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- PDB-4fi5: Crystal structure of the N-terminal domain of Hantaan virus strai... -

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Basic information

Entry
Database: PDB / ID: 4fi5
TitleCrystal structure of the N-terminal domain of Hantaan virus strain 76-118 nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Korean hemorrhagic fever virus / Hantaan virus / Hantavirus / NP / nucleoprotein / antibody epitope / N-terminal domain / ssRNA negative strand virus / Bunyaviridae / human host / Eurasian field mouse host / virion
Function / homology
Function and homology information


symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / helical viral capsid / viral nucleocapsid / host cell Golgi apparatus / endonuclease activity / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Hantavirus nucleocapsid protein / Hantavirus nucleocapsid protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHantaan virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the N-terminal domain of Hantaan virus strain 76-118 nucleoprotein
Authors: Edwards, T.E. / Abendroth, J. / Altamura, L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJun 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)12,8291
Polymers12,8291
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.400, 77.400, 36.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 12829.333 Da / Num. of mol.: 1 / Fragment: unp residues 3-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hantaan virus / Strain: 76-118 / Gene: N / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: P05133
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HahaA.17785.a.A16.PS01490 at 20 mg/mL against Morpheus screen condition g8, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 20 mM Na-formate, 20 mM Na-citrate, 20 mM Ammonium acetate, 20 mM NaK ...Details: HahaA.17785.a.A16.PS01490 at 20 mg/mL against Morpheus screen condition g8, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 20 mM Na-formate, 20 mM Na-citrate, 20 mM Ammonium acetate, 20 mM NaK tartrate, 100 mM MOPS/HEPES-Na pH 7.5, crystal tracking ID 234641g8, puck ID hky1-5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.003317 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003317 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 6619 / Num. obs: 6604 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 37.089 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.260.5793.93560483100
2.26-2.320.4694.943387461100
2.32-2.390.4185.373334452100
2.39-2.460.3386.753241438100
2.46-2.540.3057.333297449100
2.54-2.630.2239.353053417100
2.63-2.730.2199.942905396100
2.73-2.840.14713.982879390100
2.84-2.970.12116.462756374100
2.97-3.110.08721.942622359100
3.11-3.280.07625.362452333100
3.28-3.480.0630.97235632799.7
3.48-3.720.04440.192269310100
3.72-4.020.03548.032014280100
4.02-4.40.03251.681868261100
4.4-4.920.03547.71683243100
4.92-5.680.03641.951505219100
5.68-6.960.03940.44127618799.5
6.96-9.840.02262.97991145100
9.840.01769.874948086

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.35 Å
Translation3 Å19.35 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb ID 2ic9

2ic9


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2087 / WRfactor Rwork: 0.1708 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8625 / SU B: 7.962 / SU ML: 0.11 / SU R Cruickshank DPI: 0.191 / SU Rfree: 0.1766 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 645 9.8 %RANDOM
Rwork0.1915 ---
obs0.1957 6594 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.23 Å2 / Biso mean: 35.4455 Å2 / Biso min: 18.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å21.08 Å2-0 Å2
2--2.15 Å2-0 Å2
3----3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms566 0 0 71 637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019577
X-RAY DIFFRACTIONr_bond_other_d0.0020.02408
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.973775
X-RAY DIFFRACTIONr_angle_other_deg0.9513992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.121572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0624.54533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03515118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.423158
X-RAY DIFFRACTIONr_chiral_restr0.0780.289
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02108
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 52 -
Rwork0.244 388 -
all-440 -
obs--99.55 %
Refinement TLS params.Method: refined / Origin x: 30.1016 Å / Origin y: 12.5975 Å / Origin z: -0.2086 Å
111213212223313233
T0.0797 Å2-0.0244 Å2-0.0009 Å2-0.0265 Å20.0085 Å2--0.0171 Å2
L0.1588 °2-0.294 °2-0.4638 °2-0.6551 °21.3391 °2--3.4483 °2
S0.0191 Å °-0.0417 Å °-0.0144 Å °0.0174 Å °0.039 Å °0.0034 Å °0.1464 Å °-0.0511 Å °-0.0581 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 70
2X-RAY DIFFRACTION1A101 - 171

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