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- PDB-2g30: beta appendage of AP2 complexed with ARH peptide -

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Basic information

Entry
Database: PDB / ID: 2g30
Titlebeta appendage of AP2 complexed with ARH peptide
Components
  • 16-mer peptide from Low density lipoprotein receptor adapter protein 1
  • AP-2 complex subunit beta-1
  • peptide sequence AAF
KeywordsENDOCYTOSIS/EXOCYTOSIS / alpha-helical ARH peptide / platform domain / sandwich domain / endocytosis / adaptor / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


AP-1 adaptor complex binding / neurofilament / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of low-density lipoprotein particle clearance / receptor-mediated endocytosis involved in cholesterol transport / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / AP-2 adaptor complex binding / Trafficking of GluR2-containing AMPA receptors ...AP-1 adaptor complex binding / neurofilament / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of low-density lipoprotein particle clearance / receptor-mediated endocytosis involved in cholesterol transport / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / AP-2 adaptor complex binding / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / low-density lipoprotein particle clearance / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Chylomicron clearance / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / LDL clearance / clathrin adaptor activity / regulation of protein binding / positive regulation of cholesterol metabolic process / clathrin-dependent endocytosis / membrane organization / cholesterol transport / coronary vasculature development / signal sequence binding / endolysosome membrane / Nef Mediated CD4 Down-regulation / amyloid precursor protein metabolic process / aorta development / ventricular septum development / low-density lipoprotein particle receptor binding / clathrin binding / Recycling pathway of L1 / cellular response to cytokine stimulus / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / regulation of protein localization to plasma membrane / signaling adaptor activity / vesicle-mediated transport / positive regulation of vascular associated smooth muscle cell proliferation / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / VLDLR internalisation and degradation / cholesterol metabolic process / phosphotyrosine residue binding / receptor-mediated endocytosis / basal plasma membrane / kidney development / cholesterol homeostasis / intracellular protein transport / clathrin-coated endocytic vesicle membrane / receptor internalization / recycling endosome / cytoplasmic side of plasma membrane / positive regulation of receptor-mediated endocytosis / endocytic vesicle membrane / signaling receptor complex adaptor activity / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / amyloid-beta binding / postsynapse / Potential therapeutics for SARS / early endosome / axon / glutamatergic synapse / membrane / plasma membrane / cytosol
Similarity search - Function
Phosphotyrosine interaction domain (PTB/PID) / Immunoglobulin-like - #1150 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Coatomer/calthrin adaptor appendage, C-terminal subdomain ...Phosphotyrosine interaction domain (PTB/PID) / Immunoglobulin-like - #1150 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / PTB/PI domain / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TATA-Binding Protein / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AP-2 complex subunit beta / Low density lipoprotein receptor adapter protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEdeling, M.A. / Collins, B.M. / Traub, L.M. / Owen, D.J.
CitationJournal: Dev.Cell / Year: 2006
Title: Molecular Switches Involving the AP-2 beta2 Appendage Regulate Endocytic Cargo Selection and Clathrin Coat Assembly
Authors: Edeling, M.A. / Mishra, S.K. / Keyel, P.A. / Steinhauser, A.L. / Collins, B.M. / Roth, R. / Heuser, J.E. / Owen, D.J. / Traub, L.M.
History
DepositionFeb 17, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BETA-ADAPTIN PROTEIN IS PART OF THE ASSEMBLY PROTEIN COMPLEX 2, (AP-2) THAT IS A HETEROTETRAMER COMPOSED OF TWO LARGE CHAINS (ALPHA AND BETA), A MEDIUM CHAIN (AP50) AND A SMALL CHAIN (AP17).

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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: 16-mer peptide from Low density lipoprotein receptor adapter protein 1
S: peptide sequence AAF


Theoretical massNumber of molelcules
Total (without water)31,1793
Polymers31,1793
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.750, 36.313, 98.982
Angle α, β, γ (deg.)90.00, 92.91, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit (chains A, P and S) represent the biological unit

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Components

#1: Protein AP-2 complex subunit beta-1 / Adapter-related protein complex 2 beta-1 subunit / Beta-adaptin / Plasma membrane adaptor HA2/AP2 ...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 / Beta appendage


Mass: 29088.453 Da / Num. of mol.: 1 / Fragment: residues 701-937
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP2B1, CLAPB1 / Plasmid: pMW172His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: P63010
#2: Protein/peptide 16-mer peptide from Low density lipoprotein receptor adapter protein 1 / Autosomal recessive hypercholesterolemia protein / ARH peptide


Mass: 1782.865 Da / Num. of mol.: 1 / Fragment: residues 1-16 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in human(ARH residues 252-267).
References: UniProt: Q5SW96
#3: Protein/peptide peptide sequence AAF


Mass: 307.345 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in human. Probably represents the residues EAF(257-259) of degraded ARH peptide sequence in the crystal
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 8000, 100mM HEPES pH 7.5, 4mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.6→49.45 Å / Num. all: 35656 / Num. obs: 35656 / Observed criterion σ(I): 10 / Redundancy: 5.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5081

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Phasing

Phasing MRRfactor: 0.461 / Cor.coef. Fo:Fc: 0.467 / Cor.coef. Io to Ic: 0.13
Highest resolutionLowest resolution
Rotation3 Å99.015 Å
Translation3 Å99.015 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+42 / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.346 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1781 5 %RANDOM
Rwork0.215 ---
all0.216 35493 --
obs0.216 35493 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.967 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-1.28 Å2
2--1.82 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 0 144 2134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222028
X-RAY DIFFRACTIONr_bond_other_d0.0020.021828
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9492753
X-RAY DIFFRACTIONr_angle_other_deg0.80434272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165249
X-RAY DIFFRACTIONr_chiral_restr0.0930.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022231
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02380
X-RAY DIFFRACTIONr_nbd_refined0.2160.2331
X-RAY DIFFRACTIONr_nbd_other0.2450.22007
X-RAY DIFFRACTIONr_nbtor_other0.0840.21210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7530.23
X-RAY DIFFRACTIONr_mcbond_it1.0721.51260
X-RAY DIFFRACTIONr_mcangle_it1.96522041
X-RAY DIFFRACTIONr_scbond_it2.7983768
X-RAY DIFFRACTIONr_scangle_it4.5764.5712
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.336 119
Rwork0.292 2356
obs-2475

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