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- PDB-6her: Mouse prion protein in complex with Nanobody 484 -

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Basic information

Entry
Database: PDB / ID: 6her
TitleMouse prion protein in complex with Nanobody 484
Components
  • Major prion protein
  • Nanobody 484
KeywordsPROTEIN BINDING / Prion / Nanobody / aggregation / B-sheet
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / negative regulation of interleukin-17 production ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / nucleobase-containing compound metabolic process / response to copper ion / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / activation of protein kinase activity / 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 / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / side of membrane / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / protein sequestering activity / tubulin binding / negative regulation of protein phosphorylation / molecular condensate scaffold activity / 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 / regulation of protein localization / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / mitochondrial outer membrane / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / learning or memory / membrane raft / copper ion binding / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 Å
AuthorsSoror, S.H. / Abskharon, R. / Wohlkonig, A.
CitationJournal: Plos Pathog. / Year: 2019
Title: Structural evidence for the critical role of the prion protein hydrophobic region in forming an infectious prion.
Authors: Abskharon, R. / Wang, F. / Wohlkonig, A. / Ruan, J. / Soror, S. / Giachin, G. / Pardon, E. / Zou, W. / Legname, G. / Ma, J. / Steyaert, J.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein
B: Nanobody 484
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8046
Polymers26,4232
Non-polymers3804
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-46 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.328, 74.646, 116.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12918.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prnp, Prn-p, Prp / Production host: Escherichia coli (E. coli) / References: UniProt: P04925
#2: Antibody Nanobody 484


Mass: 13504.972 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8, 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.199→37.323 Å / Num. obs: 96266 / % possible obs: 93.59 % / Redundancy: 5.4 % / Biso Wilson estimate: 18.2 Å2 / Net I/σ(I): 26.9
Reflection shellResolution: 1.2→1.26 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MA8

4ma8


Resolution: 1.199→37.323 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 18.55
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 4810 5 %RANDOM
Rwork0.1686 ---
obs0.1699 96167 93.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.199→37.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 21 177 1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051889
X-RAY DIFFRACTIONf_angle_d0.7812556
X-RAY DIFFRACTIONf_dihedral_angle_d12.503889
X-RAY DIFFRACTIONf_chiral_restr0.075257
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1993-1.2130.25621280.21242432X-RAY DIFFRACTION75
1.213-1.22720.25711410.21422670X-RAY DIFFRACTION83
1.2272-1.24220.24481390.20712662X-RAY DIFFRACTION83
1.2422-1.25790.20321450.19712745X-RAY DIFFRACTION85
1.2579-1.27450.21441440.19112740X-RAY DIFFRACTION86
1.2745-1.29190.21171490.18852818X-RAY DIFFRACTION87
1.2919-1.31040.20861490.18112839X-RAY DIFFRACTION89
1.3104-1.330.21421520.17672895X-RAY DIFFRACTION89
1.33-1.35070.20851550.16762928X-RAY DIFFRACTION92
1.3507-1.37290.17571570.16362987X-RAY DIFFRACTION92
1.3729-1.39660.18711580.1523007X-RAY DIFFRACTION94
1.3966-1.42190.17681610.15483051X-RAY DIFFRACTION95
1.4219-1.44930.15821610.15373045X-RAY DIFFRACTION95
1.4493-1.47890.18851640.15313115X-RAY DIFFRACTION96
1.4789-1.5110.16531610.15183068X-RAY DIFFRACTION95
1.511-1.54620.18711620.1473082X-RAY DIFFRACTION96
1.5462-1.58490.16781680.14163174X-RAY DIFFRACTION98
1.5849-1.62770.15231640.14343143X-RAY DIFFRACTION96
1.6277-1.67560.1681660.1543155X-RAY DIFFRACTION98
1.6756-1.72970.14891680.14813175X-RAY DIFFRACTION98
1.7297-1.79150.18381660.15433162X-RAY DIFFRACTION97
1.7915-1.86320.19311680.15753187X-RAY DIFFRACTION98
1.8632-1.9480.19071690.16043204X-RAY DIFFRACTION98
1.948-2.05070.18731690.15783216X-RAY DIFFRACTION99
2.0507-2.17920.19221700.15913225X-RAY DIFFRACTION98
2.1792-2.34740.19711710.1623253X-RAY DIFFRACTION98
2.3474-2.58360.19941720.17453252X-RAY DIFFRACTION99
2.5836-2.95730.20331730.18593301X-RAY DIFFRACTION99
2.9573-3.72540.21771760.17933345X-RAY DIFFRACTION99
3.7254-37.34110.19391840.17463481X-RAY DIFFRACTION99

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