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- PDB-3md4: Prion peptide -

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Basic information

Entry
Database: PDB / ID: 3md4
TitlePrion peptide
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN / Prion peptide / Amyloid / Cell membrane / Disulfide bond / Glycoprotein / Golgi apparatus / GPI-anchor / Lipoprotein / Membrane / Prion
Function / homology
Function and homology information


negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / NCAM1 interactions / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding ...negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / NCAM1 interactions / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of protein processing / negative regulation of dendritic spine maintenance / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of membrane / negative regulation of interleukin-2 production / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / response to amyloid-beta / cuprous ion binding / 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 / inclusion body / neuron projection maintenance / tubulin binding / positive regulation of calcium-mediated signaling / cellular response to copper ion / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to xenobiotic stimulus / cellular response to amyloid-beta / terminal bouton / positive regulation of neuron apoptotic process / signaling receptor activity / protein-folding chaperone binding / amyloid-beta binding / response to oxidative stress / protease binding / nuclear membrane / microtubule binding / molecular adaptor activity / transmembrane transporter binding / learning or memory / postsynapse / regulation of cell cycle / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / 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/Doppel alpha-helical domain
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.15 Å
AuthorsYee, V.C. / Lee, S.
CitationJournal: To be Published
Title: Diversity in the cross-beta spine structure of prion peptides
Authors: Lee, S. / Yee, V.C.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Major prion protein


Theoretical massNumber of molelcules
Total (without water)1,2532
Polymers1,2532
Non-polymers00
Water1629
1
A: Major prion protein


  • defined by author
  • 627 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6271
Polymers6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major prion protein


  • defined by author
  • 627 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6271
Polymers6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-2 kcal/mol
Surface area1490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)9.439, 17.792, 44.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTwo molecules in the asymmetric unit, but the biological unit is believed to be a monomer

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Components

#1: Protein/peptide Major prion protein / PrP


Mass: 626.724 Da / Num. of mol.: 2 / Fragment: PrP 127-132 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P04156
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 1.49 Å3/Da / Density % sol: 17.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 2627 / % possible obs: 87.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.102 / Χ2: 1.001 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.15-1.1930.1861971.094165.2
1.19-1.243.20.1712010.981175.8
1.24-1.33.90.1592401.13180.3
1.3-1.364.40.162381.064181
1.36-1.455.20.1482660.952195
1.45-1.565.70.122890.959196.3
1.56-1.726.40.1182750.937195.2
1.72-1.976.90.1072980.971196.1
1.97-2.487.50.0833070.977199
2.48-507.20.0813161.07190.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0088refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.15→22.28 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 1.155 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.169 116 4.4 %RANDOM
Rwork0.149 ---
obs0.15 2612 87.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 30.33 Å2 / Biso mean: 6.768 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2--0.36 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.15→22.28 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms86 0 0 9 95
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02192
X-RAY DIFFRACTIONr_angle_refined_deg1.4542.103121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.404512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.937202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.671517
X-RAY DIFFRACTIONr_chiral_restr0.1250.211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0268
X-RAY DIFFRACTIONr_mcbond_it1.8391.559
X-RAY DIFFRACTIONr_mcangle_it2.939288
X-RAY DIFFRACTIONr_scbond_it3.258333
X-RAY DIFFRACTIONr_scangle_it4.1564.532
X-RAY DIFFRACTIONr_rigid_bond_restr1.508392
X-RAY DIFFRACTIONr_sphericity_free9.673312
X-RAY DIFFRACTIONr_sphericity_bonded5.066391
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 7 -
Rwork0.15 136 -
all-143 -
obs--60.59 %

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