[English] 日本語
Yorodumi
- PDB-5fpi: Mu2 adaptin subunit of the AP2 adaptor (C-terminal domain) comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fpi
TitleMu2 adaptin subunit of the AP2 adaptor (C-terminal domain) complexed with Integrin alpha4 internalisation peptide QYKSILQE
Components
  • AP-2 COMPLEX SUBUNIT MU
  • INTEGRIN ALPHA-4 SUBUNIT
KeywordsENDOCYTOSIS / CLATHRIN ADAPTOR
Function / homology
Function and homology information


clathrin-dependent extracellular exosome endocytosis / negative regulation of protein homodimerization activity / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / diapedesis / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / Gap junction degradation / Formation of annular gap junctions ...clathrin-dependent extracellular exosome endocytosis / negative regulation of protein homodimerization activity / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / diapedesis / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / 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 / positive regulation of leukocyte tethering or rolling / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / axonogenesis involved in innervation / Recycling pathway of L1 / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / protein antigen binding / leukocyte tethering or rolling / vesicle budding from membrane / clathrin-dependent endocytosis / RUNX3 Regulates Immune Response and Cell Migration / signal sequence binding / integrin complex / positive regulation of vascular endothelial cell proliferation / heterotypic cell-cell adhesion / neuron projection extension / negative regulation of vasoconstriction / low-density lipoprotein particle receptor binding / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering / cellular response to cytokine stimulus / endodermal cell differentiation / Trafficking of GluR2-containing AMPA receptors / fibronectin binding / positive regulation of receptor internalization / synaptic vesicle endocytosis / positive regulation of endothelial cell apoptotic process / Integrin cell surface interactions / negative regulation of protein localization to plasma membrane / positive regulation of T cell migration / coreceptor activity / cell adhesion molecule binding / clathrin-coated pit / substrate adhesion-dependent cell spreading / B cell differentiation / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / intracellular protein transport / terminal bouton / cell-cell adhesion / receptor internalization / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / disordered domain specific binding / integrin binding / synaptic vesicle / growth cone / protein-containing complex assembly / cytoplasmic vesicle / Potential therapeutics for SARS / transmembrane transporter binding / postsynapse / external side of plasma membrane / focal adhesion / neuronal cell body / synapse / lipid binding / glutamatergic synapse / cell surface / extracellular exosome / metal ion binding / membrane / 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 / Clathrin adaptor complex small chain ...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 / Clathrin adaptor complex small chain / Adaptor complexes medium subunit family / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / : / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Integrin alpha-4 / AP-2 complex subunit mu / Integrin alpha-4 subunit
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsOwen, D.J. / Evans, P.R. / Ivaska, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Selective Integrin Endocytosis is Driven by Alpha Chain:Ap2 Interactions
Authors: De Franceschi, N. / Arjonen, A. / Elkhatib, N. / Denessiouk, K. / Wrobel, A.G. / Wilson, T.A. / Pouwels, J. / Montagnac, G. / Owen, D.J. / Ivaska, J.
History
DepositionNov 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AP-2 COMPLEX SUBUNIT MU
B: INTEGRIN ALPHA-4 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)52,0532
Polymers52,0532
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-3.6 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.650, 125.650, 74.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein AP-2 COMPLEX SUBUNIT MU / AP-2 MU CHAIN / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT MU / ADAPTOR-RELATED PROTEIN COMPLEX 2 SUBUNIT ...AP-2 MU CHAIN / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT MU / ADAPTOR-RELATED PROTEIN COMPLEX 2 SUBUNIT MU / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MU MEDIUM CHAIN / CLATHRIN COAT ASSEMBLY PROTEIN AP50 / CLATHRIN COAT-ASSOCIATED PROTEIN AP50 / HA2 50 KDA SUBUNIT / MU2- ADAPTIN / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN


Mass: 51044.113 Da / Num. of mol.: 1 / Fragment: INTERNALISATION SIGNAL BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PLASMID / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P84092
#2: Protein/peptide INTEGRIN ALPHA-4 SUBUNIT


Mass: 1009.134 Da / Num. of mol.: 1 / Fragment: INTERNALISATION SIGNAL PEPTIDE, RESIDUES 150-157 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q8IU71, UniProt: P13612*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.26 Å3/Da / Density % sol: 62.24 % / Description: NONE
Crystal growpH: 6.5
Details: 2.2M NACL, 0.4M NAKPHOSPHATE, 20% V/V GLYCEROL, 0.1M MES PH6.5, 5MM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54182
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 2.75→74 Å / Num. obs: 17034 / % possible obs: 97.2 % / Observed criterion σ(I): -9.9 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.7 / % possible all: 80.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BXX

1bxx


Resolution: 2.77→108.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.982 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 893 5.3 %RANDOM
Rwork0.17443 ---
obs0.17697 16115 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.116 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.23 Å20 Å2
2---0.45 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.77→108.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 0 45 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192171
X-RAY DIFFRACTIONr_bond_other_d0.0020.022195
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9812918
X-RAY DIFFRACTIONr_angle_other_deg1.06135059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.415260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07222.72788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.60515427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8161519
X-RAY DIFFRACTIONr_chiral_restr0.1090.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212340
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02477
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4875.7371052
X-RAY DIFFRACTIONr_mcbond_other5.4865.7361051
X-RAY DIFFRACTIONr_mcangle_it7.8688.5651308
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.1796.491119
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.773→2.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 54 -
Rwork0.321 1085 -
obs--90.54 %

+
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