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- PDB-6aq7: Structure of POM6 FAB fragment complexed with mouse PrPc -

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Basic information

Entry
Database: PDB / ID: 6aq7
TitleStructure of POM6 FAB fragment complexed with mouse PrPc
Components
  • Major prion protein
  • POM6 FAB Heavy CHAIN
  • POM6 FAB light CHAIN
KeywordsIMMUNE SYSTEM / Prion / antibody / chaperone / antigen-antibody
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 / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / 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 / protein sequestering activity / 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 / 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 / mitochondrial outer membrane / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / learning or memory / membrane raft / copper ion binding / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / membrane / identical protein binding / metal ion binding / plasma membrane / 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
3,3',3''-phosphanetriyltripropanoic acid / Major prion protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBaral, P.K. / Swayampakula, M. / James, M.N.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Alberta innovates Canada
CitationJournal: FEBS J. / Year: 2018
Title: Structural characterization of POM6 Fab and mouse prion protein complex identifies key regions for prions conformational conversion.
Authors: Baral, P.K. / Swayampakula, M. / Aguzzi, A. / James, M.N.G.
History
DepositionAug 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 7, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein
H: POM6 FAB Heavy CHAIN
L: POM6 FAB light CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9076
Polymers61,4733
Non-polymers4343
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-26 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.040, 82.420, 103.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11H-559-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 14481.103 Da / Num. of mol.: 1 / Fragment: UNP residues 127-225
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

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Antibody , 2 types, 2 molecules HL

#2: Antibody POM6 FAB Heavy CHAIN


Mass: 23203.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody POM6 FAB light CHAIN


Mass: 23788.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)

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Non-polymers , 3 types, 463 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Sodium malonate pH 7.0, 12% PEG8000 along with 5mM TCEP, 5mM Praseodymium acetate and ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.83→48 Å / Num. obs: 54971 / % possible obs: 99.8 % / Redundancy: 9.3 % / Net I/σ(I): 9.29

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J8R

4j8r


Resolution: 1.83→48 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.97
RfactorNum. reflection% reflection
Rfree0.2299 2750 5 %
Rwork0.1967 --
obs0.1984 54971 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4139 0 28 460 4627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084270
X-RAY DIFFRACTIONf_angle_d1.015807
X-RAY DIFFRACTIONf_dihedral_angle_d6.5712550
X-RAY DIFFRACTIONf_chiral_restr0.054643
X-RAY DIFFRACTIONf_plane_restr0.005740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.86150.40341320.3662493X-RAY DIFFRACTION96
1.8615-1.89540.36091330.33882537X-RAY DIFFRACTION99
1.8954-1.93190.34051360.33132572X-RAY DIFFRACTION100
1.9319-1.97130.36431350.28732572X-RAY DIFFRACTION100
1.9713-2.01420.29321370.25872599X-RAY DIFFRACTION100
2.0142-2.0610.28471370.23622603X-RAY DIFFRACTION100
2.061-2.11260.28311360.23312588X-RAY DIFFRACTION100
2.1126-2.16970.26191360.22172578X-RAY DIFFRACTION100
2.1697-2.23350.27921360.21392585X-RAY DIFFRACTION100
2.2335-2.30560.23591380.21352624X-RAY DIFFRACTION100
2.3056-2.3880.27221360.21112584X-RAY DIFFRACTION100
2.388-2.48360.23241380.20582614X-RAY DIFFRACTION100
2.4836-2.59660.24411380.20652620X-RAY DIFFRACTION100
2.5966-2.73350.271370.20322607X-RAY DIFFRACTION100
2.7335-2.90480.22651370.19692601X-RAY DIFFRACTION100
2.9048-3.1290.22971390.18772643X-RAY DIFFRACTION100
3.129-3.44380.21551390.18132644X-RAY DIFFRACTION100
3.4438-3.94190.17141400.16292649X-RAY DIFFRACTION100
3.9419-4.96560.17541420.14312691X-RAY DIFFRACTION100
4.9656-48.07970.20171480.18022817X-RAY DIFFRACTION100

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