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- PDB-4f37: Structure of the tethered N-terminus of Alzheimer's disease A peptide -

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Basic information

Entry
Database: PDB / ID: 4f37
TitleStructure of the tethered N-terminus of Alzheimer's disease A peptide
Components
  • Colicin-E7 immunity protein
  • Fab WO2 anti-amyloid-beta antibody Fab fragment
  • Im7 immunity protein
KeywordsIMMUNE SYSTEM / amyloid-beta / Alzheimer's disease
Function / homology
Function and homology information


bacteriocin immunity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / toxic substance binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / extracellular space ...bacteriocin immunity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / toxic substance binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
If kappa light chain / Ig gamma-2A chain C region, A allele / Colicin-E7 immunity protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsNisbet, R.M. / Nuttall, S.D. / Caine, J.M. / Rober, R. / Hittaki, M. / Pearce, L.A. / Davydova, N. / Masters, C.L. / Varghese, J.N. / Streltsov, V.A.
CitationJournal: Proteins / Year: 2013
Title: Structural studies of the tethered N-terminus of the Alzheimer's disease amyloid-beta peptide.
Authors: Nisbet, R.M. / Nuttall, S.D. / Robert, R. / Caine, J.M. / Dolezal, O. / Hattarki, M. / Pearce, L.A. / Davydova, N. / Masters, C.L. / Varghese, J.N. / Streltsov, V.A.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Colicin-E7 immunity protein
B: Colicin-E7 immunity protein
F: Im7 immunity protein
H: Im7 immunity protein
K: Fab WO2 anti-amyloid-beta antibody Fab fragment
L: Fab WO2 anti-amyloid-beta antibody Fab fragment


Theoretical massNumber of molelcules
Total (without water)126,3806
Polymers126,3806
Non-polymers00
Water4,774265
1
A: Colicin-E7 immunity protein
H: Im7 immunity protein
L: Fab WO2 anti-amyloid-beta antibody Fab fragment


Theoretical massNumber of molelcules
Total (without water)63,1903
Polymers63,1903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Colicin-E7 immunity protein
F: Im7 immunity protein
K: Fab WO2 anti-amyloid-beta antibody Fab fragment


Theoretical massNumber of molelcules
Total (without water)63,1903
Polymers63,1903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.642, 82.836, 89.196
Angle α, β, γ (deg.)90.05, 92.51, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Colicin-E7 immunity protein / ImmE7 / Microcin-E7 immunity protein


Mass: 14154.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q03708
#2: Antibody Im7 immunity protein


Mass: 24841.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: in vitro / Cell: HYBRIDOMA / References: UniProt: P01863*PLUS
#3: Antibody Fab WO2 anti-amyloid-beta antibody Fab fragment


Mass: 24193.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: serum free medium (Invitrogen) / Cell: HYBRIDOMA / References: UniProt: A2NHM3*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium malonate, 20% (w/v) PEG 3350, 0.1M Bis-tris propane pH 8.5, 0.2M 1-methylimidazolium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.94721 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94721 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.489
11-H, K, -L20.391
11-h,-k,l30.12
ReflectionResolution: 2.57→44.56 Å / Num. all: 28836 / Num. obs: 28836 / % possible obs: 89.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.2
Reflection shellResolution: 2.57→2.64 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→44.46 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.871 / SU B: 23.477 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26885 1374 4.7 %RANDOM
Rwork0.22341 ---
obs0.22564 27954 77.9 %-
all-28836 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.459 Å2
Baniso -1Baniso -2Baniso -3
1--74.14 Å29.37 Å2-0.97 Å2
2---53.25 Å25.2 Å2
3---127.39 Å2
Refinement stepCycle: LAST / Resolution: 2.57→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8504 0 0 265 8769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228712
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.95111850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.62251084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95124.202376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.915151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461544
X-RAY DIFFRACTIONr_chiral_restr0.1080.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216580
X-RAY DIFFRACTIONr_mcbond_it0.31.55428
X-RAY DIFFRACTIONr_mcangle_it0.54228828
X-RAY DIFFRACTIONr_scbond_it0.96333284
X-RAY DIFFRACTIONr_scangle_it1.5034.53022
LS refinement shellResolution: 2.469→2.533 Å / Num. reflection Rwork: 0 / Total num. of bins used: 20
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)
10.03280.0128-0.01240.0286-0.0182-0.03680.0353-0.0520.06280.1207-0.02010.0101-0.0691-0.0081-0.01520.50330.06250.04710.4628-0.01290.0979-30.23570.222468.6793
2-0.0344-0.00190.034-0.0080.0266-0.0274-0.02040.0360.0212-0.08240.01510.0201-0.05060.08370.00530.48660.04190.04560.48240.02770.111826.733141.613520.2852
30.53570.1657-0.00110.39890.0567-0.07080.0133-0.05560.03680.0599-0.0092-0.02510.00770.0111-0.00410.36150.05390.02840.32290.00790.0046-9.22934.195452.2736
40.87120.51950.28260.24110.12870.559-0.0182-0.00320.03190.0439-0.01780.0231-0.0685-0.1020.03610.44330.03240.05670.440.00590.0055-34.236850.374476.0249
50.7556-0.0495-0.11371.0329-0.0676-0.016-0.0130.03190.0127-0.0590.0224-0.01740.0080.0497-0.00950.31520.04780.03250.3328-0.0145-0.00025.2938-7.209736.9466
60.8433-0.3557-0.02020.1476-0.05970.1063-0.00280.0924-0.0624-0.0826-0.0606-0.0323-0.03130.11090.06330.48170.0390.05940.41380.00980.052730.04429.021713.0331
70.05150.28620.13320.9790.47590.17860.0396-0.0078-0.01060.0415-0.0055-0.05940.00520.0026-0.0340.30710.04480.05710.29640.00970.0104-6.878855.431449.2094
80.11890.11850.15920.4754-0.42491.3212-0.0124-0.083-0.02360.058-0.0497-0.07530.04920.10540.06210.50180.06360.060.4503-0.00850.0175-22.907660.103482.016
91.27880.1816-0.17040.57490.220.11890.01180.10430.08720.09660.01030.01860-0.0339-0.02210.30030.04690.04310.24450.02650.01013.055714.007139.8769
100.5097-0.2709-0.38860.15710.17631.39010.03170.1206-0.0254-0.0763-0.08520.0427-0.107-0.25880.05360.46080.020.02890.42150.01120.045118.649918.47846.8592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 102
2X-RAY DIFFRACTION2B1 - 102
3X-RAY DIFFRACTION3F1 - 125
4X-RAY DIFFRACTION4F126 - 225
5X-RAY DIFFRACTION5H1 - 125
6X-RAY DIFFRACTION6H126 - 225
7X-RAY DIFFRACTION7K1 - 113
8X-RAY DIFFRACTION8K114 - 218
9X-RAY DIFFRACTION9L1 - 113
10X-RAY DIFFRACTION10L114 - 218

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