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- PDB-2w9e: Structure of ICSM 18 (anti-Prp therapeutic antibody) Fab fragment... -

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Basic information

Entry
Database: PDB / ID: 2w9e
TitleStructure of ICSM 18 (anti-Prp therapeutic antibody) Fab fragment complexed with human Prp fragment 119-231
Components
  • ICSM 18-ANTI-PRP THERAPEUTIC FAB HEAVY CHAIN
  • ICSM 18-ANTI-PRP THERAPEUTIC FAB LIGHT CHAIN
  • MAJOR PRION PROTEIN
KeywordsIMMUNE SYSTEM / FAB / PRP / PRION / MEMBRANE / GPI-ANCHOR / LIPOPROTEIN / GOLGI APPARATUS / DISEASE MUTATION / GLYCOPROTEIN / CELL MEMBRANE
Function / homology
Function and homology information


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 / glycosaminoglycan binding / NCAM1 interactions / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-17 production / cupric ion binding ...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 / glycosaminoglycan binding / NCAM1 interactions / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-17 production / cupric ion binding / ATP-dependent protein binding / negative regulation of protein processing / type 5 metabotropic glutamate receptor binding / dendritic spine maintenance / negative regulation of dendritic spine maintenance / negative regulation of activated T cell proliferation / extrinsic component of membrane / negative regulation of interleukin-2 production / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of glutamate receptor signaling pathway / negative regulation of type II interferon production / response to amyloid-beta / negative regulation of amyloid-beta formation / cuprous ion binding / negative regulation of long-term synaptic potentiation / response to cadmium ion / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / negative regulation of T cell receptor signaling pathway / long-term memory / positive regulation of calcium-mediated signaling / neuron projection maintenance / inclusion body / cellular response to copper ion / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / tubulin binding / protein homooligomerization / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / terminal bouton / amyloid-beta binding / protein-folding chaperone binding / signaling receptor activity / protease binding / response to oxidative stress / microtubule binding / molecular adaptor activity / learning or memory / regulation of cell cycle / transmembrane transporter binding / postsynapse / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / external side of plasma membrane / negative regulation of apoptotic process / dendrite / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / 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 / Major Prion Protein / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAntonyuk, S.V. / Trevitt, C.R. / Strange, R.W. / Jackson, G.S. / Sangar, D. / Batchelor, M. / Jones, S. / Georgiou, T. / Cooper, S. / Fraser, C. ...Antonyuk, S.V. / Trevitt, C.R. / Strange, R.W. / Jackson, G.S. / Sangar, D. / Batchelor, M. / Jones, S. / Georgiou, T. / Cooper, S. / Fraser, C. / Khalili-Shirazi, A. / Clarke, A.R. / Hasnain, S.S. / Collinge, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal Structure of Human Prion Protein Bound to a Therapeutic Antibody.
Authors: Antonyuk, S.V. / Trevitt, C.R. / Strange, R.W. / Jackson, G.S. / Sangar, D. / Batchelor, M. / Cooper, S. / Fraser, C. / Jones, S. / Georgiou, T. / Khalili-Shirazi, A. / Clarke, A.R. / ...Authors: Antonyuk, S.V. / Trevitt, C.R. / Strange, R.W. / Jackson, G.S. / Sangar, D. / Batchelor, M. / Cooper, S. / Fraser, C. / Jones, S. / Georgiou, T. / Khalili-Shirazi, A. / Clarke, A.R. / Hasnain, S.S. / Collinge, J.
History
DepositionJan 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)59,6574
Polymers59,5613
Non-polymers961
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-36.4 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.149, 126.149, 134.126
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein MAJOR PRION PROTEIN / PRP27-30 / PRP33-35C / ASCR / PRP


Mass: 13231.674 Da / Num. of mol.: 1 / Fragment: RESIDUES 119-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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: 23283.688 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.: 42 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 8 / Details: AMMONIUM SULPHATE, TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 7, 2008 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→27 Å / Num. obs: 13209 / % possible obs: 86.2 % / Redundancy: 8 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 70

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UW3

1uw3


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.854 / SU B: 39.624 / SU ML: 0.357 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 711 5 %RANDOM
Rwork0.207 ---
obs0.21 13392 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4077 0 5 42 4124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224230
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.9385774
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62124.358179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53515677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.591516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023216
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21809
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22824
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4081.52689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71424304
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.89731774
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5124.51463
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.407 44
Rwork0.323 814
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)
15.4784-1.8406-1.86154.6750.0344.9270.0260.48710.3078-0.2262-0.11120.3770.0204-0.27530.0852-0.36-0.0046-0.0214-0.05820.0345-0.081-43.112-5.93321.607
27.5253-0.1104-5.72016.4076-3.496814.46650.37470.9806-0.193-0.8161-0.36050.6769-1.3916-0.9848-0.01420.33650.165-0.2622-0.0254-0.19250.2631-40.3922.8629.355
33.12660.6558-0.18561.892-0.66473.9421-0.0730.19790.212-0.0473-0.2184-0.2734-0.16140.51010.2913-0.31150.004-0.0139-0.03770.059-0.075-22.018-6.04915.634
48.7764-5.1375-3.45499.23913.38375.42810.465-0.94781.4465-0.30870.0554-0.4132-1.90060.7332-0.52030.7611-0.3938-0.04480.1456-0.0980.1821-27.88730.3714.364
51.11331.3047-0.548413.7495-3.90223.0516-0.07960.2413-0.1387-0.5472-0.06860.49460.4409-0.55320.1482-0.1168-0.1204-0.0159-0.0303-0.10620-38.507-38.3623.266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 114
2X-RAY DIFFRACTION2H115 - 215
3X-RAY DIFFRACTION3L1 - 106
4X-RAY DIFFRACTION4L107 - 212
5X-RAY DIFFRACTION5A125 - 223

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