[English] 日本語
Yorodumi
- PDB-5c7z: AP2 Mu2 adaptin C-terminal domain complexed with integrin alpha-4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c7z
TitleAP2 Mu2 adaptin C-terminal domain complexed with integrin alpha-4 peptide
Components
  • AP-2 complex subunit mu
  • Integrin alpha-4
KeywordsTRANSPORT PROTEIN / clathrin adaptor
Function / homology
Function and homology information


clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / negative regulation of protein homodimerization activity / cell-cell adhesion in response to extracellular stimulus / diapedesis / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / Gap junction degradation ...clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / negative regulation of protein homodimerization activity / cell-cell adhesion in response to extracellular stimulus / diapedesis / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / 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 / protein antigen binding / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / leukocyte tethering or rolling / vesicle budding from membrane / clathrin-dependent endocytosis / RUNX3 Regulates Immune Response and Cell Migration / signal sequence binding / positive regulation of endothelial cell apoptotic process / negative regulation of protein localization to plasma membrane / heterotypic cell-cell adhesion / integrin complex / low-density lipoprotein particle receptor binding / positive regulation of vascular endothelial cell proliferation / cell adhesion mediated by integrin / neuron projection extension / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / receptor clustering / endodermal cell differentiation / cellular response to cytokine stimulus / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / fibronectin binding / positive regulation of T cell migration / Integrin cell surface interactions / coreceptor activity / clathrin-coated pit / cell adhesion molecule binding / substrate adhesion-dependent cell spreading / cell-matrix adhesion / B cell differentiation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / intracellular protein transport / terminal bouton / receptor internalization / cell-cell adhesion / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / disordered domain specific binding / integrin binding / growth cone / cytoplasmic vesicle / postsynapse / protein-containing complex assembly / Potential therapeutics for SARS / transmembrane transporter binding / external side of plasma membrane / focal adhesion / neuronal cell body / glutamatergic synapse / lipid binding / synapse / cell surface / extracellular exosome / membrane / metal ion 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. / Adaptor complexes medium subunit family / 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. / 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. / : / Integrin alpha Ig-like domain 3 / Longin-like domain superfamily / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / 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
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. / Wilson, T.A.
CitationJournal: To Be Published
Title: AP2 Mu2 adaptin C-terminal domain complexed with integrin alpha-4 peptide
Authors: Owen, D.J. / Evans, P.R. / Wilson, T.A.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AP-2 complex subunit mu
B: Integrin alpha-4


Theoretical massNumber of molelcules
Total (without water)33,9972
Polymers33,9972
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-4 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.650, 125.650, 74.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / Mu2-adaptin / Plasma membrane adaptor AP-2 50 kDa protein


Mass: 32987.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2m1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84092
#2: Protein/peptide Integrin alpha-4 / CD49 antigen-like family member D / Integrin alpha-IV / VLA-4 subunit alpha


Mass: 1009.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13612
#3: Water ChemComp-HOH / water / 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: 5.6 Å3/Da / Density % sol: 77.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 2.2M NaCl, 0.4M Na/K phosphate, 10MM DTT 0.1M MES pH 7.1, 15% glycerol, molar ratio of peptide to protein 3:1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54182 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2014
RadiationMonochromator: MIRRORS / Protocol: 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. all: 17034 / Num. obs: 17034 / % possible obs: 97.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 14.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.7 / % possible all: 80.8

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0123refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bxx

1bxx


Resolution: 2.77→74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / 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
Rfree0.2243 893 5.3 %RANDOM
Rwork0.1743 16115 --
obs0.1768 17008 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 max: 139.18 Å2 / Biso mean: 61.7828 Å2 / Biso min: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.22 Å20 Å2
2---0.44 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.77→74 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_d00.022195
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9812918
X-RAY DIFFRACTIONr_angle_other_deg3.54735059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4095260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06622.72788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.60715427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8171519
X-RAY DIFFRACTIONr_chiral_restr0.1090.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212340
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02477
X-RAY DIFFRACTIONr_mcbond_it5.4885.7371052
X-RAY DIFFRACTIONr_mcbond_other5.4865.7361051
X-RAY DIFFRACTIONr_mcangle_it7.8688.5651308
LS refinement shellResolution: 2.773→2.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 54 -
Rwork0.32 1085 -
all-1139 -
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