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- PDB-6pq5: AGAAAA segment 113-118 from human prion -

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Basic information

Entry
Database: PDB / ID: 6pq5
TitleAGAAAA segment 113-118 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
MALONATE ION / Major prion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
B: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0654
Polymers8612
Non-polymers2042
Water00
1
A: Major prion protein
B: Major prion protein
hetero molecules

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

A: Major prion protein
hetero molecules

A: Major prion protein
hetero molecules

B: Major prion protein

B: Major prion protein


Theoretical massNumber of molelcules
Total (without water)4,26016
Polymers3,4448
Non-polymers8168
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
crystal symmetry operation2_566-x,y+3/2,-z+11
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_565-x,y+3/2,-z1
Unit cell
Length a, b, c (Å)18.533, 9.508, 17.632
Angle α, β, γ (deg.)90.00, 120.54, 90.00
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: 430.456 Da / Num. of mol.: 2 / Fragment: UNP residues 113-118 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
Has ligand of interestN

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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: 1.55 Å3/Da / Density % sol: 20.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 35 mg/mL peptide in 1.92 M sodium malonate, pH 4.0 / PH range: 3.6-5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.8954 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 31, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8954 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. obs: 836 / % possible obs: 91.5 % / Redundancy: 3.4 % / Rsym value: 0.18 / Net I/σ(I): 5.42
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.4 % / Num. unique obs: 63 / Rsym value: 0.5 / % possible all: 64.9

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Processing

Software
NameVersionClassification
REFMAC5.4.0061refinement
DENZOdata reduction
SCALEPACK1.98.5data scaling
PHASER1.3.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→15.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.696 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27122 75 9 %RANDOM
Rwork0.23421 ---
obs0.23694 758 88.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å2-0.84 Å2
2---0.15 Å20 Å2
3----2.1 Å2
Refinement stepCycle: 1 / Resolution: 1.5→15.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60 0 14 0 74
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02170
X-RAY DIFFRACTIONr_bond_other_d0.0010.0228
X-RAY DIFFRACTIONr_angle_refined_deg1.1022.11792
X-RAY DIFFRACTIONr_angle_other_deg0.727370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.49510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.210
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0294
X-RAY DIFFRACTIONr_gen_planes_other00.0210
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4751.558
X-RAY DIFFRACTIONr_mcbond_other0.0761.524
X-RAY DIFFRACTIONr_mcangle_it0.782278
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.728312
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8374.514
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.494→1.668 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.329 23 -
Rwork0.292 163 -
obs--70.45 %

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