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- PDB-3nhd: GYVLGS segment 127-132 from human prion with V129 -

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Basic information

Entry
Database: PDB / ID: 3nhd
TitleGYVLGS segment 127-132 from human prion with V129
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Function / homology
Function and homology information


: / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport ...: / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of interleukin-2 production / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / negative regulation of amyloid-beta formation / cuprous ion binding / negative regulation of activated T cell proliferation / negative regulation of long-term synaptic potentiation / response to amyloid-beta / negative regulation of type II interferon production / : / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / positive regulation of protein tyrosine kinase activity / response to cadmium ion / inclusion body / regulation of peptidyl-tyrosine phosphorylation / cellular response to copper ion / molecular condensate scaffold activity / neuron projection maintenance / tubulin binding / protein sequestering activity / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / postsynapse / nuclear membrane / response to oxidative stress / protease binding / transmembrane transporter binding / postsynaptic density / learning or memory / molecular adaptor activity / regulation of cell cycle / cell cycle / copper ion binding / membrane raft / 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
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
ACETIC ACID / Major prion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 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 1.2Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major prion protein
B: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3094
Polymers1,1892
Non-polymers1202
Water362
1
A: Major prion protein
B: Major prion protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)7,85724
Polymers7,13612
Non-polymers72112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation3_455-x-1/2,y+1/2,-z1
crystal symmetry operation3_454-x-1/2,y+1/2,-z-11
crystal symmetry operation3_456-x-1/2,y+1/2,-z+11
Buried area180 Å2
ΔGint-1 kcal/mol
Surface area1740 Å2
Unit cell
Length a, b, c (Å)41.173, 18.959, 9.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 594.659 Da / Num. of mol.: 2 / Fragment: residues 127-132 / Mutation: M129V / Source method: obtained synthetically
Details: GYVLGS (residues 127-132 with V129) from human prion protein, synthesized
Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.57 Å3/Da / Density % sol: 21.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Sodium Acetate pH 5.5, PEG 10,000, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→90 Å / Num. obs: 637 / % possible obs: 91.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.193 / Χ2: 1.034 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.973.20.223311.00556.4
1.97-2.055.60.374531.01979.1
2.05-2.145.90.38601.15690.9
2.14-2.256.80.389671.003100
2.25-2.395.30.305651.05187.8
2.39-2.586.40.303581.028100
2.58-2.845.90.266700.998100
2.84-3.255.40.184771.06397.5
3.25-4.095.80.16681.00198.6
4.09-905.30.104881.01396.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.92 Å20.59 Å
Translation1.92 Å20.59 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: 1.92→20.58 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2942 / WRfactor Rwork: 0.2138 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.895 / SU B: 2.453 / SU ML: 0.077 / SU R Cruickshank DPI: 0.2994 / SU Rfree: 0.2197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 63 10.1 %RANDOM
Rwork0.2033 ---
obs0.2097 621 91.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 40.69 Å2 / Biso mean: 10.8356 Å2 / Biso min: 2.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.97 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.92→20.58 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms84 0 8 2 94
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02290
X-RAY DIFFRACTIONr_bond_other_d0.0010.0250
X-RAY DIFFRACTIONr_angle_refined_deg1.482.125118
X-RAY DIFFRACTIONr_angle_other_deg0.8013122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.083510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.255202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5281510
X-RAY DIFFRACTIONr_chiral_restr0.0930.212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02102
X-RAY DIFFRACTIONr_gen_planes_other00.0218
X-RAY DIFFRACTIONr_mcbond_it1.1311.562
X-RAY DIFFRACTIONr_mcbond_other0.2371.526
X-RAY DIFFRACTIONr_mcangle_it1.836288
X-RAY DIFFRACTIONr_scbond_it1.997328
X-RAY DIFFRACTIONr_scangle_it2.3884.530
LS refinement shellResolution: 1.92→2.144 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.268 13 -
Rwork0.148 116 -
all-129 -
obs--75.44 %

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