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- PDB-3nhc: GYMLGS segment 127-132 from human prion with M129 -

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Basic information

Entry
Database: PDB / ID: 3nhc
TitleGYMLGS segment 127-132 from human prion with M129
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Function / homology
Function and homology information


negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / positive regulation of glutamate receptor signaling pathway / lamin binding / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / type 5 metabotropic glutamate receptor binding ...negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / positive regulation of glutamate receptor signaling pathway / lamin binding / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / cupric ion binding / negative regulation of protein processing / 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 / positive regulation of protein targeting to membrane / intracellular copper ion homeostasis / long-term memory / regulation of peptidyl-tyrosine phosphorylation / negative regulation of protein phosphorylation / response to cadmium ion / inclusion body / cellular response to copper ion / neuron projection maintenance / tubulin binding / positive regulation of calcium-mediated signaling / molecular function activator activity / positive regulation of protein localization to plasma membrane / negative regulation of DNA-binding transcription factor activity / molecular condensate scaffold activity / terminal bouton / protein destabilization / protein homooligomerization / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / protease binding / microtubule binding / nuclear membrane / molecular adaptor activity / transmembrane transporter binding / response to oxidative stress / learning or memory / regulation of cell cycle / postsynapse / postsynaptic density / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsApostol, M.I. / Eisenberg, D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease.
Authors: Apostol, M.I. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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
Water724
1
A: Major prion protein
B: Major prion protein
x 6


Theoretical massNumber of molelcules
Total (without water)7,52112
Polymers7,52112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
crystal symmetry operation4_565x+1/2,-y+3/2,-z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)18.150, 9.553, 45.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 626.724 Da / Num. of mol.: 2 / Fragment: residues 127-132 / Source method: obtained synthetically
Details: GYMLGS (residues 127-132 with M129) from human prion protein, synthesized
Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.56 Å3/Da / Density % sol: 21.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Tris pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0048 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0048 Å / Relative weight: 1
ReflectionResolution: 1.55→90 Å / Num. obs: 1163 / % possible obs: 90.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.186 / Χ2: 1.066 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.55-1.615.10.398971.01678.2
1.61-1.674.90.4431001.10287.7
1.67-1.755.20.4041121.00893.3
1.75-1.845.30.3241111.23589.5
1.84-1.955.40.2421051.16582
1.95-2.160.2281101.08896.5
2.1-2.325.90.2411221.03591.7
2.32-2.655.80.1911181.05493.7
2.65-3.345.50.1541360.99997.1
3.34-904.80.1371521.00396.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å9.59 Å
Translation1.8 Å9.59 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→22.58 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.2435 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8229 / SU B: 3.961 / SU ML: 0.065 / SU R Cruickshank DPI: 0.3193 / SU Rfree: 0.1323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 120 10.5 %RANDOM
Rwork0.2213 ---
obs0.2246 1146 90.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.51 Å2 / Biso mean: 14.6467 Å2 / Biso min: 6.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å20 Å2
2---1.56 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.57→22.58 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms86 0 0 4 90
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02197
X-RAY DIFFRACTIONr_bond_other_d0.0010.0264
X-RAY DIFFRACTIONr_angle_refined_deg1.5412.122129
X-RAY DIFFRACTIONr_angle_other_deg0.8653159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.976513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.113202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6371518
X-RAY DIFFRACTIONr_chiral_restr0.1220.212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0220
X-RAY DIFFRACTIONr_mcbond_it1.3281.563
X-RAY DIFFRACTIONr_mcbond_other0.4021.528
X-RAY DIFFRACTIONr_mcangle_it2.218295
X-RAY DIFFRACTIONr_scbond_it3.555334
X-RAY DIFFRACTIONr_scangle_it4.9374.532
X-RAY DIFFRACTIONr_rigid_bond_restr1.6933161
X-RAY DIFFRACTIONr_sphericity_free5.06334
X-RAY DIFFRACTIONr_sphericity_bonded1.8573159
LS refinement shellResolution: 1.569→1.754 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.328 33 -
Rwork0.233 248 -
all-281 -
obs--84.13 %

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