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- PDB-4yx2: Crystal structure of Bovine prion protein complexed with POM1 FAB -

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Basic information

Entry
Database: PDB / ID: 4yx2
TitleCrystal structure of Bovine prion protein complexed with POM1 FAB
Components
  • Major prion protein
  • POM1 FAB HEAVY CHAIN
  • POM1 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / prion / antibody / complex / Immune system complex
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 / 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 / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / 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
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 speciesBos taurus (cattle)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å
AuthorsBaral, P.K. / Swayampakula, M. / James, M.N.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
APRI Canada
CitationJournal: J.Struct.Biol. / Year: 2015
Title: X-ray structural and molecular dynamical studies of the globular domains of cow, deer, elk and Syrian hamster prion proteins.
Authors: Baral, P.K. / Swayampakula, M. / Aguzzi, A. / James, M.N.
History
DepositionMar 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein
H: POM1 FAB HEAVY CHAIN
L: POM1 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)65,3953
Polymers65,3953
Non-polymers00
Water4,071226
1
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)18,4891
Polymers18,4891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6320 Å2
MethodPISA
2
H: POM1 FAB HEAVY CHAIN
L: POM1 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,9072
Polymers46,9072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-25 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.674, 99.764, 75.942
Angle α, β, γ (deg.)90.00, 93.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Major prion protein / PrP / Major scrapie-associated fibril protein 1


Mass: 18488.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRNP, PRP / Production host: Escherichia Coli (E. coli) / References: UniProt: P10279
#2: Antibody POM1 FAB HEAVY CHAIN


Mass: 23397.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody POM1 FAB LIGHT CHAIN


Mass: 23509.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.1 M BIS-TRIS, 0.2 M lithium sulphate

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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: Sep 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.194→50 Å / Num. obs: 33032 / % possible obs: 96.8 % / Redundancy: 3.9 % / Rsym value: 0.069 / Net I/σ(I): 18
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H88, 4DGI

4h88

4dgi


Resolution: 2.194→33.537 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2634 1662 5.03 %
Rwork0.2159 --
obs0.2183 33023 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→33.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4118 0 0 226 4344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094222
X-RAY DIFFRACTIONf_angle_d1.1985733
X-RAY DIFFRACTIONf_dihedral_angle_d16.7641523
X-RAY DIFFRACTIONf_chiral_restr0.047631
X-RAY DIFFRACTIONf_plane_restr0.005737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1939-2.25840.37311210.33252360X-RAY DIFFRACTION88
2.2584-2.33130.35231410.2982511X-RAY DIFFRACTION92
2.3313-2.41460.33431250.27962659X-RAY DIFFRACTION98
2.4146-2.51120.31081340.26452704X-RAY DIFFRACTION100
2.5112-2.62550.35551420.26922695X-RAY DIFFRACTION100
2.6255-2.76380.28151460.24642689X-RAY DIFFRACTION100
2.7638-2.93690.31341390.2572706X-RAY DIFFRACTION100
2.9369-3.16350.29261540.24582671X-RAY DIFFRACTION100
3.1635-3.48160.27471490.22982673X-RAY DIFFRACTION99
3.4816-3.98470.24911290.20632358X-RAY DIFFRACTION87
3.9847-5.01760.22561460.1622618X-RAY DIFFRACTION97
5.0176-33.54080.19631360.17022717X-RAY DIFFRACTION98

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