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- PDB-3lyf: Crystal Structure of the Rift Valley Fever Virus Nucleocapsid Protein -

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Basic information

Entry
Database: PDB / ID: 3lyf
TitleCrystal Structure of the Rift Valley Fever Virus Nucleocapsid Protein
ComponentsNucleocapsid proteinVirus
KeywordsVIRAL PROTEIN / nucleocapsid protein / N protein / Rift Valley fever virus / ribonucleoprotein / Viral nucleoprotein
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / host cell nucleus / RNA binding / identical protein binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesRift Valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å
AuthorsRaymond, D.D. / Smith, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of the Rift Valley fever virus nucleocapsid protein reveals another architecture for RNA encapsidation.
Authors: Raymond, D.D. / Piper, M.E. / Gerrard, S.R. / Smith, J.L.
History
DepositionFeb 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8358
Polymers109,4664
Non-polymers3684
Water11,097616
1
A: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9174
Polymers54,7332
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nucleocapsid protein
D: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9174
Polymers54,7332
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers27,3671
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers27,3671
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers27,3671
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers27,3671
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.110, 69.630, 80.620
Angle α, β, γ (deg.)78.45, 69.72, 60.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleocapsid protein / Virus


Mass: 27366.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift Valley fever virus / Strain: ZH-501 / Gene: N / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI/pRARE2 / References: UniProt: D3K5I7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 26% PEG 3350, 100 mM Na/K phosphate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.9794,0.9796
SYNCHROTRONAPS 23-ID-D21.033
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDJun 3, 2009K-B pair of biomorph mirrors for vertical and horizontal focusing
MARMOSAIC 300 mm CCD2CCDDec 16, 2009K-B pair of biomorph mirrors for vertical and horizontal focusing
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal MonochromatorMADMx-ray1
2Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
31.0331
ReflectionResolution: 1.93→50 Å / Num. all: 90337 / Num. obs: 87736 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.1 / Num. unique all: 12642 / % possible all: 95.7

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Processing

Software
NameVersionClassification
Blu-IceEpicsdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.93→46.51 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.64 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25428 4393 5 %RANDOM
Rwork0.2115 ---
all0.21361 ---
obs0.21361 83342 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.134 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å2-0.08 Å2-0.48 Å2
2---1.18 Å20.23 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.93→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7557 0 24 616 8197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227727
X-RAY DIFFRACTIONr_bond_other_d0.0010.025404
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.96610412
X-RAY DIFFRACTIONr_angle_other_deg0.902313113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2525960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99623.411343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.777151381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3811566
X-RAY DIFFRACTIONr_chiral_restr0.0770.21138
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218544
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021570
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_it0.8511.54821
X-RAY DIFFRACTIONr_mcbond_other0.1961.51943
X-RAY DIFFRACTIONr_mcangle_it1.53827690
X-RAY DIFFRACTIONr_scbond_it2.29732906
X-RAY DIFFRACTIONr_scangle_it3.6724.52721
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 323 -
Rwork0.281 6041 -
obs--95.27 %

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