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- PDB-1oks: Crystal structure of the measles virus phosphoprotein XD domain -

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Basic information

Entry
Database: PDB / ID: 1oks
TitleCrystal structure of the measles virus phosphoprotein XD domain
ComponentsRNA POLYMERASE ALPHA SUBUNIT
KeywordsTRANSFERASE / RNA-DIRECTED RNA POLYMERASE / NUCLEOCAPSID / PHOSPHORYLATION.
Function / homology
Function and homology information


protein folding chaperone / viral genome replication / molecular condensate scaffold activity / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding
Similarity search - Function
RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMEASLES VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsJohansson, K. / Bourhis, J.-M. / Campanacci, V. / Cambillau, C. / Canard, B. / Longhi, S.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of the Measles Virus Phosphoprotein Domain Responsible for the Induced Folding of the C-Terminal Domain of the Nucleoprotein
Authors: Johansson, K. / Bourhis, J.-M. / Campanacci, V. / Cambillau, C. / Canard, B. / Longhi, S.
History
DepositionJul 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA POLYMERASE ALPHA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1002
Polymers6,8931
Non-polymers2071
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.109, 50.109, 47.127
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RNA POLYMERASE ALPHA SUBUNIT / PHOSPHOPROTEIN / NUCLEOCAPSID PHOSPHOPROTEIN


Mass: 6892.544 Da / Num. of mol.: 1 / Fragment: XD-DOMAIN, RESIDUES 459-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MEASLES VIRUS / Strain: EDMONSTON B / Description: SELENOMETHIONINE / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C41[DE3]PLYSS / References: UniProt: P03422, RNA-directed RNA polymerase
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: N NUCLEOSIDE TRIPHOSPHATE = N DIPHOSPHATE + {RNA}(N).
Has protein modificationY
Sequence detailsTHIS CONFLICT IS DUE TO THE FACT THAT THE P GENE USED AS TEMPLATE TO AMPLIFY THE MEASLES VIRUS ...THIS CONFLICT IS DUE TO THE FACT THAT THE P GENE USED AS TEMPLATE TO AMPLIFY THE MEASLES VIRUS PHOSPHOPROTEIN XD GENE FRAGMENT IS THE PLASMID PSC6/P (RADECKE ET AL. EMBO, 1995) WHICH CONTAINS THIS MUTATION. HOWEVER, THIS MUTATED PHOSPHOPROTEIN IS FUNCTIONAL, AS INDICATED BY THE FACT THAT IT ALLOWS RESCUE OF MEASLES VIRUS IN A REVERSE GENETICS SYSTEM.

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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: 2.36 Å3/Da / Density % sol: 47.5 %
Crystal growpH: 8.5 / Details: 0.1 M CHES PH 8.5, 1.25 M NA CITRATE
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
20.1 MCHES1reservoirpH8.5
31.25 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→12 Å / Num. obs: 6611 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 6.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.6 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 12 Å / Num. measured all: 44883 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 100 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.323 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 310 4.7 %RANDOM
Rwork0.198 ---
obs0.2 6291 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20.67 Å20 Å2
2--1.34 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 13 64 517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.5021.98609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr4.483552
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02321
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2216
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8571.5266
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2072428
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6323193
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.8994.5181
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 23
Rwork0.284 458
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 12 Å / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.63
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å

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