[English] 日本語
Yorodumi
- PDB-1bw8: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -

+
Open data


ID or keywords:

Loading...

-
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 / AP-2 adaptor complex ...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 / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / positive regulation of synaptic vesicle endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / diterpenoid metabolic process / ovulation cycle / epidermal growth factor receptor activity / positive regulation of mucus secretion / low-density lipoprotein particle receptor binding / epidermal growth factor binding / response to UV-A / tongue development / midgut development / hydrogen peroxide metabolic process / ERBB2-EGFR signaling pathway / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / digestive tract morphogenesis / morphogenesis of an epithelial fold / response to lipid / intracellular vesicle / protein tyrosine kinase activator activity / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / response to cobalamin / eyelid development in camera-type eye / positive regulation of receptor internalization / cerebral cortex cell migration / Trafficking of GluR2-containing AMPA receptors / regulation of JNK cascade / endocytic vesicle / negative regulation of mitotic cell cycle / synaptic vesicle endocytosis / hair follicle development / epidermis development / embryonic placenta development / positive regulation of bone resorption / negative regulation of protein localization to plasma membrane / positive regulation of G1/S transition of mitotic cell cycle / salivary gland morphogenesis / positive regulation of phosphorylation / regulation of peptidyl-tyrosine phosphorylation / clathrin-coated pit / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / cellular response to cadmium ion / transmembrane receptor protein tyrosine kinase activity / positive regulation of DNA repair / regulation of ERK1 and ERK2 cascade / cellular response to dexamethasone stimulus / receptor-mediated endocytosis / neurogenesis / positive regulation of synaptic transmission, glutamatergic / positive regulation of epithelial cell proliferation / liver development / neuron projection morphogenesis / basal plasma membrane / epithelial cell proliferation / positive regulation of superoxide anion generation / positive regulation of DNA replication / cellular response to estradiol stimulus / synaptic membrane / astrocyte activation / liver regeneration / cellular response to amino acid stimulus / positive regulation of protein localization to plasma membrane / intracellular protein transport / lung development / positive regulation of smooth muscle cell proliferation / epidermal growth factor receptor signaling pathway / cell morphogenesis / negative regulation of protein catabolic process / cellular response to growth factor stimulus / kinase binding / terminal bouton / receptor internalization / response to organic cyclic compound / positive regulation of miRNA transcription / cell-cell adhesion / ruffle membrane / cellular response to mechanical stimulus
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. / : / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit ...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. / : / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / 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
Epidermal growth factor receptor / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more