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- PDB-2iv8: beta appendage in complex with b-arrestin peptide -

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Basic information

Entry
Database: PDB / ID: 2iv8
Titlebeta appendage in complex with b-arrestin peptide
Components
  • AP-2 COMPLEX SUBUNIT BETA-1
  • BETA-ARRESTIN-1
KeywordsENDOCYTOSIS/REGULATOR / ENDOCYTOSIS-REGULATOR COMPLEX / SENSORY TRANSDUCTION / RECEPTOR / COATED PITS / ADAPTOR COMPLEX-REGULATOR
Function / homology
Function and homology information


Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / angiotensin receptor binding / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization ...Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / angiotensin receptor binding / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / TGFBR3 regulates TGF-beta signaling / Retrograde neurotrophin signalling / Activation of SMO / clathrin-coated endocytic vesicle / clathrin coat assembly / LDL clearance / negative regulation of interleukin-8 production / clathrin-dependent endocytosis / signal sequence binding / Nef Mediated CD4 Down-regulation / positive regulation of protein localization to membrane / coronary vasculature development / arrestin family protein binding / G protein-coupled receptor internalization / endolysosome membrane / neurotransmitter secretion / ventricular septum development / aorta development / clathrin binding / Lysosome Vesicle Biogenesis / : / stress fiber assembly / positive regulation of cardiac muscle hypertrophy / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / pseudopodium / Recycling pathway of L1 / negative regulation of interleukin-6 production / positive regulation of receptor internalization / EPH-ephrin mediated repulsion of cells / negative regulation of Notch signaling pathway / positive regulation of endocytosis / synaptic vesicle endocytosis / vesicle-mediated transport / insulin-like growth factor receptor binding / clathrin-coated pit / MHC class II antigen presentation / negative regulation of protein ubiquitination / enzyme inhibitor activity / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / cytoplasmic vesicle membrane / VLDLR internalisation and degradation / intracellular protein transport / kidney development / clathrin-coated endocytic vesicle membrane / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / G protein-coupled receptor binding / cytoplasmic side of plasma membrane / positive regulation of protein phosphorylation / 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 / synaptic vesicle / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / Cargo recognition for clathrin-mediated endocytosis / protein transport / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / G alpha (s) signalling events / ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / Ub-specific processing proteases / nuclear body / protein ubiquitination / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / protein-containing complex binding / glutamatergic synapse / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Immunoglobulin-like - #1150 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain ...Immunoglobulin-like - #1150 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / 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 / TATA-Binding Protein / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Immunoglobulin E-set / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-arrestin-1 / AP-2 complex subunit beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFord, M.G.J. / Schmid, E.M. / McMahon, H.T.
CitationJournal: Plos Biol. / Year: 2006
Title: Role of the Ap2 Beta-Appendage Hub in Recruiting Partners for Clathrin-Coated Vesicle Assembly.
Authors: Schmid, E.M. / Ford, M.G.J. / Burtey, A. / Praefcke, G.J.K. / Peak-Chew, S. / Mills, I.G. / Benmerah, A. / Mcmahon, H.T.
History
DepositionJun 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-2 COMPLEX SUBUNIT BETA-1
P: BETA-ARRESTIN-1
Q: BETA-ARRESTIN-1


Theoretical massNumber of molelcules
Total (without water)31,7343
Polymers31,7343
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-8 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.952, 35.484, 190.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AP-2 COMPLEX SUBUNIT BETA-1 / BETA2-APPENDAGE / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-1 SUBUNIT / BETA-ADAPTIN / PLASMA MEMBRANE ...BETA2-APPENDAGE / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-1 SUBUNIT / BETA-ADAPTIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN / AP105B


Mass: 26899.055 Da / Num. of mol.: 1 / Fragment: RESIDUES 700-937
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BRAIN / Plasmid: PET-15B / Production host: ESCHERICIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P63010
#2: Protein/peptide BETA-ARRESTIN-1 / B-ARRESTIN2


Mass: 2417.651 Da / Num. of mol.: 2 / Fragment: RESIDUES 383-402 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P49407
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.4
Details: 0.2M MG FORMATE 30% PEG 3350 OTHER REMARKS: THIS WAS THE ONLY CRYSTAL OBTAINED DESPITE HEROIC ATTEMPTS. THE CRYSTAL WAS HIGHLY MOSAIC, AND EPITAXIALLY SPLIT, LIMITING THE AMOUNT OF DATA ...Details: 0.2M MG FORMATE 30% PEG 3350 OTHER REMARKS: THIS WAS THE ONLY CRYSTAL OBTAINED DESPITE HEROIC ATTEMPTS. THE CRYSTAL WAS HIGHLY MOSAIC, AND EPITAXIALLY SPLIT, LIMITING THE AMOUNT OF DATA WHICH COULD BE COLLECTED., pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→19.78 Å / Num. obs: 4759 / % possible obs: 70.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5 / % possible all: 63.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E42, CHAIN A

1e42


Resolution: 2.8→19.78 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.781 / SU B: 23.134 / SU ML: 0.455 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.788 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.369 215 4.5 %RANDOM
Rwork0.213 ---
obs0.22 4512 70.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 0 16 2018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2461.9582797
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7295251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.23725.5198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.01515359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.835157
X-RAY DIFFRACTIONr_chiral_restr0.1330.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021558
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3050.21033
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3410.21376
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3490.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9731.51301
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69122048
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2753873
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7484.5747
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.566 6
Rwork0.238 289
Refinement TLS params.Method: refined / Origin x: -4.9825 Å / Origin y: -4.053 Å / Origin z: -11.088 Å
111213212223313233
T-0.0988 Å2-0.0428 Å2-0.0107 Å2-0.0486 Å2-0.0354 Å2---0.1143 Å2
L0.2184 °2-0.1097 °2-0.7835 °2-0.0579 °20.4901 °2--6.0894 °2
S-0.3225 Å °0.0706 Å °0.0376 Å °0.1401 Å °0.0628 Å °-0.2298 Å °0.1961 Å °-0.3487 Å °0.2597 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A828 - 905
2X-RAY DIFFRACTION1A906 - 937
3X-RAY DIFFRACTION1P1 - 14

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