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- PDB-6sv2: Human prion protein (PrP) fragment 119-231 (G127V M129 variant) c... -

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Basic information

Entry
Database: PDB / ID: 6sv2
TitleHuman prion protein (PrP) fragment 119-231 (G127V M129 variant) complexed to ICSM 18 (anti-Prp therapeutic antibody) Fab fragment
Components
  • ICSM 18-ANTI-PRP THERAPEUTIC FAB HEAVY CHAIN
  • ICSM 18-ANTI-PRP THERAPEUTIC FAB LIGHT CHAIN
  • Major prion protein
KeywordsPROTEIN BINDING / Prion
Function / homology
Function and homology information


positive regulation of glutamate receptor signaling pathway / 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 / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions ...positive regulation of glutamate receptor signaling pathway / 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 / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / 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 T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of interleukin-2 production / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / cuprous ion binding / response to amyloid-beta / 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 / long-term memory / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / tubulin binding / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / negative regulation of DNA-binding transcription factor activity / protein homooligomerization / terminal bouton / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / protein-folding chaperone binding / signaling receptor activity / amyloid-beta binding / microtubule binding / protease binding / nuclear membrane / postsynapse / transmembrane transporter binding / response to oxidative stress / molecular adaptor activity / postsynaptic density / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / 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
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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsConners, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UU_00024/6 United Kingdom
CitationJournal: Commun Biol / Year: 2020
Title: Structural effects of the highly protective V127 polymorphism on human prion protein.
Authors: Hosszu, L.L.P. / Conners, R. / Sangar, D. / Batchelor, M. / Sawyer, E.B. / Fisher, S. / Cliff, M.J. / Hounslow, A.M. / McAuley, K. / Leo Brady, R. / Jackson, G.S. / Bieschke, J. / Waltho, J.P. / Collinge, J.
History
DepositionSep 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: 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_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ICSM 18-ANTI-PRP THERAPEUTIC FAB LIGHT CHAIN
H: ICSM 18-ANTI-PRP THERAPEUTIC FAB HEAVY CHAIN
A: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6994
Polymers59,6033
Non-polymers961
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-30 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.076, 128.076, 135.642
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Antibody ICSM 18-ANTI-PRP THERAPEUTIC FAB LIGHT CHAIN


Mass: 23283.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody ICSM 18-ANTI-PRP THERAPEUTIC FAB HEAVY CHAIN


Mass: 23045.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Major prion protein / PrP / ASCR / PrP27-30 / PrP33-35C


Mass: 13273.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRNP, ALTPRP, PRIP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P04156
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.8 M and 1.5 M ammonium sulphate, 0.1 M Tris (pH 7.5 and 8.0)

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→57.93 Å / Num. obs: 26908 / % possible obs: 88.5 % / Redundancy: 4.2 % / Rpim(I) all: 0.103 / Net I/σ(I): 24.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2626 / Rpim(I) all: 1.224

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w9e

2w9e


Resolution: 2.3→57.93 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 15.727 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.249
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1362 5.2 %RANDOM
Rwork0.1999 ---
obs0.2026 24982 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.82 Å2 / Biso mean: 47.674 Å2 / Biso min: 16.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.32 Å20 Å2
2---0.32 Å20 Å2
3---1.03 Å2
Refinement stepCycle: final / Resolution: 2.3→57.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4037 0 5 67 4109
Biso mean--24.6 36.25 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194176
X-RAY DIFFRACTIONr_bond_other_d0.0010.023746
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9375694
X-RAY DIFFRACTIONr_angle_other_deg0.8673.0028664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94524.181177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23315666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4041516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02964
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 87 -
Rwork0.327 1671 -
all-1758 -
obs--81.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.03950.0401-0.14693.2866-1.06092.7258-0.04570.21860.3418-0.0959-0.12420.0967-0.26970.01430.16990.1357-0.066-0.06490.07940.04880.088858.235288.467715.7033
29.15370.9278-1.82753.1225-0.56652.0671-0.0377-0.12761.10010.377-0.06670.7219-0.4401-0.44280.10440.55480.2293-0.00860.4489-0.14290.430624.0368101.705314.3163
34.64042.04810.1423.3891-1.51832.7398-0.17770.2844-0.0774-0.15990.07430.28220.0796-0.07670.10340.0785-0.0319-0.00880.0327-0.03010.096747.405270.067322.2127
44.6365-0.58380.79574.9733-2.14783.9980.16260.5895-0.4074-0.54750.05340.3810.1175-0.6313-0.2160.33120.03690.00720.5315-0.16570.419824.170385.991210.4062
55.1491-4.99291.67775.1046-1.2981.02140.29910.2864-0.2015-0.295-0.28740.20290.18710.0241-0.01170.1896-0.02180.05450.1682-0.01160.094878.205257.470923.8309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 106
2X-RAY DIFFRACTION2L107 - 212
3X-RAY DIFFRACTION3H1 - 114
4X-RAY DIFFRACTION4H115 - 215
5X-RAY DIFFRACTION5A125 - 223

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