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- PDB-7mrn: Mouse CNTN5 APP complex -

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Basic information

Entry
Database: PDB / ID: 7mrn
TitleMouse CNTN5 APP complex
Components
  • Contactin-5
  • N-APP
KeywordsCELL ADHESION / Ig superfamily / amyloid precursor protein
Function / homology
Function and homology information


Formyl peptide receptors bind formyl peptides and many other ligands / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of presynapse assembly / Advanced glycosylation endproduct receptor signaling / cytosolic mRNA polyadenylation / ECM proteoglycans / synaptic assembly at neuromuscular junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / TRAF6 mediated NF-kB activation / Lysosome Vesicle Biogenesis ...Formyl peptide receptors bind formyl peptides and many other ligands / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of presynapse assembly / Advanced glycosylation endproduct receptor signaling / cytosolic mRNA polyadenylation / ECM proteoglycans / synaptic assembly at neuromuscular junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / TRAF6 mediated NF-kB activation / Lysosome Vesicle Biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / smooth endoplasmic reticulum calcium ion homeostasis / TAK1-dependent IKK and NF-kappa-B activation / G alpha (q) signalling events / presynapse assembly / G alpha (i) signalling events / Platelet degranulation / ciliary rootlet / Mitochondrial protein degradation / COPII-coated ER to Golgi transport vesicle / suckling behavior / collateral sprouting in absence of injury / axo-dendritic transport / regulation of synapse structure or activity / axon midline choice point recognition / central nervous system neuron differentiation / presynaptic active zone / mating behavior / Golgi-associated vesicle / neuromuscular process controlling balance / neuron remodeling / negative regulation of neuron differentiation / spindle midzone / intracellular vesicle / forebrain development / dendrite development / smooth endoplasmic reticulum / signaling receptor activator activity / transition metal ion binding / intracellular copper ion homeostasis / regulation of multicellular organism growth / positive regulation of G2/M transition of mitotic cell cycle / cholesterol metabolic process / side of membrane / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / axonogenesis / adult locomotory behavior / neuromuscular junction / locomotory behavior / serine-type endopeptidase inhibitor activity / sensory perception of sound / neuron cellular homeostasis / recycling endosome / GABA-ergic synapse / visual learning / G2/M transition of mitotic cell cycle / cognition / memory / long-term synaptic potentiation / endocytosis / neuron differentiation / neuron projection development / apical part of cell / synaptic vesicle / cell-cell junction / mitotic cell cycle / heparin binding / regulation of translation / presynaptic membrane / growth cone / regulation of gene expression / response to oxidative stress / cytoplasmic vesicle / neuron apoptotic process / perikaryon / gene expression / early endosome / receptor complex / cell adhesion / neuron projection / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / axon / protein kinase binding / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
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. / 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 ...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. / 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 / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein / Contactin-5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBouyain, S. / Karuppan, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R15NS108371-01 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Members of the vertebrate contactin and amyloid precursor protein families interact through a conserved interface.
Authors: Karuppan, S.J. / Vogt, A. / Fischer, Z. / Ladutska, A. / Swiastyn, J. / McGraw, H.F. / Bouyain, S.
History
DepositionMay 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contactin-5
C: N-APP
B: Contactin-5
D: N-APP


Theoretical massNumber of molelcules
Total (without water)106,2524
Polymers106,2524
Non-polymers00
Water00
1
A: Contactin-5
C: N-APP


Theoretical massNumber of molelcules
Total (without water)53,1262
Polymers53,1262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Contactin-5
D: N-APP


Theoretical massNumber of molelcules
Total (without water)53,1262
Polymers53,1262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.010, 137.010, 385.372
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Contactin-5 / Neural recognition molecule NB-2


Mass: 33395.023 Da / Num. of mol.: 2 / Fragment: FN1-FN3 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn5 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P68500
#2: Protein N-APP


Mass: 19730.727 Da / Num. of mol.: 2 / Fragment: E1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: App / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: P12023
Has protein modificationY

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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: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Na-citrate pH 5.5, 10% Isopropanol, 25% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→74.79 Å / Num. obs: 17993 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 114.08 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.073 / Rrim(I) all: 0.229 / Net I/σ(I): 8.8
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.323 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4233 / CC1/2: 0.728 / Rpim(I) all: 0.444 / Rrim(I) all: 1.396 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KTM, 5E52

3ktm

5e52


Resolution: 3.5→64.64 Å / SU ML: 0.4177 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.6588
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2909 1799 10 %
Rwork0.2433 16183 -
obs0.248 17982 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 136.01 Å2
Refinement stepCycle: LAST / Resolution: 3.5→64.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 0 0 6326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196477
X-RAY DIFFRACTIONf_angle_d0.4888806
X-RAY DIFFRACTIONf_chiral_restr0.0435988
X-RAY DIFFRACTIONf_plane_restr0.00351126
X-RAY DIFFRACTIONf_dihedral_angle_d10.46452336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.32631370.30621234X-RAY DIFFRACTION100
3.59-3.70.39541350.27621219X-RAY DIFFRACTION100
3.7-3.820.34821360.27861222X-RAY DIFFRACTION99.93
3.82-3.960.32731370.26911230X-RAY DIFFRACTION100
3.96-4.110.30651350.26461219X-RAY DIFFRACTION100
4.12-4.30.26011390.22631243X-RAY DIFFRACTION100
4.3-4.530.2571360.2121229X-RAY DIFFRACTION99.93
4.53-4.810.25091380.20451241X-RAY DIFFRACTION100
4.81-5.180.2361380.18621242X-RAY DIFFRACTION100
5.19-5.710.23641380.19911241X-RAY DIFFRACTION100
5.71-6.530.29511400.24751263X-RAY DIFFRACTION100
6.53-8.220.3331410.23931264X-RAY DIFFRACTION100
8.23-64.640.29631490.27871336X-RAY DIFFRACTION99.46
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.350301881480.8514445772020.4052676099069.09118470329-2.377973488533.79246066176-0.190941886816-0.287295519596-0.09866444569610.06350362193950.4550415246151.119109820850.00417251155433-0.222852701701-0.1816185517190.760029523680.05577380790860.02769100020440.6042416031190.09089404507110.78856443181-26.988607102363.9859677867-47.2864674118
21.79191031633-2.040109786020.3314412157077.934091174253.763681894084.450374654580.3802811076170.2389263646650.244988351881-0.315122370517-0.2927835811740.185069677475-0.3822464594610.138949098647-0.1002018877880.7981706341260.03977711693542.62322109086E-50.4906267373670.1118601445920.700251917697-8.5313222375935.0918705138-53.8170290307
32.266842163560.228258813155-2.84937811547-0.779197111492-0.432031881513.32597403627-0.3123325837360.097590760364-0.536427722048-0.169822600680.422560776904-0.1513206690661.442993757260.357905154144-0.09171571515971.137843125360.1551127961630.06226221578520.758202647277-0.007314141027480.821816204919-4.2712355721225.0469248987-60.7643204887
49.57856653256-2.12888482137-1.363787188139.06300327937-1.378174424734.154317347840.2581489477660.582324343083-0.172157808468-0.352703490587-0.2927486642760.603621944016-0.07981731111480.329767386881-0.05408831370221.106003704630.434967239694-0.1391535007620.815359606384-0.1447943624070.555643024487.1787152878625.832606209-92.3205372876
51.20962671962-2.316964242491.793114812036.531899177431.907941765852.07326612149-2.907375609111.41094378939-4.29574714558-0.984063392094-2.49477964972-2.89245023582-0.765167307392.952118340060.3326171414781.398775936560.1049556898550.6860730015391.65448189178-0.896901126654.7877065193724.067132864319.8320740066-45.2551388044
60.756036325247-1.460545372980.6630593680033.561582042850.09052244987084.705797124830.656300673245-1.826500962031.82751457447-0.627738879642.333652277-4.683005550681.277474554212.58265064962-1.572373169580.8899204777210.272768091914-0.02214015747632.32164900577-0.7315245250962.8652878602922.79690704730.1204918949-43.7554767101
77.468404925280.07567067985483.72940398755.47459385521-2.323840715783.87431526575-0.421323267986-0.962813837807-0.784321634745-0.7588191892760.8766075130320.203435504152.03943368938-0.29512187122-0.5406891727732.124194120910.334870563626-0.2574501459671.10717872430.06246624611611.4708317823318.231721220819.1324267471-38.0358642753
83.141708372960.623798531684-2.846455042153.245289417143.295670744238.02833478974-1.15394173670.0969566664897-0.332552751206-2.1175379020.1823677551650.802846615689-0.1608215447710.220459470271.152494442981.330769478850.082433419737-0.01037650556770.8418446914790.1449185444950.984721032215-1.3086760445525.4596095734-46.0878118205
93.192293575213.15475017584-1.771340584794.374228598521.70761035066.827476135910.947972040067-0.680300616938-0.1891223244031.41572972406-0.5098581075890.1181825785490.3398325459210.172098171641-0.4938912492751.06230945345-0.061633162646-0.09472195406330.5916059849220.1520679790860.732282626492-0.59950973104430.8239743106-35.5765530341
108.76966122854-5.901720557020.4551710888816.636477708711.746387250256.94999436791-0.141816478776-0.3448408597990.0273008425696-0.3536032183810.471892905852-0.2269016854640.4154850433321.65092624736-0.1794990809591.564358364910.324710698293-0.1434221098431.426513908850.05277492724640.72107452938110.315054454527.0102964332-13.4407763005
116.1991486380.740718561559-2.515586647750.6985419133831.856829709731.90427627569-0.184088725555-0.8258085840540.2748037586910.3715991255460.3030280631920.01511041666390.689828385891-0.0557190387578-0.05440473810721.294869575730.0175279687318-0.1502432465221.072047322020.6200736040971.21168918184-19.671773718634.5519861879-11.9968218361
122.08152845914-0.221266287251-3.27916532788-1.265487051730.7401636931873.81982473388-0.0228792309901-0.2272339837470.070238017347-0.2256417593340.318731157330.121118570690.622697991609-0.555274541429-0.2374731044591.50175397749-0.0933036428086-0.1795904403051.648406047810.7409933833741.36072121352-32.883141014633.9759612273-11.1417590181
139.099465483531.36451820717-4.632971189862.39804205611.896280929544.40812049195-0.01454499905430.2492871164092.240129915470.1924370464210.739918431842-0.349818718838-0.560218913095-1.14131345412-0.746630762321.344269703710.153632057568-0.5249726542211.005472259710.2118164963081.78499825147-49.452603425838.204963255921.259906888
145.39547923078-2.361528878374.423550935541.20684297603-1.33097233853.08151171824-1.00098731042-2.213888051020.6375108883480.7560123831470.4980737604471.33555387853-0.0959230293212-1.91291971830.6704528871661.083251087490.3104147842950.4419307624342.11045723774-0.1028374471882.31969163852-44.449433597960.5819692312-20.7171829582
158.19037744292-1.52302328731.809387219177.33298298771-0.0506657823939.075205512640.0254997772005-1.186218088860.05886839733990.09714710449870.6949452162720.9983756949620.324336845035-1.54355168663-0.6373053208650.900130742254-0.02983921407420.06477962553711.147223455050.3914957820620.957619933321-28.489752340347.6207810311-27.1658404139
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 670 through 763 )AA670 - 7631 - 89
22chain 'A' and (resid 764 through 831 )AA764 - 83190 - 157
33chain 'A' and (resid 832 through 881 )AA832 - 881158 - 207
44chain 'A' and (resid 882 through 968 )AA882 - 968208 - 285
55chain 'C' and (resid 32 through 57 )CB32 - 571 - 20
66chain 'C' and (resid 58 through 87 )CB58 - 8721 - 44
77chain 'C' and (resid 88 through 119 )CB88 - 11945 - 61
88chain 'C' and (resid 120 through 133 )CB120 - 13362 - 75
99chain 'C' and (resid 134 through 189 )CB134 - 18976 - 131
1010chain 'B' and (resid 669 through 762 )BC669 - 7621 - 83
1111chain 'B' and (resid 763 through 814 )BC763 - 81484 - 135
1212chain 'B' and (resid 815 through 881 )BC815 - 881136 - 197
1313chain 'B' and (resid 882 through 969 )BC882 - 969198 - 267
1414chain 'D' and (resid 30 through 109 )DD30 - 1091 - 48
1515chain 'D' and (resid 110 through 188 )DD110 - 18849 - 127

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