interleukin-6 production / clathrin binding / positive regulation of Rho protein signal transduction / negative regulation of protein phosphorylation / pseudopodium / phototransduction / positive regulation of receptor internalization / cysteine-type endopeptidase inhibitor activity / insulin-like growth factor receptor binding / negative regulation of protein ubiquitination / clathrin-coated pit / intracellular glucose homeostasis / positive regulation of protein ubiquitination / nuclear estrogen receptor binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / GTPase activator activity / phosphoprotein binding / negative regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / endocytosis / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / protein transport / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / molecular adaptor activity / dendritic spine / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / regulation of apoptotic process / positive regulation of MAPK cascade / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / transcription coactivator activity / postsynaptic membrane / endosome / postsynaptic density / response to xenobiotic stimulus / protein ubiquitination / G protein-coupled receptor signaling pathway / signaling receptor binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / regulation of DNA-templated transcription / chromatin / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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 / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.794 Å
AuthorsKang, H. / Choi, H.J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2018R1A2B6001554 Korea, Republic Of
National Research Foundation (Korea)NRF-2012R1A5A2A28671860 Korea, Republic Of
National Research Foundation (Korea)NRF-2016R1A2B4013488 Korea, Republic Of
CitationJournal: Structure / Year: 2020
Title: Conformational Dynamics and Functional Implications of Phosphorylated beta-Arrestins.
Authors: Kang, H. / Yang, H.S. / Ki, A.Y. / Ko, S.B. / Kim, K.W. / Shim, C.Y. / Kim, K. / Choi, H.J. / Chung, K.Y.
History
DepositionJul 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-arrestin-1
B: Beta-arrestin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8378
Polymers95,0882
Non-polymers7496
Water70339
1
A: Beta-arrestin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0185
Polymers47,5441
Non-polymers4744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-arrestin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8193
Polymers47,5441
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.441, 76.835, 119.456
Angle α, β, γ (deg.)90.000, 100.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 47543.977 Da / Num. of mol.: 2 / Mutation: S13D, T275D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29066
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.05 M HEPES 7.5, 70 mM BaCl2, 9% PEG 3550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.794→40 Å / Num. obs: 27394 / % possible obs: 98.68 % / Redundancy: 4 % / Biso Wilson estimate: 65.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07279 / Rpim(I) all: 0.04162 / Rrim(I) all: 0.0841 / Net I/σ(I): 12.89
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.5517 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2715 / CC1/2: 0.887 / Rpim(I) all: 0.3086 / Rrim(I) all: 0.6336 / % possible all: 98.15

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å39.1 Å
Translation2.9 Å39.1 Å

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
HKL-2000718data reduction
SCALEPACKdata scaling
PHASER2.8.0phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WTR

2wtr


Resolution: 2.794→39.096 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 1315 4.8 %
Rwork0.2184 26079 -
obs0.2211 27394 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.09 Å2 / Biso mean: 95.914 Å2 / Biso min: 30.24 Å2
Refinement stepCycle: final / Resolution: 2.794→39.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5449 0 9 39 5497
Biso mean--131.99 58.3 -
Num. residues----685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.794-2.90540.33781550.3023284397
2.9054-3.03750.33861450.2813285998
3.0375-3.19760.32541200.25291899
3.1976-3.39780.28541440.2437287899
3.3978-3.660.33591420.237290899
3.66-4.0280.34191260.2298289799
4.028-4.61010.27281740.1898287799
4.6101-5.80520.22851610.1893292399
5.8052-39.0960.22641480.207297699
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)
12.87310.11410.02847.42265.94839.65650.00810.3231-0.1191-0.8640.1635-0.3692-0.09720.4612-0.14450.44730.10780.02130.48410.07310.409628.3529-10.19483.128
22.0327-7.5019-4.07469.90086.22289.54341.11180.63941.2981-1.2964-0.1052-1.6331-0.82251.2706-0.96190.56530.0010.09890.8812-0.01750.681233.3103-6.50953.4742
35.4062-1.6867-4.56812.11921.97467.30840.0537-0.11520.0506-0.192-0.2150.2213-0.0173-0.62150.15190.315-0.0091-0.13770.6251-0.02640.57158.61291.132527.7984
42.09070.7638-2.07622.0778-0.49966.3093-0.0539-2.1384-0.18041.042-0.10030.41720.1279-1.4290.18840.968-0.14970.09292.4244-0.28810.956212.77555.163683.0608
52.6845-0.91231.76453.765-1.6088.97890.0377-1.06270.33940.40350.1051-0.0192-0.021-0.0768-0.16120.4336-0.0932-0.02941.5187-0.24340.769114.33638.219373.0908
62.7424-0.3797-0.35895.756-0.40454.5628-0.1188-1.4549-0.28190.8316-0.07811.06390.1343-0.75840.19830.6556-0.13560.05291.9224-0.26480.795813.04725.351775.0267
73.43630.5293-4.56950.85080.13267.7031-0.3018-0.4431-0.15280.0705-0.0676-0.1280.50220.89350.3530.37820.0719-0.17441.027-0.13830.779136.88351.288944.8095
88.7271-1.0868-6.13340.99250.76227.99330.1633-0.63660.56050.08430.1035-0.0053-0.42040.2398-0.26720.3897-0.0224-0.1220.8614-0.22830.709329.78159.401752.5684
92.42310.2115-0.64831.97181.02726.34550.2424-1.10780.4860.6938-0.3206-0.0687-0.6421-0.31030.06340.7189-0.128-0.11461.2035-0.26080.772128.06259.769267.0146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 139 )A5 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 172 )A140 - 172
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 396 )A173 - 396
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 105 )B5 - 105
5X-RAY DIFFRACTION5chain 'B' and (resid 106 through 139 )B106 - 139
6X-RAY DIFFRACTION6chain 'B' and (resid 140 through 184 )B140 - 184
7X-RAY DIFFRACTION7chain 'B' and (resid 185 through 213 )B185 - 213
8X-RAY DIFFRACTION8chain 'B' and (resid 214 through 329 )B214 - 329
9X-RAY DIFFRACTION9chain 'B' and (resid 330 through 397 )B330 - 397

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