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- PDB-4n9o: Probing the N-terminal beta-sheet conversion in the crystal struc... -

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Basic information

Entry
Database: PDB / ID: 4n9o
TitleProbing the N-terminal beta-sheet conversion in the crystal structure of the human prion protein bound to a Nanobody
Components
  • Major prion protein
  • Nanobody Nb484
KeywordsMEMBRANE PROTEIN/PROTEIN BINDING / Prion-like fold / antibody / nanobody / MEMBRANE PROTEIN-PROTEIN BINDING complex
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 / terminal bouton / protein destabilization / 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, 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsAbskharon, R.N.N. / Giachin, G. / Wohlkonig, A. / Soror, S.H. / Pardon, E. / Legname, G. / Steyaert, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Probing the N-Terminal beta-Sheet Conversion in the Crystal Structure of the Human Prion Protein Bound to a Nanobody.
Authors: Abskharon, R.N. / Giachin, G. / Wohlkonig, A. / Soror, S.H. / Pardon, E. / Legname, G. / Steyaert, J.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major prion protein
B: Nanobody Nb484


Theoretical massNumber of molelcules
Total (without water)30,4182
Polymers30,4182
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.857, 45.781, 45.092
Angle α, β, γ (deg.)90.000, 96.230, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16168.997 Da / Num. of mol.: 1 / Fragment: C-terminal 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
#2: Antibody Nanobody Nb484


Mass: 14248.748 Da / Num. of mol.: 1 / Fragment: Nb484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES-Na pH 7, 15% PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→65.54 Å / Num. all: 42399 / Num. obs: 42399 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.058 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.584.10.242.82490760920.2497.8
1.58-1.684.10.16842385357790.16898.2
1.68-1.794.10.1235.42245654550.12398.5
1.79-1.944.10.096.52094251110.0998.8
1.94-2.124.10.0648.81925847270.06499.3
2.12-2.3740.0569.71731342890.05699.5
2.37-2.7440.0559.71515337940.05599.7
2.74-3.353.90.04510.71258232250.04599.7
3.35-4.743.80.04310.9958925160.04399.4
4.74-25.18540.0479.5563614110.04798.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.15 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.18 Å
Translation2.5 Å25.18 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W9E

2w9e


Resolution: 1.5→24.93 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1913 / WRfactor Rwork: 0.1534 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8918 / SU B: 2.126 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0688 / SU Rfree: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1843 2137 5.1 %RANDOM
Rwork0.1497 ---
obs0.1514 42305 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.17 Å2 / Biso mean: 16.7219 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 171 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191861
X-RAY DIFFRACTIONr_bond_other_d0.0010.021686
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.932512
X-RAY DIFFRACTIONr_angle_other_deg0.89233866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2285233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.40223.26395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7815310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1181517
X-RAY DIFFRACTIONr_chiral_restr0.1230.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_mcbond_it2.5781.395926
X-RAY DIFFRACTIONr_mcbond_other2.5731.392925
X-RAY DIFFRACTIONr_mcangle_it2.9722.0941155
X-RAY DIFFRACTIONr_rigid_bond_restr5.52933547
X-RAY DIFFRACTIONr_sphericity_free19.241562
X-RAY DIFFRACTIONr_sphericity_bonded9.2253616
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 166 -
Rwork0.166 2857 -
all-3023 -
obs--97.17 %

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