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- PDB-1i4m: Crystal structure of the human prion protein reveals a mechanism ... -

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Basic information

Entry
Database: PDB / ID: 1i4m
TitleCrystal structure of the human prion protein reveals a mechanism for oligomerization
ComponentsMAJOR PRION PROTEIN
KeywordsMEMBRANE PROTEIN / DOMAIN-SWAPPED DIMER
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 / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport ...: / 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 / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of interleukin-2 production / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / negative regulation of amyloid-beta formation / cuprous ion binding / negative regulation of activated T cell proliferation / negative regulation of long-term synaptic potentiation / response to amyloid-beta / negative regulation of type II interferon production / : / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / positive regulation of protein tyrosine kinase activity / response to cadmium ion / inclusion body / regulation of peptidyl-tyrosine phosphorylation / cellular response to copper ion / neuron projection maintenance / molecular condensate scaffold activity / tubulin binding / protein sequestering 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 / response to oxidative stress / protease binding / transmembrane transporter binding / postsynaptic density / learning or memory / molecular adaptor activity / regulation of cell cycle / cell cycle / copper ion binding / membrane raft / 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 / MIR / Resolution: 2 Å
AuthorsKnaus, K.J. / Morillas, M. / Swietnicki, W. / Malone, M. / Surewicz, W.K. / Yee, V.C.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of the human prion protein reveals a mechanism for oligomerization.
Authors: Knaus, K.J. / Morillas, M. / Swietnicki, W. / Malone, M. / Surewicz, W.K. / Yee, V.C.
History
DepositionFeb 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR PRION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9754
Polymers12,7151
Non-polymers2603
Water2,036113
1
A: MAJOR PRION PROTEIN
hetero molecules

A: MAJOR PRION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9518
Polymers25,4302
Non-polymers5216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area6800 Å2
ΔGint-89 kcal/mol
Surface area11690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.441, 85.707, 40.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-37-

HOH

DetailsThe second half of the dimer is generated by the two fold axis: x, -y, -z+1

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Components

#1: Protein MAJOR PRION PROTEIN / PRP


Mass: 12715.145 Da / Num. of mol.: 1 / Fragment: FRAGMENT 119-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: SODIUM CHLORIDE, TRIS HYDROCHLORIDE, CADMIUM CHLORIDE, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
20.1 MTris-HCl1reservoirpH8.
33 M1reservoirNaCl
45 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0688 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 24, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0688 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 10079 / Num. obs: 10069 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 36
Reflection shellResolution: 2→2.07 Å / Redundancy: 6 % / Rmerge(I) obs: 0.239 / % possible all: 84.8
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 84.8 % / Mean I/σ(I) obs: 5.5

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→27.1 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1594254.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 728 7.2 %RANDOM
Rwork0.206 ---
all0.225 10412 --
obs0.206 10069 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.37 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1-17.28 Å20 Å20 Å2
2---4.71 Å20 Å2
3----12.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-30 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 3 113 1005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3186 37 6.8 %
Rwork0.2537 1372 -
obs-571 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 7.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
% reflection Rfree: 6.8 %

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