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- PDB-2hh0: Structure of an Anti-PrP Fab, P-Clone, in Complex with its Cognat... -

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Basic information

Entry
Database: PDB / ID: 2hh0
TitleStructure of an Anti-PrP Fab, P-Clone, in Complex with its Cognate Bovine Peptide Epitope.
Components
  • Heavy Chain, P-Clone Fab, Chimera
  • Light Chain, P-Clone Fab, Chimera
  • Prion protein
KeywordsIMMUNE SYSTEM / prion / prp / fab
Function / homology
Function and homology information


type 5 metabotropic glutamate receptor binding / cuprous ion binding / side of membrane / inclusion body / cellular response to copper ion / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / positive regulation of neuron apoptotic process / cellular response to amyloid-beta ...type 5 metabotropic glutamate receptor binding / cuprous ion binding / side of membrane / inclusion body / cellular response to copper ion / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / amyloid-beta binding / G-quadruplex RNA binding / microtubule binding / nuclear membrane / membrane raft / copper ion binding / dendrite / protein-containing complex binding / Golgi apparatus / cell surface / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Immunoglobulins ...Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / 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
Major prion protein / Major prion protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 Å
AuthorsKanyo, Z.K.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation
Authors: Luginbuhl, B. / Kanyo, Z. / Jones, R.M. / Fletterick, R.J. / Prusiner, S.B. / Cohen, F.E. / Williamson, R.A. / Burton, D.R. / Pluckthun, A.
#1: Journal: Nat.Biotechnol. / Year: 2002
Title: Measuring Prions Causing Bovine Spongiform Encephalopathy or Chronic Wasting Disease by Immunoassays and Transgenic Mice.
Authors: Safar, J.G. / Scott, M. / Monaghan, J. / Deering, C. / Didorenko, S. / Vergara, J. / Ball, H. / Legname, G. / Leclerc, E. / Solforosi, L. / Serban, H. / Groth, D. / Burton, D.R. / Prusiner, ...Authors: Safar, J.G. / Scott, M. / Monaghan, J. / Deering, C. / Didorenko, S. / Vergara, J. / Ball, H. / Legname, G. / Leclerc, E. / Solforosi, L. / Serban, H. / Groth, D. / Burton, D.R. / Prusiner, S.B. / Williamson, R.A.
History
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.percent_possible_all / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light Chain, P-Clone Fab, Chimera
H: Heavy Chain, P-Clone Fab, Chimera
P: Prion protein


Theoretical massNumber of molelcules
Total (without water)47,3673
Polymers47,3673
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.834, 119.834, 95.534
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody Light Chain, P-Clone Fab, Chimera


Mass: 23039.572 Da / Num. of mol.: 1 / Fragment: 2-109 (mouse), 110-271 (human)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: Escherichia coli (E. coli)
#2: Antibody Heavy Chain, P-Clone Fab, Chimera


Mass: 23242.982 Da / Num. of mol.: 1 / Mutation: 1-106 (mouse), 107-271 (human)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Prion protein


Mass: 1084.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in bovines. / References: UniProt: Q5UK71, UniProt: P10279*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 4.18 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Well: 57% saturated ammonium sulfate Drop: 10/1 protein solution/well solution, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→43.391 Å / Num. all: 18457 / Num. obs: 18459 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.85-32.70.2982.6731627250.298100
3-3.192.70.1854.1684925420.18599
3.19-3.412.70.1226.1648924130.12299.9
3.41-3.682.70.0828.4599222180.08298.5
3.68-4.032.70.06510.1556720590.06598.9
4.03-4.512.70.05212.1500018440.05297.9
4.51-5.22.70.05111.5439716390.05197.9
5.2-6.372.50.05112.3345813700.05196.5
6.37-9.012.50.0599.3265910600.05995.1
9.01-43.392.50.0569.614935890.05692.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.85→43.391 Å / FOM work R set: 0.744 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1267 6.7 %Random
Rwork0.222 ---
all0.222 18457 --
obs0.222 18457 97.9 %-
Solvent computationBsol: 34.012 Å2
Displacement parametersBiso mean: 56.124 Å2
Refinement stepCycle: LAST / Resolution: 2.85→43.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 0 69 3403
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.41
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.85-2.890.441490.401694743
2.89-2.930.48450.382704749
2.93-2.970.362540.358665719
2.97-3.020.476390.364691730
3.02-3.070.491440.369719763
3.07-3.120.378590.334663722
3.12-3.180.389630.324697760
3.18-3.240.483530.292675728
3.24-3.310.268460.275704750
3.31-3.380.389450.25674719
3.38-3.460.399380.267709747
3.46-3.540.294570.262686743
3.54-3.640.28450.225707752
3.64-3.750.287500.21687737
3.75-3.870.26540.206664718
3.87-4.010.228480.185695743
4.01-4.170.309690.185664733
4.17-4.360.228500.172694744
4.36-4.590.185410.142691732
4.59-4.870.206520.157686738
4.87-5.250.197510.138684735
5.25-5.780.201660.17666732
5.78-6.610.247550.212688743
6.61-8.320.295520.229676728
8.32-510.29420.245707749
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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