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- PDB-3l81: Crystal structure of adaptor protein complex 4 (AP-4) mu4 subunit... -

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Basic information

Entry
Database: PDB / ID: 3l81
TitleCrystal structure of adaptor protein complex 4 (AP-4) mu4 subunit C-terminal domain, in complex with a sorting peptide from the amyloid precursor protein (APP)
Components
  • AP-4 complex subunit mu-1
  • Amyloid beta A4 protein
KeywordsTRANSPORT PROTEIN / immunoglobulin-like beta-sandwich / Coated pit / Golgi apparatus / Membrane / Phosphoprotein / Protein transport / Transport / Alzheimer disease / Amyloid / Amyloidosis
Function / homology
Function and homology information


AP-4 adaptor complex / protein localization to basolateral plasma membrane / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Golgi to lysosome 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 / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Golgi to lysosome transport / Golgi to endosome transport / protein targeting to lysosome / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / regulation of synapse structure or activity / hippocampal neuron apoptotic process / 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 / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / PTB domain binding / positive regulation of amyloid fibril formation / Golgi-associated vesicle / astrocyte projection / Lysosome Vesicle Biogenesis / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / transition metal ion binding / The NLRP3 inflammasome / transmembrane protein transporter activity / regulation of multicellular organism growth / main axon / modulation of excitatory postsynaptic potential / intracellular copper ion homeostasis / ECM proteoglycans / response to insulin-like growth factor stimulus / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / autophagosome assembly / protein targeting / cellular response to manganese ion / positive regulation of chemokine production / Notch signaling pathway / vesicle-mediated transport / swimming behavior / neuron projection maintenance / extracellular matrix organization / clathrin-coated pit / astrocyte activation / axonogenesis / positive regulation of mitotic cell cycle / Mitochondrial protein degradation / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / platelet alpha granule lumen / response to interleukin-1 / regulation of neuron apoptotic process / cellular response to cAMP / cellular response to copper ion / positive regulation of glycolytic process / endosome lumen / positive regulation of long-term synaptic potentiation / trans-Golgi network membrane / central nervous system development / dendritic shaft / positive regulation of interleukin-1 beta production / protein serine/threonine kinase binding / learning / adult locomotory behavior / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / trans-Golgi network / locomotory behavior / microglial cell activation / cellular response to nerve growth factor stimulus / intracellular protein transport / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / visual learning / regulation of long-term neuronal synaptic plasticity / positive regulation of interleukin-6 production / recycling endosome / Golgi lumen / positive regulation of JNK cascade
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, heparin-binding / Amyloid A4 N-terminal heparin-binding / 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, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / 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 / MAD / Resolution: 1.6 Å
AuthorsMardones, G.A. / Rojas, A.L. / Burgos, P.V. / Dasilva, L.L.P. / Prabhu, Y. / Bonifacino, J.S. / Hurley, J.H.
CitationJournal: Dev.Cell / Year: 2010
Title: Sorting of the Alzheimer's disease amyloid precursor protein mediated by the AP-4 complex.
Authors: Burgos, P.V. / Mardones, G.A. / Rojas, A.L. / daSilva, L.L. / Prabhu, Y. / Hurley, J.H. / Bonifacino, J.S.
History
DepositionDec 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3525
Polymers34,0762
Non-polymers2763
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-4 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.672, 56.910, 60.664
Angle α, β, γ (deg.)90.000, 106.530, 90.000
Int Tables number4
Space group name H-MP1211
Detailsauthors state that the biological unit of the protein-peptide complex is better called monomer.

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Components

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


Mass: 33112.645 Da / Num. of mol.: 1 / Fragment: C-terminus, residues 160-453 / Mutation: C235S,C431S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP4M1, MUARP2 / Plasmid: pGST-Parallel-1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: O00189
#2: Protein/peptide Amyloid beta A4 protein / Alzheimer disease amyloid protein / ABPP / APPI / APP / PreA4 / Cerebral vascular amyloid peptide / ...Alzheimer disease amyloid protein / ABPP / APPI / APP / PreA4 / Cerebral vascular amyloid peptide / CVAP / 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 / Gamma-CTF(59) / Amyloid intracellular domain 59 / AICD-59 / AID(59) / Gamma-secretase C-terminal fragment 57 / Gamma-CTF(57) / Amyloid intracellular domain 57 / AICD-57 / AID(57) / Gamma-secretase C-terminal fragment 50 / Gamma-CTF(50) / Amyloid intracellular domain 50 / AICD-50 / AID(50) / C31


Mass: 963.063 Da / Num. of mol.: 1 / Fragment: C-terminus, residues 761-767 / Source method: obtained synthetically / References: UniProt: P05067
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2745.73
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, hanging drop710% PEG 3350, 10mM magnesium chloride, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
2952vapor diffusion, hanging drop715% PEG 6000, 3% trimethylamine N-oxide dihydrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.9794, 0.9796, 0.9719
SYNCHROTRONAPS 22-ID21
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDMar 20, 2009
MARMOSAIC 300 mm CCD2CCDMar 20, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.97191
411
ReflectionRedundancy: 7.1 % / Number: 157813 / Rmerge(I) obs: 0.076 / Χ2: 1.04 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 22201 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.25099.710.0551.0417.4
3.334.299.710.061.067.4
2.913.3310010.0691.057.7
2.652.9110010.0851.0367.6
2.462.6510010.1141.0717.6
2.312.4610010.1341.0237.5
2.22.3199.910.1951.0277.1
2.12.299.710.21.0096.9
2.022.197.710.2351.0256.2
1.952.0297.510.2891.0265.7
ReflectionResolution: 1.6→50 Å / Num. all: 39566 / Num. obs: 39268 / % possible obs: 97.3 % / Observed criterion σ(I): 1.48 / Redundancy: 4.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97944.25-9.92
3 wavelength120.97960.26-8.7
3 wavelength130.97193.77-4.47
Phasing dmFOM : 0.66 / FOM acentric: 0.65 / FOM centric: 0.72 / Reflection: 20985 / Reflection acentric: 20053 / Reflection centric: 932
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.6-44.8670.950.950.921011876135
3.5-5.60.950.950.9530072803204
2.8-3.50.870.870.8237413570171
2.4-2.80.720.720.6737033558145
2.1-2.40.490.50.4862076007200
2-2.10.290.290.33316323977

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.6→41.67 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.283 / WRfactor Rwork: 0.239 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.802 / SU B: 2.211 / SU ML: 0.077 / SU R Cruickshank DPI: 0.094 / SU Rfree: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1972 5 %RANDOM
Rwork0.207 ---
obs0.209 39268 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 27.823 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 18 153 2209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222098
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9942830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6325253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23322.63295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4931521
X-RAY DIFFRACTIONr_chiral_restr0.1250.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021580
X-RAY DIFFRACTIONr_nbd_refined0.2120.2794
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.215
X-RAY DIFFRACTIONr_mcbond_it1.4741.51316
X-RAY DIFFRACTIONr_mcangle_it2.3622062
X-RAY DIFFRACTIONr_scbond_it3.0873869
X-RAY DIFFRACTIONr_scangle_it4.8174.5768
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 120 -
Rwork0.333 2302 -
all-2422 -
obs--83.2 %

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