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- PDB-7fhq: Solution structure of the pathogenic mutant G131V of Human prion ... -

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Basic information

Entry
Database: PDB / ID: 7fhq
TitleSolution structure of the pathogenic mutant G131V of Human prion protein (91-231)
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN
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)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, H. / Lin, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670741 China
CitationJournal: To Be Published
Title: Solution structure of the pathogenic mutant G131V of Human prion protein
Authors: Zhang, H. / Lin, D.
History
DepositionJul 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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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)16,2851
Polymers16,2851
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 16285.220 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRNP, ALTPRP, PRIP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P04156

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
1111isotropic12D (HB)CB(CGCD)HD
1121isotropic12D (HB)CB(CGCDCE)HE
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCA
161isotropic13D HN(CO)CA
171isotropic13D HNCO
181isotropic13D HN(CA)CO
1151isotropic13D HBHA(CO)NH
1161isotropic13D H(CCO)NH
191isotropic13D (H)CCH-TOCSY
1141isotropic13D C(CO)NH
1131isotropic13D 1H-15N TOCSY
1101isotropic13D (H)CCH-TOCSY
1183isotropic13D 1H-15N NOESY
1172isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 % v/v [U-100% 2H] D2O, 90 % v/v H2O, 20 mM sodium acetate, 0.02 % w/v sodium azide, 0.65 mM [U-99% 13C; U-99% 15N] HuPrP G131V, 90% H2O/10% D2O15N/13C_sample90% H2O/10% D2O
solution310 % v/v [U-100% 2H] D2O, 90 % v/v H2O, 20 mM sodium acetate, 0.02 % w/v sodium azide, 0.65 mM [U-99% 15N] HuPrP G131V, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution2100 % v/v [U-100% 2H] D2O, 20 mM sodium acetate, 0.02 % w/v sodium azide, 0.65 mM [U-99% 13C; U-99% 15N] HuPrP G131V, 100% D2O15N/13C_sample_100%D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 % v/vD2O[U-100% 2H]1
90 % v/vH2Onatural abundance1
20 mMsodium acetatenatural abundance1
0.02 % w/vsodium azidenatural abundance1
0.65 mMHuPrP G131V[U-99% 13C; U-99% 15N]1
10 % v/vD2O[U-100% 2H]3
90 % v/vH2Onatural abundance3
20 mMsodium acetatenatural abundance3
0.02 % w/vsodium azidenatural abundance3
0.65 mMHuPrP G131V[U-99% 15N]3
100 % v/vD2O[U-100% 2H]2
20 mMsodium acetatenatural abundance2
0.02 % w/vsodium azidenatural abundance2
0.65 mMHuPrP G131V[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 20 mM / Label: NMR_condition / pH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKY1.4.7Lee W., Tonelli M., Markley J. L.chemical shift assignment
CNSAria2.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSAria2.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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