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- PDB-4j4s: Triple mutant SFTAVN -

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Basic information

Entry
Database: PDB / ID: 4j4s
TitleTriple mutant SFTAVN
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / nucleocapsid protein / nucleoprotein / nucleocapsid
Function / homology
Function and homology information


viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesPhlebovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.442 Å
AuthorsJiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Zhu, Y. / Zhang, F. ...Jiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Zhu, Y. / Zhang, F. / Wang, T. / Li, C. / Zuo, X. / Luan, C.H. / Li, D. / Liu, Z.J.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of severe Fever with thrombocytopenia syndrome virus nucleocapsid protein in complex with suramin reveals therapeutic potential
Authors: Jiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Peng, Y. / Zhu, Y. / Zhang, F. / Wang, T. / Li, C. / Zuo, X. / Luan, C.H. / Li, D. / Liu, Z.J.
History
DepositionFeb 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 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 / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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)109,06112
Polymers108,8774
Non-polymers1848
Water1,40578
1
A: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5768
Polymers54,4382
Non-polymers1386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-62 kcal/mol
Surface area23860 Å2
MethodPISA
2
C: Nucleocapsid protein
D: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4844
Polymers54,4382
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-58 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.489, 108.479, 221.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Nucleocapsid protein / SFTSVN


Mass: 27219.201 Da / Num. of mol.: 4 / Mutation: R64D, K67D, K74D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phlebovirus / Strain: JS2010-018 / Production host: Escherichia coli (E. coli) / References: UniProt: I6WJ72
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3M NaCl, 0.1M NaAc, 0.2M Li2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.442→43.81 Å / Num. all: 42167 / Num. obs: 43028 / % possible obs: 97.92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 45.1 Å2
Reflection shellResolution: 2.45→2.5 Å / % possible all: 73

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4R

4j4r


Resolution: 2.442→43.809 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.7011 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 34.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 1998 4.74 %RANDOM
Rwork0.2084 ---
obs0.2111 42171 97.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 278.82 Å2 / Biso mean: 71.0312 Å2 / Biso min: 26.19 Å2
Refinement stepCycle: LAST / Resolution: 2.442→43.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 8 78 7500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157578
X-RAY DIFFRACTIONf_angle_d1.46710277
X-RAY DIFFRACTIONf_chiral_restr0.1041169
X-RAY DIFFRACTIONf_plane_restr0.011314
X-RAY DIFFRACTIONf_dihedral_angle_d16.7472795
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4418-2.50280.3411050.28562108221373
2.5028-2.57050.37641420.26552867300999
2.5705-2.64610.34081440.254328993043100
2.6461-2.73150.38041420.257328763018100
2.7315-2.82910.32621450.253428903035100
2.8291-2.94240.33031450.264729093054100
2.9424-3.07630.32531440.266829053049100
3.0763-3.23840.33041450.253929153060100
3.2384-3.44120.30191460.231329413087100
3.4412-3.70680.26911450.207329083053100
3.7068-4.07960.25421460.191829313077100
4.0796-4.66930.21141470.16729483095100
4.6693-5.88060.22341480.186629883136100
5.8806-43.81630.20361540.170130883242100
Refinement TLS params.Method: refined / Origin x: 7.1056 Å / Origin y: -30.7575 Å / Origin z: -25.4299 Å
111213212223313233
T0.3136 Å20.0217 Å2-0.0179 Å2-0.3433 Å2-0.0347 Å2--0.3522 Å2
L-0.1299 °20.138 °20.1661 °2-0.0495 °20.0445 °2--0.4545 °2
S0.0227 Å °-0.012 Å °0.0405 Å °0.0012 Å °-0.0377 Å °0.0468 Å °0.0723 Å °0.0535 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA0 - 245
2X-RAY DIFFRACTION1ALLB0 - 245
3X-RAY DIFFRACTION1ALLC1 - 245
4X-RAY DIFFRACTION1ALLD1 - 245
5X-RAY DIFFRACTION1ALLA301 - 303
6X-RAY DIFFRACTION1ALLB301 - 303
7X-RAY DIFFRACTION1ALLC301
8X-RAY DIFFRACTION1ALLD301
9X-RAY DIFFRACTION1ALLA401 - 445
10X-RAY DIFFRACTION1ALLB401 - 415
11X-RAY DIFFRACTION1ALLC401 - 411
12X-RAY DIFFRACTION1ALLD401 - 406

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