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- PDB-3heq: Human prion protein variant D178N with M129 -

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Basic information

Entry
Database: PDB / ID: 3heq
TitleHuman prion protein variant D178N with M129
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN / Prion protein / Cell membrane / Disease mutation / Disulfide bond / Glycoprotein / Golgi apparatus / GPI-anchor / Lipoprotein / Membrane / Polymorphism / Prion
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 / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions ...: / 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 / positive regulation of protein targeting to membrane / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / positive regulation of protein tyrosine kinase activity / long-term memory / response to cadmium ion / inclusion body / regulation of peptidyl-tyrosine phosphorylation / cellular response to copper ion / neuron projection maintenance / tubulin binding / protein sequestering activity / molecular condensate scaffold 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 / protease binding / response to oxidative stress / transmembrane transporter binding / postsynaptic density / learning or memory / molecular adaptor activity / regulation of cell cycle / cell cycle / membrane raft / copper ion binding / 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/Doppel protein, beta-ribbon domain / Major Prion Protein / 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 protein, beta-ribbon domain / Major Prion Protein / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Major prion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.8 Å
AuthorsLee, S. / Antony, L. / Hartmann, R. / Knaus, K.J. / Surewicz, K. / Surewicz, W.K. / Yee, V.C.
CitationJournal: Embo J. / Year: 2010
Title: Conformational diversity in prion protein variants influences intermolecular beta-sheet formation.
Authors: Lee, S. / Antony, L. / Hartmann, R. / Knaus, K.J. / Surewicz, K. / Surewicz, W.K. / Yee, V.C.
History
DepositionMay 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)32,5614
Polymers32,3362
Non-polymers2252
Water3,909217
1
A: Major prion protein
hetero molecules

B: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5614
Polymers32,3362
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y+1/2,-z+3/41
Buried area1720 Å2
ΔGint-18 kcal/mol
Surface area11740 Å2
MethodPISA
2
A: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2802
Polymers16,1681
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2802
Polymers16,1681
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.489, 57.489, 168.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 16168.013 Da / Num. of mol.: 2 / Fragment: UNP residues 90-231 / Mutation: D178N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRNP, PRIP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P04156
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, 0.2 M Mg acetate, 5% PEG4K, 5mM CdCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorDate: Mar 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 26006 / % possible obs: 95.8 % / Rmerge(I) obs: 0.052 / Χ2: 0.993 / Net I/σ(I): 36.939
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.860.18721321.05480.3
1.86-1.940.20723531.03389.1
1.94-2.030.14725520.98296.8
2.03-2.130.11126231.02597.3
2.13-2.270.0925841.00297.9
2.27-2.440.06526580.99399.1
2.44-2.690.05526850.97199.2
2.69-3.080.04527181.04199.7
3.08-3.880.04827670.96399.2
3.88-1000.04229340.96598.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SIR / Resolution: 1.8→40.12 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.358 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1312 5.1 %RANDOM
Rwork0.206 ---
obs0.207 25974 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.32 Å2 / Biso mean: 26.635 Å2 / Biso min: 9.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 2 217 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211773
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.922396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2295204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33723.874111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45915307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7221516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211418
X-RAY DIFFRACTIONr_mcbond_it1.0431.51014
X-RAY DIFFRACTIONr_mcangle_it1.90221653
X-RAY DIFFRACTIONr_scbond_it2.3393759
X-RAY DIFFRACTIONr_scangle_it3.7014.5740
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 76 -
Rwork0.265 1451 -
all-1527 -
obs--78.11 %

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