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- PDB-6hhd: Mouse Prion Protein in complex with Nanobody 484 -

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Basic information

Entry
Database: PDB / ID: 6hhd
TitleMouse Prion Protein in complex with Nanobody 484
Components
  • (Major prion protein) x 2
  • (Nanobody 484) x 2
KeywordsPROTEIN BINDING / Prion / Nanobody / aggregation / B-sheet
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/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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsSoror, S. / Abskharon, R. / Wohlkonig, A.
CitationJournal: Plos Pathog. / Year: 2019
Title: Structural evidence for the critical role of the prion protein hydrophobic region in forming an infectious prion.
Authors: Abskharon, R. / Wang, F. / Wohlkonig, A. / Ruan, J. / Soror, S. / Giachin, G. / Pardon, E. / Zou, W. / Legname, G. / Ma, J. / Steyaert, J.
History
DepositionAug 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 13, 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
B: Nanobody 484
C: Major prion protein
D: Nanobody 484
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,05513
Polymers52,4494
Non-polymers6069
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-74 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.130, 63.798, 69.792
Angle α, β, γ (deg.)90.00, 101.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AC

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


Mass: 12732.195 Da / Num. of mol.: 1
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
#3: Protein Major prion protein / PrP / PrP27-30 / PrP33-35C


Mass: 12569.021 Da / Num. of mol.: 1
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

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Antibody , 2 types, 2 molecules BD

#2: Antibody Nanobody 484


Mass: 13504.972 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#4: Antibody Nanobody 484


Mass: 13643.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 294 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.15 M ammonium sulfate, 0.1 M MES pH6.0, 15% w/v PEG 40000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→57.85 Å / Num. obs: 29594 / % possible obs: 99.54 % / Redundancy: 5 % / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.2 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MA7

4ma7


Resolution: 2.102→57.846 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1481 5 %RANDOM
Rwork0.206 ---
obs0.208 29594 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→57.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 30 285 3975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033805
X-RAY DIFFRACTIONf_angle_d0.555144
X-RAY DIFFRACTIONf_dihedral_angle_d15.6552238
X-RAY DIFFRACTIONf_chiral_restr0.04522
X-RAY DIFFRACTIONf_plane_restr0.003676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1024-2.17030.35291290.30992458X-RAY DIFFRACTION97
2.1703-2.24780.34981340.28852547X-RAY DIFFRACTION100
2.2478-2.33790.28531340.26742530X-RAY DIFFRACTION99
2.3379-2.44430.28211340.2512553X-RAY DIFFRACTION100
2.4443-2.57310.25221360.23692576X-RAY DIFFRACTION100
2.5731-2.73430.27331330.21882531X-RAY DIFFRACTION100
2.7343-2.94540.23671350.21452573X-RAY DIFFRACTION100
2.9454-3.24180.23551350.19452558X-RAY DIFFRACTION100
3.2418-3.71090.23351360.1832589X-RAY DIFFRACTION100
3.7109-4.6750.1991350.15412554X-RAY DIFFRACTION99
4.675-57.86830.22031400.18892644X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.8402 Å / Origin y: -24.4808 Å / Origin z: -15.3606 Å
111213212223313233
T0.1844 Å20.0177 Å2-0.0003 Å2-0.2161 Å20.0005 Å2--0.1829 Å2
L-0.1096 °2-0.0491 °20.0015 °2-1.1431 °20.0244 °2--0.0798 °2
S0.0193 Å °-0.0003 Å °-0.0026 Å °-0.0157 Å °-0.0413 Å °0.0465 Å °-0.0033 Å °-0.0001 Å °-0 Å °
Refinement TLS groupSelection details: all

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