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- PDB-4ma7: Crystal structure of mouse prion protein complexed with Promazine -

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Basic information

Entry
Database: PDB / ID: 4ma7
TitleCrystal structure of mouse prion protein complexed with Promazine
Components
  • Major prion protein
  • POM1 heavy chain
  • POM1 light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Fab / Antibody / Mouse prion protein
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / nucleobase-containing compound metabolic process / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / response to amyloid-beta / cuprous ion binding / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / response to cadmium ion / side of membrane / inclusion body / neuron projection maintenance / positive regulation of calcium-mediated signaling / cellular response to copper ion / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to xenobiotic stimulus / cellular response to amyloid-beta / terminal bouton / positive regulation of neuron apoptotic process / signaling receptor activity / regulation of protein localization / protein-folding chaperone binding / amyloid-beta binding / response to oxidative stress / protease binding / nuclear membrane / microtubule binding / molecular adaptor activity / transmembrane transporter binding / learning or memory / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / metal ion binding / identical protein binding / membrane / plasma membrane / cytosol
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
Promazine / Major prion protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBaral, P.K. / Swayampakula, M. / James, M.N.G.
CitationJournal: Structure / Year: 2014
Title: Structural basis of prion inhibition by phenothiazine compounds.
Authors: Baral, P.K. / Swayampakula, M. / Rout, M.K. / Kav, N.N. / Spyracopoulos, L. / Aguzzi, A. / James, M.N.
History
DepositionAug 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 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
H: POM1 heavy chain
L: POM1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5524
Polymers60,2683
Non-polymers2841
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.211, 106.038, 75.733
Angle α, β, γ (deg.)90.00, 95.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13360.877 Da / Num. of mol.: 1 / Fragment: UNP residues 116-229
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 POM1 heavy chain


Mass: 23397.078 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Details: hybridoma / Source: (gene. exp.) Mus musculus (house mouse) / Cell: hybridoma
#3: Antibody POM1 light chain


Mass: 23509.701 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Details: hybridoma / Source: (gene. exp.) Mus musculus (house mouse) / Cell: hybridoma
#4: Chemical ChemComp-P2Z / Promazine / N,N-dimethyl-3-(10H-phenothiazin-10-yl)propan-1-amine


Mass: 284.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2011
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 52155 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 85.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H88

4h88


Resolution: 1.97→34.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.154 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24687 2298 5 %RANDOM
Rwork0.21578 ---
obs0.21741 43247 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.636 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.34 Å2
2--0.08 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.97→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 20 409 4625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024334
X-RAY DIFFRACTIONr_bond_other_d0.0020.023881
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.9435899
X-RAY DIFFRACTIONr_angle_other_deg0.7863.0048969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03424.444189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45315689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8271518
X-RAY DIFFRACTIONr_chiral_restr0.0660.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021004
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_it1.2124.012163
X-RAY DIFFRACTIONr_mcbond_other1.2124.0082162
X-RAY DIFFRACTIONr_mcangle_it2.0316.0052699
X-RAY DIFFRACTIONr_mcangle_other2.0165.9742685
X-RAY DIFFRACTIONr_scbond_it1.3994.1192170
X-RAY DIFFRACTIONr_scbond_other1.4094.1072158
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3086.0963181
X-RAY DIFFRACTIONr_long_range_B_refined5.30632.6035350
X-RAY DIFFRACTIONr_long_range_B_other4.82932.1585156
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.965→2.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 127 -
Rwork0.266 2379 -
obs--73.27 %

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