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- PDB-7mqy: Zebrafish CNTN4 APLP2 complex -

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Basic information

Entry
Database: PDB / ID: 7mqy
TitleZebrafish CNTN4 APLP2 complex
ComponentsFusion protein of CNTN4 and APLP2
KeywordsCELL ADHESION / Ig superfamily / amyloid precursor protein
Function / homology
Function and homology information


cell-cell adhesion mediator activity / transition metal ion binding / side of membrane / endomembrane system / axonogenesis / axon guidance / central nervous system development / serine-type endopeptidase inhibitor activity / cell-cell adhesion / heparin binding ...cell-cell adhesion mediator activity / transition metal ion binding / side of membrane / endomembrane system / axonogenesis / axon guidance / central nervous system development / serine-type endopeptidase inhibitor activity / cell-cell adhesion / heparin binding / axon / membrane / 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. / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus ...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. / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Amyloid beta (A4) precursor-like protein 2 / Contactin-4 precursor
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 1.3Nov 13, 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: Fusion protein of CNTN4 and APLP2


Theoretical massNumber of molelcules
Total (without water)43,7211
Polymers43,7211
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.660, 44.980, 99.829
Angle α, β, γ (deg.)90.000, 95.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Fusion protein of CNTN4 and APLP2 / Contactin-4 / Amyloid beta (A4) precursor-like protein 2 / Zgc:153573 / Aplp2 protein


Mass: 43721.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cntn4, zgc:153573, aplp2 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08C52, UniProt: A2BID8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na-acetate pH 5.2, 30% (w/v) PEG 8,000

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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: RAYONIX MX300-HS / Detector: CCD / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→99.31 Å / Num. obs: 20199 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 41.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.035 / Rrim(I) all: 0.096 / Net I/σ(I): 15.6
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 7 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2266 / CC1/2: 0.909 / Rpim(I) all: 0.243 / Rrim(I) all: 0.646 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E4S, 3KTM

5e4s

3ktm


Resolution: 2.46→49.96 Å / SU ML: 0.3052 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.6289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2209 1959 9.92 %
Rwork0.1891 17780 -
obs0.1923 19739 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.7 Å2
Refinement stepCycle: LAST / Resolution: 2.46→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 0 120 2945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042921
X-RAY DIFFRACTIONf_angle_d0.67633983
X-RAY DIFFRACTIONf_chiral_restr0.0475434
X-RAY DIFFRACTIONf_plane_restr0.0047517
X-RAY DIFFRACTIONf_dihedral_angle_d12.98061073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.520.33821290.25791152X-RAY DIFFRACTION91.24
2.52-2.590.31311320.24681213X-RAY DIFFRACTION93.99
2.59-2.660.23771390.23371253X-RAY DIFFRACTION95.54
2.66-2.750.29221340.23541216X-RAY DIFFRACTION96.5
2.75-2.850.28141410.22871262X-RAY DIFFRACTION97.3
2.85-2.960.31111370.22691248X-RAY DIFFRACTION97.12
2.96-3.10.25931400.23321267X-RAY DIFFRACTION98.53
3.1-3.260.23611400.20731290X-RAY DIFFRACTION99.37
3.26-3.470.19521420.19571293X-RAY DIFFRACTION99.45
3.47-3.730.21951430.18971301X-RAY DIFFRACTION99.72
3.73-4.110.19451440.1761298X-RAY DIFFRACTION99.79
4.11-4.70.18371420.15271287X-RAY DIFFRACTION100
4.7-5.920.1881460.15481333X-RAY DIFFRACTION100
5.92-49.960.19531500.1671367X-RAY DIFFRACTION99.74
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)
11.14305726569-0.1063837048271.266656797580.5360039163340.002031376565054.28425543591-0.1299749247130.3674694754730.0875313214580.09036100903230.127398758377-0.0611386308208-0.4851963515471.4074523198-0.004904470214440.817787146946-0.177111389302-0.006063009778431.031972004110.06200032087860.35428659266843.90413661720.7153595452103.463669437
23.756377604860.4514308800950.971722660295.98076367686-1.147309393264.895347615230.094833291486-0.4667532508820.3695561243990.348437045947-0.3211453169440.542910282821-0.374606582535-0.5758343013810.193336697670.2337443075270.00884967268380.04656752268360.377527487939-0.1086366366350.36429319849133.741808667231.481009338365.5743865698
33.581927701190.317429228319-0.2797547194933.907937285510.9509109815184.3406473086-0.08268166993230.4826863904020.0420765474111-0.3315953257790.1613134426680.136138042829-0.0297384116039-0.0499946044449-0.06444700595720.237364300135-0.02239397428130.01320955578560.152269690160.01611564336820.33236796824153.115780768119.250127985839.747740081
45.030387254641.351541895060.06001974930344.03787433605-0.07200423830492.703896119080.172185322523-0.806303354707-1.002540575910.0829371355395-0.147500021744-0.007649738533910.460364822571-0.324870096377-0.01777367454470.292087899144-0.0538842693339-0.008530896866330.2912209093560.1297590433690.35184178309738.793364708614.511732319959.947773692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 598 through 702 )
2X-RAY DIFFRACTION2chain 'A' and (resid 703 through 801 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1036 through 1126 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1127 through 1199 )

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