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- PDB-4yxk: Crystal structure of Elk prion protein complexed with POM1 FAB -

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Basic information

Entry
Database: PDB / ID: 4yxk
TitleCrystal structure of Elk 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


side of membrane / protein homooligomerization / copper ion binding / Golgi apparatus / plasma membrane
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 speciesCervus elaphus nelsoni (American elk)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 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)62,8624
Polymers62,8393
Non-polymers231
Water1,31573
1
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)15,9321
Polymers15,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6840 Å2
MethodPISA
2
H: POM1 FAB HEAVY CHAIN
L: POM1 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9303
Polymers46,9072
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-29 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.674, 105.509, 76.112
Angle α, β, γ (deg.)90.00, 95.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Major prion protein / PrP


Mass: 15931.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cervus elaphus nelsoni (American elk) / Gene: PRNP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P67986
#2: Antibody POM1 FAB HEAVY CHAIN


Mass: 23397.078 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.: 73 / 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: 2.8 Å3/Da / Density % sol: 56.08 %
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: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15989 / % possible obs: 98.4 % / Redundancy: 3.9 % / Rsym value: 0.11 / Net I/σ(I): 10.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.4 / % possible all: 99.3

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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: 2.805→42.161 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3526 809 5.07 %
Rwork0.2998 --
obs0.3026 15958 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.805→42.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 1 73 4208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154238
X-RAY DIFFRACTIONf_angle_d2.2095756
X-RAY DIFFRACTIONf_dihedral_angle_d16.2371528
X-RAY DIFFRACTIONf_chiral_restr0.102633
X-RAY DIFFRACTIONf_plane_restr0.013742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8046-2.98030.44181530.34272388X-RAY DIFFRACTION94
2.9803-3.21040.40331480.31982507X-RAY DIFFRACTION97
3.2104-3.53330.34391150.29852557X-RAY DIFFRACTION98
3.5333-4.04420.31071360.30172555X-RAY DIFFRACTION99
4.0442-5.09390.32261270.27292534X-RAY DIFFRACTION97
5.0939-42.16580.37021300.30722608X-RAY DIFFRACTION98

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