[English] 日本語
Yorodumi
- PDB-4ikn: Crystal structure of adaptor protein complex 3 (AP-3) mu3A subuni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ikn
TitleCrystal structure of adaptor protein complex 3 (AP-3) mu3A subunit C-terminal domain, in complex with a sorting peptide from TGN38
Components
  • AP-3 complex subunit mu-1
  • Trans-Golgi network integral membrane protein TGN38
KeywordsPROTEIN TRANSPORT / immunoglobulin-like beta-sandwich / signal recognition / cytosolic tail of transmembrane proteins / adaptor protein
Function / homology
Function and homology information


anterograde synaptic vesicle transport / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Retrograde transport at the Trans-Golgi-Network / small GTPase binding => GO:0031267 / clathrin adaptor complex / Golgi to endosome transport / Golgi Associated Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis ...anterograde synaptic vesicle transport / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Retrograde transport at the Trans-Golgi-Network / small GTPase binding => GO:0031267 / clathrin adaptor complex / Golgi to endosome transport / Golgi Associated Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / trans-Golgi network transport vesicle / anterograde axonal transport / vesicle-mediated transport / axon cytoplasm / intracellular protein transport / cytoplasmic vesicle membrane / trans-Golgi network / endocytosis / cytoplasmic vesicle / endosome / intracellular membrane-bounded organelle / Golgi apparatus / membrane / cytosol
Similarity search - Function
Keratinocyte-associated gene product / Mu homology domain, subdomain B / 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 ...Keratinocyte-associated gene product / Mu homology domain, subdomain B / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Trans-Golgi network integral membrane protein TGN38 / AP-3 complex subunit mu-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.851 Å
AuthorsMardones, G.A. / Kloer, D.P. / Burgos, P.V. / Bonifacino, J.S. / Hurley, J.H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural basis for the recognition of tyrosine-based sorting signals by the mu 3A subunit of the AP-3 adaptor complex.
Authors: Mardones, G.A. / Burgos, P.V. / Lin, Y. / Kloer, D.P. / Magadan, J.G. / Hurley, J.H. / Bonifacino, J.S.
History
DepositionDec 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Sep 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AP-3 complex subunit mu-1
B: Trans-Golgi network integral membrane protein TGN38


Theoretical massNumber of molelcules
Total (without water)30,1222
Polymers30,1222
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-5 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.454, 44.301, 86.013
Angle α, β, γ (deg.)90.000, 127.840, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein AP-3 complex subunit mu-1 / AP-3 adapter complex mu3A subunit / Adapter-related protein complex 3 mu-1 subunit / Clathrin ...AP-3 adapter complex mu3A subunit / Adapter-related protein complex 3 mu-1 subunit / Clathrin assembly protein assembly protein complex 1 medium chain homolog 1 / Clathrin coat assembly protein AP47 homolog 1 / Clathrin coat-associated protein AP47 homolog 1 / Golgi adaptor AP-1 47 kDa protein homolog 1 / HA1 47 kDa subunit homolog 1 / Mu-adaptin 3A / Mu3A-adaptin / P47A


Mass: 29339.959 Da / Num. of mol.: 1 / Fragment: C-terminus, residues 165-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap3m1 / Plasmid: pHis-Parallel-1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: P53676
#2: Protein/peptide Trans-Golgi network integral membrane protein TGN38


Mass: 781.835 Da / Num. of mol.: 1 / Fragment: C-terminus, residues 348-353 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P19814
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate, 1.75 M sodium formate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→67.93 Å / Num. obs: 28591 / % possible obs: 97.6 %
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2497 / Rsym value: 0.323 / % possible all: 85.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 26.14 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.19 Å
Translation2.5 Å45.19 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BXX

1bxx


Resolution: 1.851→67.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2501 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8401 / SU B: 2.77 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1244 / SU Rfree: 0.1274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1463 5.1 %RANDOM
Rwork0.1914 ---
obs0.1937 28570 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.07 Å2 / Biso mean: 25.5004 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20.68 Å2
2---0.5 Å2-0 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.851→67.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 0 136 2161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222069
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.9682797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3075250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59824.04589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66915370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5021512
X-RAY DIFFRACTIONr_chiral_restr0.1710.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211538
X-RAY DIFFRACTIONr_mcbond_it1.4361.51267
X-RAY DIFFRACTIONr_mcangle_it2.68422067
X-RAY DIFFRACTIONr_scbond_it4.0313802
X-RAY DIFFRACTIONr_scangle_it6.7664.5730
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 76 -
Rwork0.253 1700 -
all-1776 -
obs--83.3 %

+
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://pdbjlvh1.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