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- PDB-4yxl: Crystal structure of Syrian hamster prion protein complexed with ... -

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Basic information

Entry
Database: PDB / ID: 4yxl
TitleCrystal structure of Syrian hamster prion protein complexed with POM1 FAB
Components
  • Major prion protein
  • POM1 FAB HEAVY CHAIN
  • POM1 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / prion / antibody / Immune system complex
Function / homology
Function and homology information


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 / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade ...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 / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / 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 / negative regulation of type II interferon production / cuprous ion binding / positive regulation of protein targeting to membrane / side of membrane / inclusion body / neuron projection maintenance / positive regulation of calcium-mediated signaling / molecular function activator activity / cellular response to copper ion / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein homooligomerization / protein destabilization / cellular response to xenobiotic stimulus / cellular response to amyloid-beta / terminal bouton / positive regulation of neuron apoptotic process / signaling receptor activity / presynapse / amyloid-beta binding / response to oxidative stress / protease binding / nuclear membrane / microtubule binding / amyloid fibril formation / learning or memory / regulation of cell cycle / 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 / identical protein binding / 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
Biological speciesMesocricetus auratus (golden hamster)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsBaral, P.K. / Swayampakula, M. / James, M.N.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
APRI Canada
CitationJournal: J.Struct.Biol. / Year: 2015
Title: X-ray structural and molecular dynamical studies of the globular domains of cow, deer, elk and Syrian hamster prion proteins.
Authors: Baral, P.K. / Swayampakula, M. / Aguzzi, A. / James, M.N.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein
H: POM1 FAB HEAVY CHAIN
L: POM1 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7964
Polymers65,7733
Non-polymers231
Water1,36976
1
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)18,8961
Polymers18,8961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6750 Å2
MethodPISA
2
H: POM1 FAB HEAVY CHAIN
L: POM1 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9003
Polymers46,8772
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-32 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.916, 105.969, 76.326
Angle α, β, γ (deg.)90.00, 95.37, 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: 18896.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Gene: PRNP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P04273
#2: Antibody POM1 FAB HEAVY CHAIN


Mass: 23367.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody POM1 FAB LIGHT CHAIN


Mass: 23509.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.1 M BIS-TRIS, 0.2 M lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 19709 / % possible obs: 97.4 % / Redundancy: 4 % / Rsym value: 0.08 / Net I/σ(I): 15.46
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.44 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H88, 4DGI

4h88

4dgi


Resolution: 2.604→35.241 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3101 1012 5.14 %
Rwork0.2619 --
obs0.2645 19692 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.604→35.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 1 76 4223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134251
X-RAY DIFFRACTIONf_angle_d1.9725773
X-RAY DIFFRACTIONf_dihedral_angle_d14.9851531
X-RAY DIFFRACTIONf_chiral_restr0.088632
X-RAY DIFFRACTIONf_plane_restr0.012745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6042-2.74150.35441270.35232292X-RAY DIFFRACTION84
2.7415-2.91320.39471630.34242703X-RAY DIFFRACTION98
2.9132-3.1380.37861390.30422687X-RAY DIFFRACTION98
3.138-3.45350.32571460.28532715X-RAY DIFFRACTION98
3.4535-3.95270.33041330.25752772X-RAY DIFFRACTION99
3.9527-4.97770.25381410.23762731X-RAY DIFFRACTION99
4.9777-35.24460.30611630.24532780X-RAY DIFFRACTION99

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