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- PDB-6suz: Human prion protein (PrP) fragment 119-231 (G127V V129 variant) c... -

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Basic information

Entry
Database: PDB / ID: 6suz
TitleHuman prion protein (PrP) fragment 119-231 (G127V V129 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 / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / negative regulation of interleukin-17 production ...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 / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / 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 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 / cellular response to amyloid-beta / 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 / protease binding / nuclear membrane / response to oxidative stress / transmembrane transporter binding / postsynapse / 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: 2.5 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 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,1834
Polymers58,0873
Non-polymers961
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-35 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.951, 127.951, 135.797
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11L-314-

HOH

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Components

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


Mass: 11887.236 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
#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: Antibody ICSM 18-ANTI-PRP THERAPEUTIC FAB LIGHT CHAIN


Mass: 23154.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#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.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 55.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 5 - 6 mg/mL PrP in 0.4 M and 0.75 M ammonium sulphate, 0.05 M Tris (pH 7.5 and 8.0) were equilibrated over wells containing 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: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→111 Å / Num. obs: 23111 / % possible obs: 99.4 % / Redundancy: 5.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.063 / Rrim(I) all: 0.156 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.65.91.0591512225540.6090.4641.1622.699.6
9.01-85.855.20.07630315780.990.0350.08423.197.6

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W9E

2w9e


Resolution: 2.5→111 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 17.163 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.236
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1161 5 %RANDOM
Rwork0.1607 ---
obs0.1633 21923 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.45 Å2 / Biso mean: 57.011 Å2 / Biso min: 22.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å20 Å2
2---0.35 Å20 Å2
3---1.14 Å2
Refinement stepCycle: final / Resolution: 2.5→111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 5 66 4149
Biso mean--36.51 39.45 -
Num. residues----525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024210
X-RAY DIFFRACTIONr_bond_other_d0.0010.023776
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.9385742
X-RAY DIFFRACTIONr_angle_other_deg0.92238747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7655529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02524.413179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.05915673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4321516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02968
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 88 -
Rwork0.267 1599 -
all-1687 -
obs--99.65 %
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)
10.63272.1202-0.41737.2787-1.59471.1881-0.10350.03810.0731-0.41390.10090.29670.1831-0.240.00260.0825-0.0227-0.01350.1075-0.02950.0715-39.3679-38.827623.8159
21.06870.3477-0.70345.1066-1.92493.27620.03060.19010.3475-0.3386-0.04570.3723-0.4815-0.11660.01510.17550.0239-0.0960.1687-0.01520.2102-42.57687.001316.5632
30.975-0.42970.0222.9974-0.571.7281-0.0385-0.10550.4571-0.1308-0.1619-0.2784-0.67330.2430.20040.3151-0.0852-0.09440.20780.03830.2586-25.187212.452615.1387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 223
2X-RAY DIFFRACTION2H1 - 215
3X-RAY DIFFRACTION3L1 - 211

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