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- PDB-3nve: MMHFGN segment 138-143 from Syrian Hamster prion -

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Basic information

Entry
Database: PDB / ID: 3nve
TitleMMHFGN segment 138-143 from Syrian Hamster prion
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Function / homology
Function and homology information


regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan 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 / negative regulation of calcineurin-NFAT signaling cascade ...regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan 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 / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / : / negative regulation of type II interferon production / positive regulation of protein targeting to membrane / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / 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 / 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 / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / amyloid fibril formation / learning or memory / regulation of cell cycle / membrane raft / cell cycle / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / 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
Similarity search - Domain/homology
Biological speciesMesocricetus auratus (golden hamster)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsApostol, M.I. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Biochemistry / Year: 2011
Title: Atomic structures suggest determinants of transmission barriers in Mammalian prion disease.
Authors: Apostol, M.I. / Wiltzius, J.J. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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)1,4742
Polymers1,4742
Non-polymers00
Water543
1
A: Major prion protein
B: Major prion protein
x 6


Theoretical massNumber of molelcules
Total (without water)8,84312
Polymers8,84312
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area430 Å2
ΔGint-2 kcal/mol
Surface area1550 Å2
Unit cell
Length a, b, c (Å)9.513, 11.784, 36.541
Angle α, β, γ (deg.)90.000, 93.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 736.882 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: MMHFGN (UNP residues 138-143) from Syrian hamster prion
Source: (synth.) Mesocricetus auratus (golden hamster) / References: UniProt: P04273
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.39 Å3/Da / Density % sol: 11.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2 M Ammonium sulfate, 200 mM BisTris pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→80 Å / Num. obs: 939 / % possible obs: 97.2 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.162 / Χ2: 1.021 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.765.80.15730.99588
1.76-1.838.80.2051011.0199
1.83-1.9110.60.156940.98691.3
1.91-2.0211.30.143820.98798.8
2.02-2.1411.70.157941.044100
2.14-2.3111.50.149991.001100
2.31-2.5411.40.159931.0695.9
2.54-2.9111.40.149930.99898.9
2.911-3.6611.20.1671051.093100
3.662-8010.70.163105199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.73 Å18.24 Å
Translation1.73 Å18.24 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.3382 / WRfactor Rwork: 0.226 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7689 / SU B: 3.692 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1837 / SU Rfree: 0.1752 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 139 14.9 %RANDOM
Rwork0.1958 ---
obs0.206 935 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 39.51 Å2 / Biso mean: 20.7686 Å2 / Biso min: 14.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.12 Å2
2---0.11 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms100 0 0 3 103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02102
X-RAY DIFFRACTIONr_bond_other_d0.0010.0266
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.871132
X-RAY DIFFRACTIONr_angle_other_deg0.9483158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.404510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.63623.3336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3711518
X-RAY DIFFRACTIONr_chiral_restr0.0850.210
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0224
X-RAY DIFFRACTIONr_mcbond_it1.11.558
X-RAY DIFFRACTIONr_mcbond_other0.291.524
X-RAY DIFFRACTIONr_mcangle_it2.024288
X-RAY DIFFRACTIONr_scbond_it3.55344
X-RAY DIFFRACTIONr_scangle_it4.7214.544
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.601 9 -
Rwork0.291 45 -
all-54 -
obs--85.71 %

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