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- PDB-4e1i: Fragment of human prion protein -

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Basic information

Entry
Database: PDB / ID: 4e1i
TitleFragment of human prion protein
Components(Major prion protein) x 2
KeywordsCELL CYCLE / beta prism / amyloid-related oligomer / PROTEIN FIBRIL
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 / molecular replacement / Resolution: 2.03 Å
AuthorsApostol, M.I. / Surewicz, W.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Crystal structure of a human prion protein fragment reveals a motif for oligomer formation.
Authors: Apostol, M.I. / Perry, K. / Surewicz, W.K.
History
DepositionMar 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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
C: Major prion protein
D: Major prion protein
E: Major prion protein
F: Major prion protein
G: Major prion protein
H: Major prion protein
I: Major prion protein
J: Major prion protein
K: Major prion protein
L: Major prion protein


Theoretical massNumber of molelcules
Total (without water)8,54812
Polymers8,54812
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-57 kcal/mol
Surface area4520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.338, 41.217, 46.600
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/peptide
Major prion protein / PrP / ASCR / PrP27-30 / PrP33-35C


Mass: 700.784 Da / Num. of mol.: 6 / Fragment: UNP residues 177-182 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#2: Protein/peptide
Major prion protein / PrP / ASCR / PrP27-30 / PrP33-35C


Mass: 723.858 Da / Num. of mol.: 6 / Fragment: UNP residues 211-216 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFRAGMENT OF HUMAN PRION PROTEIN FROM HELIX 2 AND 3
Has protein modificationY
Source detailsSEGMENTS CORRESPONDING TO RESIDUES 177-182 AND 211-216 OF HUMAN PRION WAS LINKED BY DISULFIDE BOND ...SEGMENTS CORRESPONDING TO RESIDUES 177-182 AND 211-216 OF HUMAN PRION WAS LINKED BY DISULFIDE BOND BETWEEN 179 AND 214 DURING SYNTHESIS

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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: 1.99 Å3/Da / Density % sol: 38.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Bis Tris pH 5.5, 25% PEG 3350, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.028→30.873 Å / Num. all: 4685 / Num. obs: 4685 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rsym value: 0.064 / Net I/σ(I): 20.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.028-2.143.80.1963.923126050.19690.7
2.14-2.2760.1744.438066370.17499.9
2.27-2.426.10.145.536696060.14100
2.42-2.626.20.1067.234695640.106100
2.62-2.876.10.0937.932085220.093100
2.87-3.216.10.05812.529254800.058100
3.21-3.76.10.04415.425864260.044100
3.7-4.535.90.03817.421853720.03899.9
4.53-6.415.70.03715.316522890.03799.8
6.41-41.21750.03816.19141840.03898.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.03 Å26.83 Å
Translation2.03 Å26.83 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementResolution: 2.03→23.3 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.172 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.253 212 4.6 %RANDOM
Rwork0.187 ---
obs0.19 4649 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.03→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms576 0 0 67 643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021594
X-RAY DIFFRACTIONr_bond_other_d00.02334
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.945800
X-RAY DIFFRACTIONr_angle_other_deg0.6493849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.208563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.90427.81332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08515111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.298
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02624
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0276
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_it1.5341.5368
X-RAY DIFFRACTIONr_mcbond_other0.4121.5134
X-RAY DIFFRACTIONr_mcangle_it2.6072602
X-RAY DIFFRACTIONr_scbond_it4.2823226
X-RAY DIFFRACTIONr_scangle_it6.294.5197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 14 -
Rwork0.205 275 -
obs--81.18 %
Refinement TLS params.Method: refined / Origin x: -12.5408 Å / Origin y: 1.9013 Å / Origin z: 8.8177 Å
111213212223313233
T0.073 Å20.0483 Å20.0413 Å2-0.0573 Å20.015 Å2--0.0245 Å2
L3.966 °21.2601 °23.8912 °2-2.7367 °20.905 °2--5.5905 °2
S0.0837 Å °-0.071 Å °-0.0777 Å °0.1232 Å °0.2043 Å °-0.038 Å °-0.2999 Å °-0.3194 Å °-0.288 Å °

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