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- PDB-7mrs: Zebrafish CNTN4 APPb complex -

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Basic information

Entry
Database: PDB / ID: 7mrs
TitleZebrafish CNTN4 APPb complex
Components
  • Amyloid-beta A4 protein
  • Contactin-4
KeywordsCELL ADHESION / Ig superfamily / amyloid precursor protein
Function / homology
Function and homology information


convergent extension / regulation of Notch signaling pathway / cell-cell adhesion mediator activity / vasculature development / axon extension / regulation of neuron differentiation / Golgi-associated vesicle / transition metal ion binding / axonogenesis / central nervous system development ...convergent extension / regulation of Notch signaling pathway / cell-cell adhesion mediator activity / vasculature development / axon extension / regulation of neuron differentiation / Golgi-associated vesicle / transition metal ion binding / axonogenesis / central nervous system development / axon guidance / brain development / cell-cell adhesion / neuron projection development / heparin binding / membrane => GO:0016020 / axon / plasma membrane
Similarity search - Function
Amyloid-beta precursor protein / 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 / Amyloid precursor protein (APP) E1 domain profile. ...Amyloid-beta precursor protein / 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 / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 A4 / Amyloidogenic glycoprotein / 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 / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Amyloid-beta A4 protein / Contactin-4 precursor
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 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 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contactin-4
B: Amyloid-beta A4 protein


Theoretical massNumber of molelcules
Total (without water)54,3432
Polymers54,3432
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-8 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.980, 88.190, 89.770
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: Protein Contactin-4 / Contactin 4


Mass: 33217.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cntn4, zgc:153573 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08C52
#2: Protein Amyloid-beta A4 protein


Mass: 21126.209 Da / Num. of mol.: 1 / Fragment: E1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: appb / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: B0CM02
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 277 K / Method: batch mode / Details: 75 mM NaCl, 10 mM Na-HEPES pH 7.5

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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: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.93→89.77 Å / Num. obs: 13383 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 58.35 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.053 / Rrim(I) all: 0.174 / Net I/σ(I): 9.8
Reflection shellResolution: 2.93→3.1 Å / Redundancy: 10 % / Rmerge(I) obs: 1.163 / Mean I/σ(I) obs: 2 / Num. unique obs: 2111 / CC1/2: 0.697 / Rpim(I) all: 0.384 / Rrim(I) all: 1.227 / % 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, 5E4S

3ktm

5e4s


Resolution: 2.93→44.09 Å / SU ML: 0.3882 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.1231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2828 1281 10.03 %
Rwork0.2399 11496 -
obs0.2441 12777 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.82 Å2
Refinement stepCycle: LAST / Resolution: 2.93→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 0 17 2831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032890
X-RAY DIFFRACTIONf_angle_d0.58663938
X-RAY DIFFRACTIONf_chiral_restr0.0498434
X-RAY DIFFRACTIONf_plane_restr0.0049510
X-RAY DIFFRACTIONf_dihedral_angle_d9.58641053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.040.39751290.38491134X-RAY DIFFRACTION87.22
3.04-3.180.36331380.33751183X-RAY DIFFRACTION91.1
3.18-3.350.33291370.28121233X-RAY DIFFRACTION94.55
3.35-3.560.36871340.27241265X-RAY DIFFRACTION94.78
3.56-3.830.30841430.24221285X-RAY DIFFRACTION98.08
3.84-4.220.2641450.22651287X-RAY DIFFRACTION97.15
4.22-4.830.23431500.19361323X-RAY DIFFRACTION98.99
4.83-6.080.23261470.19671358X-RAY DIFFRACTION99.87
6.08-44.090.25751580.23161428X-RAY DIFFRACTION99.87
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)
13.499800915572.89307939608-1.368332271973.58080357948-1.045905626871.71676489420.314141176183-0.1494001390560.2696580447680.622953694023-0.1858927752890.358134434087-0.220623824415-0.121601938456-0.1517150797590.4631594095350.004085776019130.1253227382130.284707106737-0.03592812979550.74089236834568.259547889155.512615368136.6891021392
20.6832273277070.805193231602-0.06001067180284.618783158820.7568037363132.096778838430.274577472338-0.3132574905240.1876775920030.103304103496-0.219185202280.0686638092936-0.2599394386180.0533574261147-0.01607928784490.253701088504-0.003913953862380.04980248401020.28794054254-0.001335567328890.71211436839595.945694343976.404466385919.8363886458
34.822971134720.329619606235-0.08548582881864.843508378733.110544473975.975675397070.0425216797905-0.6641887695990.01017935786680.1293136316660.2052081489040.084561986328-0.5731411746810.190714081272-0.2763646528830.533998371638-0.06950586249860.2411768451730.498522885483-0.06927695852420.9970794342108.190548084101.85675341539.9050852615
44.24163057021-0.518947254870.2569478056695.42415770159-1.21561126083.27412668907-0.281956475456-0.5214318284670.0041887895588-0.396934932684-0.365697326654-0.3187820627380.09187052280260.0279082660120.627069839510.3948986651510.1321778673170.2227834688090.3294185712150.05286043947081.3863006289696.623240376662.231734727915.0125777983
54.61057814673-0.9113346934782.389172462650.68745923241.185673580416.742991858010.252967460764-0.117384591143-1.736282311180.111271539780.0384769716538-0.07317782591451.9402233103-0.11492239967-0.2796718586180.6011205528090.05494386577580.002222830101290.3898869261580.06245655227911.57729013847100.38299621451.93902069216.4643534972
61.84068264614-1.227192710270.9560921593053.72579176222-1.086711975186.589296736820.0940079327460.206833081149-0.3017013966430.0643081883623-0.407585043208-0.682441256161.033012536211.085860887290.2736528601370.490667836990.281889032105-0.03594054330440.3596615721090.01080681732231.48315499874101.45803206755.603796149918.1127551549
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 598 through 737 )AA598 - 7371 - 140
22chain 'A' and (resid 738 through 812 )AA738 - 812141 - 215
33chain 'A' and (resid 813 through 901 )AA813 - 901216 - 298
44chain 'B' and (resid 124 through 141 )BB124 - 1411 - 18
55chain 'B' and (resid 142 through 173 )BB142 - 17319 - 50
66chain 'B' and (resid 174 through 192 )BB174 - 19251 - 68

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