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- PDB-3nvf: IIHFGS segment 138-143 from human prion -

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Basic information

Entry
Database: PDB / ID: 3nvf
TitleIIHFGS segment 138-143 from human prion
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Function / homology
Function and homology information


positive regulation of glutamate receptor signaling pathway / 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 / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions ...positive regulation of glutamate receptor signaling pathway / 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 / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / response to amyloid-beta / : / negative regulation of type II interferon production / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / long-term memory / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / tubulin binding / 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 / negative regulation of DNA-binding transcription factor activity / 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 / protein-folding chaperone binding / postsynapse / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / cell cycle / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7922
Polymers6741
Non-polymers1181
Water0
1
A: Major prion protein
hetero molecules
x 10


Theoretical massNumber of molelcules
Total (without water)7,92020
Polymers6,73810
Non-polymers1,18210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_557x,y,z+21
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_553x,y,z-21
crystal symmetry operation2_657-x+1,-y,z+21
crystal symmetry operation2_656-x+1,-y,z+11
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation2_654-x+1,-y,z-11
crystal symmetry operation2_653-x+1,-y,z-21
Unit cell
Length a, b, c (Å)27.546, 31.017, 4.804
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: 673.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IIHFGS (UNP residues 138-143) from human prion / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

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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: 1.52 Å3/Da / Density % sol: 19.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100mM Tris pH 7.4, 25% MPD, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 225 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. obs: 443 / % possible obs: 85.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.216 / Χ2: 1.137 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.941.70.395631.42467
1.94-2.132.30.327831.29485.6
2.13-2.443.20.314890.96478.8
2.44-3.085.40.244871.062100
3.08-905.10.1971211.19994.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å20.6 Å
Translation2.2 Å20.6 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2521 / WRfactor Rwork: 0.2013 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8682 / SU B: 4.009 / SU ML: 0.111 / SU R Cruickshank DPI: 0.2379 / SU Rfree: 0.1668 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 40 9.2 %RANDOM
Rwork0.2118 ---
obs0.2133 433 86.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.98 Å2 / Biso mean: 20.8202 Å2 / Biso min: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.6 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms48 0 8 0 56
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02156
X-RAY DIFFRACTIONr_bond_other_d0.0010.0235
X-RAY DIFFRACTIONr_angle_refined_deg1.6572.04375
X-RAY DIFFRACTIONr_angle_other_deg0.693384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg52.201202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.817157
X-RAY DIFFRACTIONr_chiral_restr0.0530.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0212
X-RAY DIFFRACTIONr_mcbond_it0.5231.529
X-RAY DIFFRACTIONr_mcbond_other0.1571.512
X-RAY DIFFRACTIONr_mcangle_it0.853246
X-RAY DIFFRACTIONr_scbond_it1.22327
X-RAY DIFFRACTIONr_scangle_it1.6734.529
LS refinement shellResolution: 1.8→2.011 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.33 4 -
Rwork0.382 87 -
all-91 -
obs--72.22 %

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