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- PDB-3oa1: Crystal structure of phosphoprotein/Protein P/Protein M1 residues... -

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Basic information

Entry
Database: PDB / ID: 3oa1
TitleCrystal structure of phosphoprotein/Protein P/Protein M1 residues 69-297 from Rabies virus reveals degradation to C-terminal domain only
ComponentsPhosphoprotein
KeywordsCHAPERONE / Seattle Structural Genomics Center for Infectious Disease / rabies virus / phosphoprotein / protein degredation / Rabies Virus Protein N / SSGCID
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...microtubule-dependent intracellular transport of viral material towards nucleus / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase activity / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Phosphoprotein, C-terminal domain / Phosphoprotein / Phosphoprotein, C-terminal / : / Phosphoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRabies virus strain Pasteur vaccin
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of phosphoprotein/Protein P/Protein M1 residues 69-297 from Rabies virus reveals degradation to C-terminal domain only
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Feb 21, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9507
Polymers51,4702
Non-polymers4805
Water2,342130
1
A: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0234
Polymers25,7351
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9273
Polymers25,7351
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.980, 44.080, 74.580
Angle α, β, γ (deg.)90.00, 127.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 6 / Auth seq-ID: 194 - 292 / Label seq-ID: 126 - 224

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Phosphoprotein / Protein P / Protein M1


Mass: 25735.000 Da / Num. of mol.: 2 / Fragment: UNP residues 69-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies virus strain Pasteur vaccin / Strain: Pasteur vaccins/PV / Gene: P / Production host: Escherichia coli (E. coli) / References: UniProt: P06747
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES 69 THROUGH 297 WENT INTO CRYSTALLIZATION TRIALS AS DETERMINED BY MW OF ABOUT 25,703 BY SDS-PAGE

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 6.48 mg/mL LyraA.17086.a.D14 PD00142 in 25 mM Tris pH 8, 0.2 M NaCl, 1 mM TCEP, 1% glycerol against Emerald Biosystems Wizard Full screen condition A8 2 M ammonium sulphate, 0.1 M Citrate pH ...Details: 6.48 mg/mL LyraA.17086.a.D14 PD00142 in 25 mM Tris pH 8, 0.2 M NaCl, 1 mM TCEP, 1% glycerol against Emerald Biosystems Wizard Full screen condition A8 2 M ammonium sulphate, 0.1 M Citrate pH 5.5, 16 C, 0.4 uL protein and 0.4 uL precipitant, crystal tracking ID 216420a8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 29, 2010 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 12248 / Num. obs: 11974 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 29.937 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.01
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.2-2.265.60.1799.1395586870681.3
2.26-2.320.1769.8546385995.1
2.32-2.390.13712.35779804100
2.39-2.460.13912.3607785099.1
2.46-2.540.12513.35734802100
2.54-2.630.12113.9552676599.2
2.63-2.730.116534874599.6
2.73-2.840.08917.4523572999.5
2.84-2.970.0917.5492068299.3
2.97-3.110.07718.9480767199.7
3.11-3.280.06722.64391613100
3.28-3.480.06225.9428160499
3.48-3.720.05826.9392356699.1
3.72-4.020.05730.2363451699.2
4.02-4.40.05431.1343348799.2
4.4-4.920.05530.2314444099.3
4.92-5.680.05627.8281939098.5
5.68-6.960.0627.6233032699.4
6.96-9.840.05831.5187226798.2
9.840.05531.596815296.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.16 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å37.95 Å
Translation3 Å37.95 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.64 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2174 / WRfactor Rwork: 0.1687 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8533 / SU B: 10.461 / SU ML: 0.124 / SU R Cruickshank DPI: 0.2532 / SU Rfree: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 569 4.8 %RANDOM
Rwork0.1723 ---
obs0.1749 11947 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.31 Å2 / Biso mean: 22.7096 Å2 / Biso min: 7.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.18 Å2
2---1.08 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 25 130 1778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221686
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9942284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.015215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6442572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97315310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.413159
X-RAY DIFFRACTIONr_chiral_restr0.090.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211225
X-RAY DIFFRACTIONr_mcbond_it0.7551.51051
X-RAY DIFFRACTIONr_mcangle_it1.43821685
X-RAY DIFFRACTIONr_scbond_it2.4993635
X-RAY DIFFRACTIONr_scangle_it3.9664.5594
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 747 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.255
LOOSE THERMAL1.4510
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 32 -
Rwork0.146 672 -
all-704 -
obs--81.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9103-1.02690.31471.4975-0.20260.70670.1034-0.0124-0.0035-0.0365-0.02840.01090.0048-0.0015-0.0750.031-0.0107-0.00210.0262-0.01390.051119.85336.9862.8799
20.18720.02820.12161.38091.00031.5067-0.04350.0145-0.02440.0259-0.01450.01240.02620.03840.0580.03830.00820.00880.03090.01070.01483.657216.340727.4241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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