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- PDB-4j8r: Structure of an octapeptide repeat of the prion protein bound to ... -

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Basic information

Entry
Database: PDB / ID: 4j8r
TitleStructure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody fragment
Components
  • Heavy chain of POM2 Fab
  • Light chain of POM2 Fab
  • Major prion protein
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Fab / Antibody / Octapeptide repeat / Mouse prion protein
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / positive 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 / type 5 metabotropic glutamate receptor binding ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / positive 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 / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / cupric ion binding / regulation of potassium ion transmembrane transport / nucleobase-containing compound metabolic process / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / cuprous ion binding / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / intracellular copper ion homeostasis / response to cadmium ion / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / terminal bouton / protein homooligomerization / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / regulation of protein localization / amyloid-beta binding / protein-folding chaperone binding / protease binding / microtubule binding / molecular adaptor activity / nuclear membrane / response to oxidative stress / transmembrane transporter binding / learning or memory / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / Golgi apparatus / metal ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / 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, copper binding octapeptide repeat / Copper binding octapeptide repeat region / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsSwayampakula, M. / Baral, P.K. / Kav, N.N.V. / Aguzzi, A. / James, M.N.G.
CitationJournal: Protein Sci. / Year: 2013
Title: The crystal structure of an octapeptide repeat of the Prion protein in complex with a Fab fragment of the POM2 antibody.
Authors: Swayampakula, M. / Baral, P.K. / Aguzzi, A. / Kav, N.N. / James, M.N.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 26, 2014Group: Other
Revision 1.3Sep 20, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light chain of POM2 Fab
B: Heavy chain of POM2 Fab
I: Major prion protein
C: Light chain of POM2 Fab
D: Heavy chain of POM2 Fab
J: Major prion protein


Theoretical massNumber of molelcules
Total (without water)95,9126
Polymers95,9126
Non-polymers00
Water2,972165
1
A: Light chain of POM2 Fab
B: Heavy chain of POM2 Fab
I: Major prion protein


Theoretical massNumber of molelcules
Total (without water)47,9563
Polymers47,9563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-31 kcal/mol
Surface area19460 Å2
MethodPISA
2
C: Light chain of POM2 Fab
D: Heavy chain of POM2 Fab
J: Major prion protein


Theoretical massNumber of molelcules
Total (without water)47,9563
Polymers47,9563
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-31 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.415, 71.567, 207.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Antibody Light chain of POM2 Fab


Mass: 23133.510 Da / Num. of mol.: 2 / Fragment: unp residues 67-82 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Heavy chain of POM2 Fab


Mass: 23188.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Major prion protein / PrP / PrP27-30 / PrP33-35C


Mass: 1633.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P04925
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG 1000, 0.1M HEPES, 0.2M Calcium Chloride, pH 7.5, 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: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2011
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→39.6 Å / Num. all: 44155 / Num. obs: 44080 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.24 % / Biso Wilson estimate: 47.98 Å2 / Net I/σ(I): 10.82
Reflection shellResolution: 2.3→2.35 Å / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
autoXDSdata reduction
autoXDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DGI

4dgi


Resolution: 2.303→39.597 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 27.31 / Stereochemistry target values: ML
Details: The Rmeas for the data collection is 0.161 (overall data)
RfactorNum. reflection% reflection
Rfree0.2574 2215 5.03 %
Rwork0.2468 --
obs0.2474 44006 99.83 %
all-41792 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 2.3 Å
Refinement stepCycle: LAST / Resolution: 2.303→39.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6626 0 0 165 6791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0286797
X-RAY DIFFRACTIONf_angle_d1.9339247
X-RAY DIFFRACTIONf_dihedral_angle_d15.782403
X-RAY DIFFRACTIONf_chiral_restr0.1671040
X-RAY DIFFRACTIONf_plane_restr0.0131179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3029-2.3530.34711380.34062504X-RAY DIFFRACTION98
2.353-2.40770.32091370.34982592X-RAY DIFFRACTION100
2.4077-2.46790.39551380.34012569X-RAY DIFFRACTION100
2.4679-2.53460.34021320.32872574X-RAY DIFFRACTION100
2.5346-2.60920.34461300.31692600X-RAY DIFFRACTION100
2.6092-2.69340.30351400.31722567X-RAY DIFFRACTION100
2.6934-2.78970.32931460.31042564X-RAY DIFFRACTION100
2.7897-2.90130.32041240.29822605X-RAY DIFFRACTION100
2.9013-3.03330.30671300.28082623X-RAY DIFFRACTION100
3.0333-3.19320.32081490.27432578X-RAY DIFFRACTION100
3.1932-3.39310.29911610.25672590X-RAY DIFFRACTION100
3.3931-3.6550.25481340.23832625X-RAY DIFFRACTION100
3.655-4.02240.22661500.21842625X-RAY DIFFRACTION100
4.0224-4.60370.16861310.19122650X-RAY DIFFRACTION100
4.6037-5.79730.19841380.22684X-RAY DIFFRACTION100
5.7973-39.60310.23581370.23262841X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.0193 Å / Origin y: -13.508 Å / Origin z: 27.3858 Å
111213212223313233
T0.3912 Å2-0.0266 Å2-0.037 Å2-0.3517 Å20.0073 Å2--0.4468 Å2
L-0.1498 °2-0.1973 °20.0299 °2-0.3556 °2-0.1949 °2--0.0682 °2
S-0.0202 Å °0.0084 Å °-0.0082 Å °-0.0262 Å °0.021 Å °0.0284 Å °-0.0098 Å °-0.0005 Å °-0.0011 Å °
Refinement TLS groupSelection details: all

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