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- PDB-7mrm: Chicken CNTN3 APP complex -

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Basic information

Entry
Database: PDB / ID: 7mrm
TitleChicken CNTN3 APP complex
ComponentsFusion protein of Chicken CNTN3 FN1-FN2 domains and Amyloid-beta A4 protein,Amyloid-beta A4 protein
KeywordsCELL ADHESION / Ig superfamily / amyloid precursor protein
Function / homology
Function and homology information


positive regulation of macromolecule metabolic process / secretory vesicle / regulation of protein metabolic process / Golgi-associated vesicle / transition metal ion binding / clathrin-coated pit / molecular function activator activity / serine-type endopeptidase inhibitor activity / endocytosis / heparin binding ...positive regulation of macromolecule metabolic process / secretory vesicle / regulation of protein metabolic process / Golgi-associated vesicle / transition metal ion binding / clathrin-coated pit / molecular function activator activity / serine-type endopeptidase inhibitor activity / endocytosis / heparin binding / growth cone / perikaryon / early endosome / cell adhesion / apoptotic process / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular region / nucleus / plasma membrane
Similarity search - Function
Sugar Binding Protein, Amyloid A4 Protein; Chain A / Amyloidogenic glycoprotein, heparin-binding domain / 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 ...Sugar Binding Protein, Amyloid A4 Protein; Chain A / Amyloidogenic glycoprotein, heparin-binding domain / 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 / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Amyloid-beta A4 protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fusion protein of Chicken CNTN3 FN1-FN2 domains and Amyloid-beta A4 protein,Amyloid-beta A4 protein
A: Fusion protein of Chicken CNTN3 FN1-FN2 domains and Amyloid-beta A4 protein,Amyloid-beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2156
Polymers86,8312
Non-polymers3844
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-51 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.669, 94.500, 174.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Fusion protein of Chicken CNTN3 FN1-FN2 domains and Amyloid-beta A4 protein,Amyloid-beta A4 protein


Mass: 43415.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CNTN3 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: F1NL84, UniProt: Q9DGJ7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Na-acetate pH 5.5, 1.1 M Li2SO4, 3% (w/v) sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→29.87 Å / Num. obs: 30550 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 49.22 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.073 / Rrim(I) all: 0.194 / Net I/σ(I): 7.8
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4407 / CC1/2: 0.891 / Rpim(I) all: 0.275 / Rrim(I) all: 0.753 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KTM, 5E4Q

3ktm

5e4q


Resolution: 2.75→29.87 Å / SU ML: 0.345 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2313 1999 6.56 %
Rwork0.1933 28481 -
obs0.1958 30480 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.93 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 20 139 5827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255841
X-RAY DIFFRACTIONf_angle_d0.49617982
X-RAY DIFFRACTIONf_chiral_restr0.0464878
X-RAY DIFFRACTIONf_plane_restr0.0041042
X-RAY DIFFRACTIONf_dihedral_angle_d12.27762112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.32121380.2621957X-RAY DIFFRACTION98.73
2.82-2.90.35921420.25232020X-RAY DIFFRACTION99.86
2.9-2.980.31551410.24562006X-RAY DIFFRACTION99.95
2.98-3.080.31921400.24941993X-RAY DIFFRACTION99.77
3.08-3.190.33841430.24882027X-RAY DIFFRACTION99.77
3.19-3.320.29931390.22062006X-RAY DIFFRACTION99.72
3.32-3.470.26391430.20832020X-RAY DIFFRACTION99.77
3.47-3.650.2621420.19462029X-RAY DIFFRACTION99.95
3.65-3.880.19711420.18512016X-RAY DIFFRACTION99.95
3.88-4.180.18191420.16752039X-RAY DIFFRACTION99.86
4.18-4.590.16921430.15252034X-RAY DIFFRACTION99.68
4.59-5.260.18491450.1422057X-RAY DIFFRACTION99.55
5.26-6.610.19221470.17022084X-RAY DIFFRACTION99.96
6.62-29.870.21341520.21032193X-RAY DIFFRACTION99.62
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)
14.689004787513.862720011292.711874999896.837911989091.066854706594.77831638383-0.2280750163440.4436467009910.3080403048250.196420080680.387195169668-0.195717833102-0.6938303279940.62699418458-0.1247293377560.3999850411780.0420112728164-0.06394428059880.3555927237810.1076797315190.395295796387-1.8819808794337.3561226958-18.0537783489
23.688886526452.307885888663.256655294126.888637233834.260936173379.066679823290.02213949917590.1477154761790.143797725928-0.182998854886-0.1365678536040.265658994001-0.217811870098-0.3022271219830.1334494635170.298281642056-0.005624791516190.03885841286070.3137609524220.05306511955490.370229073664-9.9401199366833.2023656844-20.8348535107
37.883493765485.06634835495-0.08439881123777.549253172120.3640845761832.592277168510.0800464652574-0.2907376466090.122544010765-0.0659019481989-0.183232146460.365185507691-0.0939168989304-0.1474073437570.1708752884990.3930035304110.06146476841330.02088158358490.328245274549-0.03763815853240.236102050106-33.953576973311.4388073624-39.6792362484
45.194988201971.578032010893.619604046635.909440324982.701594459536.37387715378-0.08633875335180.101358427163-0.2541068968970.0650371371969-0.0266174331352-0.0976967763435-0.114255691135-0.1610628232360.0831849725550.525565386546-0.08514415305170.05657302712090.326239460166-0.03080556645330.398458747173-36.8007718183-7.45029548654-24.0654850918
54.24134244362.239059848450.8392812877395.34865609116-0.3032382757724.579306636940.0956322659305-0.1230217605630.226370129623-0.142585782702-0.2088781727760.133022055874-0.0684112686604-0.1080466603010.09224183935020.3454948777220.0227379807545-0.0579794512890.3164665270830.05541556361210.323004993248-15.275547850119.4092675984-2.33464764278
66.506793622961.011805617263.705659838724.503590336841.212156946218.542541886720.177850376034-0.724141658210.4257237710540.71019671824-0.1472803542610.0646793012573-0.863951218454-0.58596607021-0.05007986687160.663858331230.009206731851290.04134929286050.45800148468-0.07245848155360.368185231848-19.03244070322.309360188130.2425029512
72.52803820478-0.1789895111430.007282577164012.73496454179-0.5026746306255.70536893713-0.000390293987305-0.251595911516-0.15978945743-0.06004537691580.0125406527534-0.03302455889380.152993326466-0.234627534408-0.02246206428630.3822315356010.00304679485595-0.01242021264960.2903352892710.05629574725920.451108142871-14.315382208313.335682046217.9891025725
82.95343350571-1.41160072887-2.502434003574.56070370153-1.466191357885.2062872863-0.119011592179-0.274894234837-0.650131328502-0.0622646596087-0.233877304575-0.200870698890.3435946966640.3873578149920.2978934380260.4061985284590.035337149086-0.04542000692790.3039705740320.05044350900570.312436781399-11.74398286055.7982235789813.18321473
96.549490644121.46442562108-2.493445528127.527624995822.95074997512.658765718140.7561767299110.579582147045-0.136902866772-0.658821842654-0.08602647317950.388254500198-0.313577108469-0.569959422252-0.5158592096990.6140064062310.166448613178-0.2677575924330.649099776985-0.1548294408860.645783436996-42.055303520513.4183108424-72.0838209669
104.43505674730.6176779925722.653929017816.38406858988-1.811999249014.689334580060.0923873474877-0.0986610218541.10824019236-0.792772140258-0.3472109031211.67260176991-0.273783610357-1.258095431140.2403720286420.7055411043510.265588831185-0.3209292274840.841165634712-0.4108225976211.03203834423-47.100644056514.9382093211-71.0189719364
114.290176613891.380535952821.948518142982.72709731996-1.453001616464.858136534140.03670882758890.3285301419620.104993218923-0.681267231933-0.3916516393060.929750355184-0.441870037763-0.5643694530480.3541403523510.6062370644480.20865137799-0.2109882438550.557129667278-0.1820240304320.619262355287-41.591292636115.2902434116-68.8558694006
126.33245883072.548439494-1.72756398958.25227207237-1.346486082016.488521839850.187006633589-0.01572733288590.0254742804559-0.107538258972-0.545724256335-0.2209172847420.08499775410550.3473499062730.3474483194710.4136345897620.089648215847-0.04365718718410.458374651568-0.06109049399890.196891074688-25.353796997112.6279106276-51.6695428722
136.3727013938-3.26077278202-0.1856622594957.13798371995-0.2054975290216.777551956840.01157966513890.323346159325-0.256861349937-0.723286628113-0.212830459755-0.4993339865910.5855006076390.4648511085710.1862087627940.3730712628490.0580465049745-0.02962006366260.381494246397-0.02757467249030.321241971246-22.59472929310.2288046686-57.352593432
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 496 through 529 )BA496 - 5291 - 34
22chain 'B' and (resid 530 through 598 )BA530 - 59835 - 103
33chain 'B' and (resid 599 through 699 )BA599 - 699104 - 204
44chain 'A' and (resid 496 through 598 )AB496 - 5981 - 103
55chain 'A' and (resid 599 through 699 )AB599 - 699104 - 204
66chain 'A' and (resid 1030 through 1102 )AC1030 - 11021 - 73
77chain 'A' and (resid 1103 through 1146 )AC1103 - 114674 - 117
88chain 'A' and (resid 1147 through 1190 )AC1147 - 1190118 - 161
99chain 'B' and (resid 1030 through 1042 )D - BD1030 - 10421 - 13
1010chain 'B' and (resid 1043 through 1065 )BD1043 - 106514 - 36
1111chain 'B' and (resid 1066 through 1119 )BD1066 - 111937 - 85
1212chain 'B' and (resid 1120 through 1146 )BD1120 - 114686 - 112
1313chain 'B' and (resid 1147 through 1190 )BD1147 - 1190113 - 156

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