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- PDB-4r7v: Crystal structure of N-lobe of human ARRDC3(1-165) -

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Basic information

Entry
Database: PDB / ID: 4r7v
TitleCrystal structure of N-lobe of human ARRDC3(1-165)
ComponentsArrestin domain-containing protein 3
KeywordsPROTEIN BINDING / arrestin fold / GPCR down regulation / beta 2 adrenergic receptor
Function / homology
Function and homology information


negative regulation of heat generation / beta-3 adrenergic receptor binding / negative regulation of locomotion involved in locomotory behavior / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of hippo signaling / heat generation / negative regulation of cold-induced thermogenesis / positive regulation of ubiquitin-protein transferase activity / fat pad development / skin development ...negative regulation of heat generation / beta-3 adrenergic receptor binding / negative regulation of locomotion involved in locomotory behavior / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of hippo signaling / heat generation / negative regulation of cold-induced thermogenesis / positive regulation of ubiquitin-protein transferase activity / fat pad development / skin development / protein transport / early endosome / lysosome / endosome / plasma membrane / cytoplasm
Similarity search - Function
: / Immunoglobulin-like - #640 / 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 ...: / Immunoglobulin-like - #640 / 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
Arrestin domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsQi, S. / Hurley, J.
CitationJournal: Protein Sci. / Year: 2014
Title: Insights into beta 2-adrenergic receptor binding from structures of the N-terminal lobe of ARRDC3.
Authors: Qi, S. / O'Hayre, M. / Gutkind, J.S. / Hurley, J.H.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arrestin domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)20,0171
Polymers20,0171
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.547, 36.158, 74.331
Angle α, β, γ (deg.)90.00, 109.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Arrestin domain-containing protein 3 / TBP-2-like inducible membrane protein / TLIMP


Mass: 20017.283 Da / Num. of mol.: 1 / Fragment: UNP residues 1-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARRDC3, KIAA1376 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96B67
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.1M Tris-HCl, 0.2M (NH4)2SO4, 50mM Guanidine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2014
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. all: 17185 / Num. obs: 17177 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.73→1.79 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→28.829 Å / SU ML: 0.15 / σ(F): 1.38 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 878 5.11 %
Rwork0.1914 --
obs0.193 17176 96.42 %
all-17185 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→28.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 0 61 1281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041280
X-RAY DIFFRACTIONf_angle_d0.9251738
X-RAY DIFFRACTIONf_dihedral_angle_d10.74466
X-RAY DIFFRACTIONf_chiral_restr0.05189
X-RAY DIFFRACTIONf_plane_restr0.003219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.84210.23821430.21812589X-RAY DIFFRACTION94
1.8421-1.98430.24951460.20672690X-RAY DIFFRACTION96
1.9843-2.18390.22391300.18862711X-RAY DIFFRACTION97
2.1839-2.49980.21341400.20132736X-RAY DIFFRACTION97
2.4998-3.14880.27051540.20562774X-RAY DIFFRACTION98
3.1488-28.8330.19491650.17622798X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 23.5046 Å / Origin y: 22.8323 Å / Origin z: 16.3766 Å
111213212223313233
T0.1701 Å2-0.0178 Å2-0.0032 Å2-0.1738 Å20.0118 Å2--0.1688 Å2
L0.4944 °2-0.1239 °2-0.2393 °2-0.5498 °2-0.2706 °2--0.612 °2
S-0.0016 Å °-0.0855 Å °0.0418 Å °0.1029 Å °0.0556 Å °0.0813 Å °0.0524 Å °-0.0976 Å °0.0025 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:170 OR RESID 201:261 ) )A4 - 170
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:170 OR RESID 201:261 ) )A201 - 261

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