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- PDB-1bw8: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1bw8
TitleMU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH EGFR INTERNALIZATION PEPTIDE FYRALM
Components
  • PROTEIN (INTERNALIZATION SIGNAL FROM EGFR)
  • PROTEIN (MU2 ADAPTIN SUBUNIT)
KeywordsPEPTIDE BINDING PROTEIN / ENDOCYTOSIS / ADAPTOR / PEPTIDE COMPLEX
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of vesicle size ...Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of vesicle size / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin-cargo adaptor activity / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / low-density lipoprotein particle receptor binding / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / negative regulation of protein localization to plasma membrane / synaptic vesicle endocytosis / clathrin-coated pit / transmembrane receptor protein tyrosine kinase activity / cell periphery / intracellular protein transport / receptor protein-tyrosine kinase / receptor internalization / disordered domain specific binding / terminal bouton / synaptic vesicle / protein-containing complex assembly / cytoplasmic vesicle / transmembrane transporter binding / postsynapse / synapse / lipid binding / glutamatergic synapse / signal transduction / ATP binding / plasma membrane
Similarity search - Function
Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family ...Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
receptor protein-tyrosine kinase / AP-2 complex subunit mu
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.65 Å
AuthorsOwen, D.J. / Evans, P.R.
CitationJournal: Science / Year: 1998
Title: A structural explanation for the recognition of tyrosine-based endocytotic signals.
Authors: Owen, D.J. / Evans, P.R.
History
DepositionSep 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (MU2 ADAPTIN SUBUNIT)
P: PROTEIN (INTERNALIZATION SIGNAL FROM EGFR)


Theoretical massNumber of molelcules
Total (without water)37,5082
Polymers37,5082
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.680, 125.680, 73.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein PROTEIN (MU2 ADAPTIN SUBUNIT) / AP50


Mass: 36706.617 Da / Num. of mol.: 1 / Fragment: INTERNALIZATION SIGNAL BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PMW172H6 / Species (production host): Escherichia coli / Gene (production host): AP50 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P84092
#2: Protein/peptide PROTEIN (INTERNALIZATION SIGNAL FROM EGFR)


Mass: 800.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED / References: UniProt: A8IP97*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 4.45 Å3/Da / Density % sol: 72.33 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.1
Details: HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.1 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.2 M1reservoirNaCl
20.4 Msodium potassium phosphate1reservoir
310 mMdithiothreitol1reservoir
415 %(v/v)glycerol1reservoir
50.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 15, 1998 / Details: MIRROR
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.65→35 Å / Num. obs: 119506 / % possible obs: 99 % / Observed criterion σ(I): 4 / Redundancy: 9.2 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 21.3
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.882 / % possible all: 97
Reflection
*PLUS
Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
SHARPphasing
SOLOMONphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.65→35 Å / SU B: 9.2 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.35 / ESU R Free: 0.29
RfactorNum. reflection% reflectionSelection details
Rfree0.296 842 4.4 %RANDOM
Rwork0.25 ---
obs0.272 19296 99.6 %-
Displacement parametersBiso mean: 60 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.63 Å20 Å2
2--1.25 Å20 Å2
3---1.111 Å2
Refinement stepCycle: LAST / Resolution: 2.65→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 51 2143
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.62
X-RAY DIFFRACTIONp_mcangle_it2.84
X-RAY DIFFRACTIONp_scbond_it3.44
X-RAY DIFFRACTIONp_scangle_it4.85
X-RAY DIFFRACTIONp_plane_restr0.00260.01
X-RAY DIFFRACTIONp_chiral_restr0.1190.15
X-RAY DIFFRACTIONp_singtor_nbd0.1980.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1850.3
X-RAY DIFFRACTIONp_planar_tor1.77
X-RAY DIFFRACTIONp_staggered_tor18.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 60 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_mcbond_it21.6
X-RAY DIFFRACTIONp_scbond_it43.4
X-RAY DIFFRACTIONp_mcangle_it42.8
X-RAY DIFFRACTIONp_scangle_it54.8

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