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- PDB-4mdr: Crystal structure of adaptor protein complex 4 (AP-4) mu4 subunit... -

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Basic information

Entry
Database: PDB / ID: 4mdr
TitleCrystal structure of adaptor protein complex 4 (AP-4) mu4 subunit C-terminal domain D190A mutant, in complex with a sorting peptide from the amyloid precursor protein (APP)
Components
  • AP-4 complex subunit mu-1
  • Amyloid beta A4 protein
KeywordsPROTEIN TRANSPORT/PROTEIN BINDING / immunoglobulin-like beta-sandwich / adaptor protein complex / Golgi apparatus / sorting signal recognition / Alzheimer's disease / amyloid precursor protein / PROTEIN TRANSPORT-PROTEIN BINDING complex
Function / homology
Function and homology information


AP-4 adaptor complex / protein localization to basolateral plasma membrane / Golgi to lysosome transport / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Golgi to endosome transport / protein targeting to lysosome / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus ...AP-4 adaptor complex / protein localization to basolateral plasma membrane / Golgi to lysosome transport / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Golgi to endosome transport / protein targeting to lysosome / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Lysosome Vesicle Biogenesis / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / transition metal ion binding / main axon / intracellular copper ion homeostasis / regulation of multicellular organism growth / protein transmembrane transporter activity / autophagosome assembly / ECM proteoglycans / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / protein targeting / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / vesicle-mediated transport / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / axonogenesis / response to interleukin-1 / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / endosome lumen / positive regulation of interleukin-1 beta production / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / adult locomotory behavior / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / intracellular protein transport / serine-type endopeptidase inhibitor activity / trans-Golgi network / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / cellular response to nerve growth factor stimulus / synapse organization / recycling endosome / visual learning / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis
Similarity search - Function
Mu homology domain, subdomain B / 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, subdomain B / 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 / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
AP-4 complex subunit mu-1 / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRoss, B.H. / Lin, Y. / Corales, E.A. / Burgos, P.V. / Mardones, G.A.
CitationJournal: Plos One / Year: 2014
Title: Structural and Functional Characterization of Cargo-Binding Sites on the mu 4-Subunit of Adaptor Protein Complex 4.
Authors: Ross, B.H. / Lin, Y. / Corales, E.A. / Burgos, P.V. / Mardones, G.A.
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-4 complex subunit mu-1
B: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)34,3722
Polymers34,3722
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-3 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.507, 56.729, 60.180
Angle α, β, γ (deg.)90.000, 106.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AP-4 complex subunit mu-1 / AP-4 adapter complex mu subunit / Adapter-related protein complex 4 mu-1 subunit / Mu subunit of AP- ...AP-4 adapter complex mu subunit / Adapter-related protein complex 4 mu-1 subunit / Mu subunit of AP-4 / Mu-adaptin-related protein 2 / mu-ARP2 / Mu4-adaptin / mu4


Mass: 33068.637 Da / Num. of mol.: 1 / Fragment: C-terminus, residues 160-453 / Mutation: D190A,C235S,C431S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP4M1, MUARP2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00189
#2: Protein/peptide Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II / N-APP / Soluble APP-alpha / S-APP-alpha / Soluble APP-beta / S-APP-beta / C99 / Beta-amyloid protein 42 / Beta-APP42 / Beta-amyloid protein 40 / Beta-APP40 / C83 / P3(42) / P3(40) / C80 / Gamma-secretase C-terminal fragment 59 / Amyloid intracellular domain 59 / AICD-59 / AID(59) / Gamma-CTF(59) / Gamma-secretase C-terminal fragment 57 / Amyloid intracellular domain 57 / AICD-57 / AID(57) / Gamma-CTF(57) / Gamma-secretase C-terminal fragment 50 / Amyloid intracellular domain 50 / AICD-50 / AID(50) / Gamma-CTF(50) / C31


Mass: 1303.394 Da / Num. of mol.: 1 / Fragment: C-terminus, residues 761-767 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 6000, 3% trimethylamine N-oxide dihydrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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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: Nov 1, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 25791 / Num. obs: 25043 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.8
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 75.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0088refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3L81

3l81


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.586 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 1283 5.1 %RANDOM
Rwork0.2135 ---
obs0.216 24999 97.42 %-
all-25661 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.49 Å2 / Biso mean: 36.567 Å2 / Biso min: 17.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å2-0 Å21.38 Å2
2--0.41 Å2-0 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 0 97 2098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222043
X-RAY DIFFRACTIONr_angle_refined_deg2.0461.9862759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6365248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2122.58193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22415359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.1381521
X-RAY DIFFRACTIONr_chiral_restr0.1430.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211537
X-RAY DIFFRACTIONr_mcbond_it1.5771.51254
X-RAY DIFFRACTIONr_mcangle_it2.82322019
X-RAY DIFFRACTIONr_scbond_it4.0193789
X-RAY DIFFRACTIONr_scangle_it6.7314.5740
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 77 -
Rwork0.27 1354 -
all-1431 -
obs--75.83 %

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