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- PDB-4h88: Structure of POM1 FAB fragment complexed with mouse PrPc Fragment... -

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Basic information

Entry
Database: PDB / ID: 4h88
TitleStructure of POM1 FAB fragment complexed with mouse PrPc Fragment 120-230
Components
  • Major prion protein
  • POM1 FAB CHAIN H
  • POM1 FAB CHAIN L
KeywordsIMMUNE SYSTEM / C-term mouse prion protein / POM1 FAB
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / nucleobase-containing compound metabolic process / response to copper ion / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / activation of protein kinase activity / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / response to amyloid-beta / : / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / side of membrane / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / negative regulation of protein phosphorylation / molecular condensate scaffold activity / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / regulation of protein localization / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / transmembrane transporter binding / molecular adaptor activity / postsynaptic density / learning or memory / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Immunoglobulins ...Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBaral, P.K. / Wieland, B. / Swayampakula, M. / James, M.N.
CitationJournal: Nature / Year: 2013
Title: The toxicity of antiprion antibodies is mediated by the flexible tail of the prion protein.
Authors: Sonati, T. / Reimann, R.R. / Falsig, J. / Baral, P.K. / O'Connor, T. / Hornemann, S. / Yaganoglu, S. / Li, B. / Herrmann, U.S. / Wieland, B. / Swayampakula, M. / Rahman, M.H. / Das, D. / ...Authors: Sonati, T. / Reimann, R.R. / Falsig, J. / Baral, P.K. / O'Connor, T. / Hornemann, S. / Yaganoglu, S. / Li, B. / Herrmann, U.S. / Wieland, B. / Swayampakula, M. / Rahman, M.H. / Das, D. / Kav, N. / Riek, R. / Liberski, P.P. / James, M.N. / Aguzzi, A.
History
DepositionSep 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 18, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major prion protein
H: POM1 FAB CHAIN H
L: POM1 FAB CHAIN L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1054
Polymers60,0823
Non-polymers231
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.406, 107.331, 75.443
Angle α, β, γ (deg.)90.00, 95.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-432-

HOH

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Components

#1: Protein Major prion protein / PrP / PrP27-30 / PrP33-35C


Mass: 13175.697 Da / Num. of mol.: 1 / Fragment: C-TERM FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prnp, Prn-p, Prp / Production host: Escherichia coli (E. coli) / References: UniProt: P04925
#2: Antibody POM1 FAB CHAIN H


Mass: 23397.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA
#3: Antibody POM1 FAB CHAIN L


Mass: 23509.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.1 M BIS-TRIS, 0.2 M lithium sulphate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2011
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 49880 / Redundancy: 4.2 % / Biso Wilson estimate: 33.23 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.008 Å / SU ML: 0.51 / σ(F): 1.35 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 2525 5.06 %random
Rwork0.1994 ---
obs0.2012 49874 95.89 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.144 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.7852 Å20 Å2-0.0948 Å2
2--2.2263 Å2-0 Å2
3----5.0114 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 1 359 4513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064260
X-RAY DIFFRACTIONf_angle_deg0.9565787
X-RAY DIFFRACTIONf_dihedral_angle_d12.2341533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93690.3062960.24851881X-RAY DIFFRACTION68
1.9369-1.97640.23051200.21832190X-RAY DIFFRACTION81
1.9764-2.01940.24981370.22042610X-RAY DIFFRACTION95
2.0194-2.06630.27011520.21362689X-RAY DIFFRACTION98
2.0663-2.1180.25191570.21522646X-RAY DIFFRACTION98
2.118-2.17530.24631320.19932728X-RAY DIFFRACTION98
2.1753-2.23930.22121250.18682706X-RAY DIFFRACTION99
2.2393-2.31150.23841300.19452709X-RAY DIFFRACTION99
2.3115-2.39410.25051380.19872701X-RAY DIFFRACTION99
2.3941-2.48990.2271280.21722750X-RAY DIFFRACTION99
2.4899-2.60320.27631370.22272733X-RAY DIFFRACTION99
2.6032-2.74040.28521510.21352689X-RAY DIFFRACTION99
2.7404-2.9120.27381730.21522687X-RAY DIFFRACTION99
2.912-3.13680.27831360.20682726X-RAY DIFFRACTION100
3.1368-3.45220.21261360.19732755X-RAY DIFFRACTION99
3.4522-3.95110.22291610.18762725X-RAY DIFFRACTION99
3.9511-4.97570.18341630.16812688X-RAY DIFFRACTION98
4.9757-35.01370.24141530.2112736X-RAY DIFFRACTION98

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