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- PDB-4r7x: Crystal structure of N-lobe of human ARRDC3(1-180) -

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Basic information

Entry
Database: PDB / ID: 4r7x
TitleCrystal structure of N-lobe of human ARRDC3(1-180)
ComponentsArrestin domain-containing protein 3
KeywordsPROTEIN BINDING / arrestin fold / GPCR downregulation / Beat 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 / positive regulation of hippo signaling / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of ubiquitin-protein transferase activity / heat generation / negative regulation of cold-induced thermogenesis / fat pad development / skin development ...negative regulation of heat generation / beta-3 adrenergic receptor binding / negative regulation of locomotion involved in locomotory behavior / positive regulation of hippo signaling / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of ubiquitin-protein transferase activity / heat generation / negative regulation of cold-induced thermogenesis / fat pad development / skin development / protein transport / lysosome / early endosome / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Arrestin domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arrestin domain-containing protein 3
B: Arrestin domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,82713
Polymers41,7832
Non-polymers1,04511
Water23413
1
A: Arrestin domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4617
Polymers20,8911
Non-polymers5706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arrestin domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3666
Polymers20,8911
Non-polymers4755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.941, 107.941, 117.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-206-

PO4

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Components

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


Mass: 20891.338 Da / Num. of mol.: 2 / Fragment: UNP residues 1-180
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: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.11 Å3/Da / Density % sol: 70.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.75M NH4H2PO4, 0.1M Sodium citrate tribasic dehydrate, 3.0% (W/V) 6-Aminohexanoic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Jun 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. all: 21676 / Num. obs: 20902 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.61→2.74 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→32.026 Å / SU ML: 0.47 / σ(F): 1.33 / Phase error: 29.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1065 5.1 %
Rwork0.2082 --
obs0.2104 20902 95.73 %
all-21676 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→32.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 55 13 2485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032521
X-RAY DIFFRACTIONf_angle_d0.6973416
X-RAY DIFFRACTIONf_dihedral_angle_d11.29888
X-RAY DIFFRACTIONf_chiral_restr0.029370
X-RAY DIFFRACTIONf_plane_restr0.004419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.72580.40771330.33772281X-RAY DIFFRACTION90
2.7258-2.86950.41281290.3292393X-RAY DIFFRACTION95
2.8695-3.04910.3681230.33022257X-RAY DIFFRACTION88
3.0491-3.28430.34241260.28712391X-RAY DIFFRACTION93
3.2843-3.61440.25171480.21452533X-RAY DIFFRACTION99
3.6144-4.13650.20291290.17872587X-RAY DIFFRACTION100
4.1365-5.20790.20491370.15342631X-RAY DIFFRACTION100
5.2079-32.02840.2311400.19632764X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.7002 Å / Origin y: 32.3354 Å / Origin z: 14.8749 Å
111213212223313233
T0.3972 Å20.0122 Å2-0.0045 Å2-0.3643 Å2-0.0233 Å2--0.3872 Å2
L0.3881 °2-0.003 °20.1431 °2-0.1915 °2-0.2246 °2--0.365 °2
S0.0669 Å °-0.0378 Å °-0.0529 Å °0.0406 Å °-0.0037 Å °-0.0064 Å °0.1707 Å °0.0387 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:168 OR RESID 201:206 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 201:205 OR RESID 3:168 OR RESID 301:308 ) )A3 - 168
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:168 OR RESID 201:206 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 201:205 OR RESID 3:168 OR RESID 301:308 ) )A201 - 206
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:168 OR RESID 201:206 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 201:205 OR RESID 3:168 OR RESID 301:308 ) )A301 - 305
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:168 OR RESID 201:206 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 201:205 OR RESID 3:168 OR RESID 301:308 ) )B201 - 205
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:168 OR RESID 201:206 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 201:205 OR RESID 3:168 OR RESID 301:308 ) )B3 - 168
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:168 OR RESID 201:206 OR RESID 301:305 ) ) OR ( CHAIN B AND ( RESID 201:205 OR RESID 3:168 OR RESID 301:308 ) )B301 - 308

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