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- PDB-3gd1: Structure of an Arrestin/Clathrin complex reveals a novel clathri... -

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Basic information

Entry
Database: PDB / ID: 3gd1
TitleStructure of an Arrestin/Clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking
Components
  • Beta-arrestin-1Arrestin
  • Clathrin heavy chain 1
  • clathrin
KeywordsENDOCYTOSIS / clathrin / arrestin / receptor trafficking / Alternative splicing / Phosphoprotein / Sensory transduction / Acetylation / Coated pit / Cytoplasmic vesicle / Membrane
Function / homology
Function and homology information


Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis ...Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / negative regulation of hyaluronan biosynthetic process / clathrin light chain binding / clathrin complex / AP-2 adaptor complex binding / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin heavy chain binding / clathrin coat of coated pit / Ub-specific processing proteases / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / clathrin coat disassembly / inositol hexakisphosphate binding / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / arrestin family protein binding / G protein-coupled receptor internalization / acetylcholine receptor binding / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / negative regulation of Notch signaling pathway / pseudopodium / phosphatidylinositol-3,4,5-trisphosphate binding / small molecule binding / positive regulation of receptor internalization / receptor-mediated endocytosis / visual perception / G protein-coupled receptor binding / intracellular protein transport / receptor internalization / spindle / autophagy / disordered domain specific binding / melanosome / protein transport / mitotic cell cycle / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / positive regulation of protein phosphorylation / cell division / protein domain specific binding / structural molecule activity / signal transduction / mitochondrion / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin-like - #840 / Clathrin heavy-chain terminal domain / Immunoglobulin-like - #640 / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker ...Immunoglobulin-like - #840 / Clathrin heavy-chain terminal domain / Immunoglobulin-like - #640 / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Tetratricopeptide-like helical domain superfamily / Immunoglobulin E-set / Armadillo-type fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-arrestin-1 / Clathrin heavy chain 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å
AuthorsKang, D.S. / Kern, R.C. / Puthenveedu, M.A. / von Zastrow, M. / Williams, J.C. / Benovic, J.L.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure of an arrestin2-clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking
Authors: Kang, D.S. / Kern, R.C. / Puthenveedu, M.A. / von Zastrow, M. / Williams, J.C. / Benovic, J.L.
History
DepositionFeb 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_fragment / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Beta-arrestin-1
E: Beta-arrestin-1
I: Clathrin heavy chain 1
Z: clathrin


Theoretical massNumber of molelcules
Total (without water)129,9034
Polymers129,9034
Non-polymers00
Water0
1
C: Beta-arrestin-1


Theoretical massNumber of molelcules
Total (without water)44,3101
Polymers44,3101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Beta-arrestin-1


Theoretical massNumber of molelcules
Total (without water)44,3101
Polymers44,3101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)40,3961
Polymers40,3961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
Z: clathrin


Theoretical massNumber of molelcules
Total (without water)8881
Polymers8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)228.960, 61.198, 159.840
Angle α, β, γ (deg.)90.00, 119.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44309.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ARRB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P17870
#2: Antibody Clathrin heavy chain 1


Mass: 40396.340 Da / Num. of mol.: 1 / Fragment: WD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CLTC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P49951
#3: Protein/peptide clathrin /


Mass: 887.975 Da / Num. of mol.: 1 / Fragment: WD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS

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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: 3.76 Å3/Da / Density % sol: 67.27 %
Crystal growTemperature: 293 K / pH: 9
Details: 100mM Bicine, 7% O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500, 6% polyethylene glycol 8000, 4% acetone, 1% ethylene glycol and 10 mM strontium chloride, pH 9.0, VAPOR ...Details: 100mM Bicine, 7% O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500, 6% polyethylene glycol 8000, 4% acetone, 1% ethylene glycol and 10 mM strontium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9833, 0.9795, 0.9791
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 29, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98331
20.97951
30.97911
ReflectionResolution: 3.5→50 Å / Num. obs: 25549 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.2
Reflection shellResolution: 3.5→3.65 Å / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 6.3 / % possible all: 91.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.5→30 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.254 1242 RANDOM
Rwork0.214 --
obs0.214 23540 -
all-24782 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.189 Å20 Å218.106 Å2
2---11.42 Å20 Å2
3---7.231 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7854 0 0 0 7854
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5511.5
X-RAY DIFFRACTIONc_mcangle_it2.8442
X-RAY DIFFRACTIONc_scbond_it1.7652
X-RAY DIFFRACTIONc_scangle_it3.0152.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.parammse_xplor.top
X-RAY DIFFRACTION3mse_xplor.par

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