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- PDB-6pqa: GAVVGG segment 119-124 from human prion -

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Basic information

Entry
Database: PDB / ID: 6pqa
TitleGAVVGG segment 119-124 from human prion
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 / lamin binding / positive 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 / NCAM1 interactions / type 5 metabotropic glutamate receptor binding ...negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / positive 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 / NCAM1 interactions / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / cupric ion binding / regulation of potassium ion transmembrane transport / 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 / cuprous ion binding / response to amyloid-beta / 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 / 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 / molecular condensate scaffold activity / protein destabilization / terminal bouton / protein homooligomerization / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / protease binding / microtubule binding / molecular adaptor activity / nuclear membrane / response to oxidative stress / 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 / protein-containing complex binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 Å
AuthorsApostol, M.I. / Sawaya, M.R. / Eisenberg, D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG029430 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG029430-05 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007185 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core.
Authors: Calina Glynn / Michael R Sawaya / Peng Ge / Marcus Gallagher-Jones / Connor W Short / Ronquiajah Bowman / Marcin Apostol / Z Hong Zhou / David S Eisenberg / Jose A Rodriguez /
Abstract: Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease- ...Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease-resistant fibril formed in vitro spontaneously by a 9.7-kDa unglycosylated fragment of the human prion protein. This human prion fibril contains two protofilaments intertwined with screw symmetry and linked by a tightly packed hydrophobic interface. Each protofilament consists of an extended beta arch formed by residues 106 to 145 of the prion protein, a hydrophobic and highly fibrillogenic disease-associated segment. Such structures of prion polymorphs serve as blueprints on which to evaluate the potential impact of sequence variants on prion disease.
History
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 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


Theoretical massNumber of molelcules
Total (without water)4591
Polymers4591
Non-polymers00
Water543
1
A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)3,6688
Polymers3,6688
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
crystal symmetry operation2_654-x+1,y+1/2,-z-11
crystal symmetry operation2_754-x+2,y+1/2,-z-11
crystal symmetry operation2_854-x+3,y+1/2,-z-11
Unit cell
Length a, b, c (Å)4.786, 12.810, 20.771
Angle α, β, γ (deg.)90.000, 92.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 458.510 Da / Num. of mol.: 1 / Fragment: UNP residues 119-124 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#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: 11.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10 mg/mL peptide in 2.4 M sodium malonate, pH 7.0 / PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9465 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 13, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9465 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 455 / % possible obs: 93.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.145 / Rsym value: 0.15 / Χ2: 1.052 / Net I/σ(I): 31.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRsym valueΧ2% possible all
1.45-1.52.80.311410.311.00693.2
1.5-1.563.70.274481.09984.2
1.56-1.634.50.187410.96280.4
1.63-1.726.10.218361.145100
1.72-1.836.50.242461.124100
1.83-1.976.10.137481.291100
1.97-2.176.20.143510.888100
2.17-2.485.90.152501.00394.3
2.48-3.126.40.132440.984100
3.12-305.40.095500.99889.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACK1.97.8data scaling
PHASER1.3.2phasing
REFMAC5.4.0061refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→20.75 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.878 / SU B: 1.099 / SU ML: 0.044 / SU R Cruickshank DPI: 0.1047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 46 10.6 %RANDOM
Rwork0.1802 ---
obs0.1867 389 92.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 33.98 Å2 / Biso mean: 4.425 Å2 / Biso min: 0.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.28 Å2
2--0.88 Å20 Å2
3----0.6 Å2
Refinement stepCycle: final / Resolution: 1.46→20.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32 0 0 3 35
Biso mean---31.46 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02231
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216
X-RAY DIFFRACTIONr_angle_refined_deg1.0812.03941
X-RAY DIFFRACTIONr_angle_other_deg0.554340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.267152
X-RAY DIFFRACTIONr_chiral_restr0.0730.25
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0239
X-RAY DIFFRACTIONr_gen_planes_other00.025
LS refinement shellResolution: 1.46→1.627 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.293 10 -
Rwork0.204 108 -
obs--83.69 %

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