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- PDB-6du9: Crystal Structure of Human Prion Protein 90-231 -

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Basic information

Entry
Database: PDB / ID: 6du9
TitleCrystal Structure of Human Prion Protein 90-231
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN / Crystallography Prion Neurodegenerative Prion Disease Human Crystal Structure
Function / homology
Function and homology information


negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / positive 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 / type 5 metabotropic glutamate receptor binding ...negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / positive 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 / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / 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 interleukin-2 production / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / cuprous ion binding / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / intracellular copper ion homeostasis / long-term memory / response to cadmium ion / inclusion body / cellular response to copper ion / neuron projection maintenance / tubulin binding / positive regulation of calcium-mediated signaling / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / terminal bouton / protein homooligomerization / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / protease binding / microtubule binding / molecular adaptor activity / nuclear membrane / response to oxidative stress / transmembrane transporter binding / learning or memory / postsynapse / regulation of cell cycle / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
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/Doppel alpha-helical domain
Similarity search - Domain/homology
: / Major prion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsNonato, M.C. / Rangel, V.L. / Pavlovici, F.A.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)141945/2018-4 Brazil
Sao Paulo Research Foundation (FAPESP)2016/22929-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)2017/26559-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of Human Prion Protein 90-231
Authors: Rangel, V.L. / Nonato, M.C. / Pavlovici, F.A.
History
DepositionJun 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 17, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / software / struct_conn / struct_keywords
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_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_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 / _software.name / _struct_conn.pdbx_dist_value / _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_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 / _struct_keywords.text
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4555
Polymers16,0821
Non-polymers3734
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-26 kcal/mol
Surface area5410 Å2
2
A: Major prion protein
hetero molecules

A: Major prion protein
hetero molecules

A: Major prion protein
hetero molecules

A: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,81820
Polymers64,3284
Non-polymers1,49116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area8110 Å2
ΔGint-147 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.170, 72.170, 158.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-301-

CD

21A-409-

HOH

31A-418-

HOH

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Components

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


Mass: 16081.919 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) / Strain (production host): ROSETTA BL21(DE3) / References: UniProt: P04156
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M Tris pH 7.6 15 mM CdCl2 2.5 M NaCl 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.31→65.71 Å / Num. obs: 6581 / % possible obs: 92 % / Redundancy: 4.4 % / CC1/2: 1 / Rrim(I) all: 0.105 / Net I/σ(I): 9.7
Reflection shellResolution: 2.31→2.56 Å / Num. unique obs: 329 / CC1/2: 0.6 / Rrim(I) all: 1.122

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HAF

3haf


Resolution: 2.33→65.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.536 / SU ML: 0.142 / Cross valid method: FREE R-VALUE / ESU R: 0.266 / ESU R Free: 0.227 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23496 660 10 %RANDOM
Rwork0.19241 ---
obs0.19672 5921 70.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0 Å2
2---0.5 Å20 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 2.33→65.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms725 0 4 18 747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.014747
X-RAY DIFFRACTIONr_bond_other_d0.0010.017586
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.671012
X-RAY DIFFRACTIONr_angle_other_deg0.9911.6361366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.998590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.43621.70247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.258156
X-RAY DIFFRACTIONr_chiral_restr0.0650.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02148
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0885.598366
X-RAY DIFFRACTIONr_mcbond_other4.0685.59365
X-RAY DIFFRACTIONr_mcangle_it5.718.398454
X-RAY DIFFRACTIONr_mcangle_other5.7078.406455
X-RAY DIFFRACTIONr_scbond_it5.2065.734381
X-RAY DIFFRACTIONr_scbond_other5.25.738382
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3478.467558
X-RAY DIFFRACTIONr_long_range_B_refined8.54664.467869
X-RAY DIFFRACTIONr_long_range_B_other8.53564.522869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.332→2.392 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 2 -
Rwork0.286 18 -
obs--3.02 %

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