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- PDB-3hj5: Human prion protein variant V129 domain swapped dimer -

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Basic information

Entry
Database: PDB / ID: 3hj5
TitleHuman prion protein variant V129 domain swapped dimer
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 / 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/Doppel protein, beta-ribbon domain / Major Prion Protein / 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 / Major Prion Protein / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 20, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)32,2742
Polymers32,2742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-64 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.658, 72.015, 125.892
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16136.933 Da / Num. of mol.: 2 / Fragment: UNP residues 90-231
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
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Succinic acid, 15% PEG 6K, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 4758 / % possible obs: 91.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.066 / Χ2: 1.006 / Net I/σ(I): 16.39
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.2140.2773750.98173
3.21-3.344.50.2243750.95978
3.34-3.494.40.1654461.06987.1
3.49-3.684.40.1084571.00891.4
3.68-3.914.40.0894861.01497.2
3.91-4.214.40.0785111.03398.8
4.21-4.634.40.0555110.984100
4.63-5.34.40.0545110.95799.8
5.3-6.674.20.0595361.02299.1
6.67-503.80.0395501.02192.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0067refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→27.94 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 1 / SU B: 25.943 / SU ML: 0.458 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.624 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.299 461 9.7 %RANDOM
Rwork0.23 ---
obs0.237 4729 91.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.01 Å2 / Biso mean: 76.202 Å2 / Biso min: 62.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.1 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.1→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 0 0 1701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211742
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.9212355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98523.942104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75315297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2341514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211376
X-RAY DIFFRACTIONr_mcbond_it0.321.51009
X-RAY DIFFRACTIONr_mcangle_it0.63221646
X-RAY DIFFRACTIONr_scbond_it0.8683733
X-RAY DIFFRACTIONr_scangle_it1.5784.5709
LS refinement shellResolution: 3.101→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 34 -
Rwork0.326 249 -
all-283 -
obs--73.51 %

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