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- PDB-4dgi: Structure of POM1 FAB fragment complexed with human PrPc Fragment... -

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Basic information

Entry
Database: PDB / ID: 4dgi
TitleStructure of POM1 FAB fragment complexed with human PrPc Fragment 120-230
Components
  • Major prion protein
  • POM1 Fab Heavy chain
  • POM1 Fab Light chain
KeywordsPROTEIN BINDING / prion / antibody
Function / homology
Function and homology information


positive regulation of glutamate receptor signaling pathway / 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 / NCAM1 interactions ...positive regulation of glutamate receptor signaling pathway / 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 / NCAM1 interactions / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / 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 / long-term memory / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / tubulin binding / 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 / 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 / postsynapse / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / transmembrane transporter binding / molecular adaptor activity / postsynaptic density / learning or memory / regulation of cell cycle / membrane raft / cell cycle / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / 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 protein, beta-ribbon domain / Major Prion Protein / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBaral, P.K. / Wieland, B. / Swayampakula, M. / James, M.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural studies on the folded domain of the human prion protein bound to the Fab fragment of the antibody POM1.
Authors: Baral, P.K. / Wieland, B. / Swayampakula, M. / Polymenidou, M. / Rahman, M.H. / Kav, N.N. / Aguzzi, A. / James, M.N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and preliminary X-ray diffraction analysis of prion protein bound to the Fab fragment of the POM1 antibody.
Authors: Baral, P.K. / Wieland, B. / Swayampakula, M. / Polymenidou, M. / Aguzzi, A. / Kav, N.N. / James, M.N.
History
DepositionJan 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 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 Heavy chain
L: POM1 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0174
Polymers59,9943
Non-polymers231
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.530, 105.920, 76.230
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13087.545 Da / Num. of mol.: 1 / Fragment: residues 120-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRNP, PRIP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P04156
#2: Antibody POM1 Fab Heavy chain


Mass: 23397.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody POM1 Fab Light chain


Mass: 23509.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#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.: 170 / 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: 56.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.1M MES, 0.1M sodium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.56 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 2.4→76.5 Å / Num. all: 26309 / Num. obs: 26309 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→35.194 Å / SU ML: 0.89 / σ(F): 1.42 / Phase error: 34.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2893 1285 5.01 %
Rwork0.2578 --
obs0.2594 25651 99.17 %
all-26309 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.445 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.166 Å20 Å20.4084 Å2
2--15.7809 Å2-0 Å2
3----13.6149 Å2
Refine analyzeLuzzati coordinate error obs: 0.83 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4105 0 1 170 4276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184209
X-RAY DIFFRACTIONf_angle_d2.0455715
X-RAY DIFFRACTIONf_dihedral_angle_d13.0561519
X-RAY DIFFRACTIONf_chiral_restr0.109628
X-RAY DIFFRACTIONf_plane_restr0.014736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49610.41331480.41662665X-RAY DIFFRACTION99
2.4961-2.60970.34921210.36852752X-RAY DIFFRACTION99
2.6097-2.74730.34671180.31732692X-RAY DIFFRACTION99
2.7473-2.91930.35911430.27942707X-RAY DIFFRACTION99
2.9193-3.14460.3171310.24192704X-RAY DIFFRACTION100
3.1446-3.46080.29141480.22762726X-RAY DIFFRACTION100
3.4608-3.9610.24731480.22382746X-RAY DIFFRACTION100
3.961-4.98810.23481690.2012687X-RAY DIFFRACTION100
4.9881-35.19820.28921590.26922687X-RAY DIFFRACTION97

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