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- PDB-4akl: Structure of the Crimean-Congo Haemorrhagic Fever Virus Nucleocap... -

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Basic information

Entry
Database: PDB / ID: 4akl
TitleStructure of the Crimean-Congo Haemorrhagic Fever Virus Nucleocapsid Protein
ComponentsNUCLEOCAPSID
KeywordsVIRAL PROTEIN / BUNYAVIRIDAE / CCHFV / CASPASE-3
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / RNA binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1110 / Nucleocapsid N protein / Nucleocapsid N protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Nucleoprotein
Similarity search - Component
Biological speciesCRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCarter, S.D. / Walter, C.T. / Surtees, R. / Bergeron, E. / Ariza, A. / Albarino, C.G. / Nichol, S.T. / Hiscox, J.A. / Edwards, T.A. / Barr, J.N.
CitationJournal: J.Virol. / Year: 2012
Title: Structure, Function, and Evolution of the Crimean-Congo Hemorrhagic Fever Virus Nucleocapsid Protein.
Authors: Carter, S.D. / Surtees, R. / Walter, C.T. / Ariza, A. / Bergeron, E. / Nichol, S.T. / Hiscox, J.A. / Edwards, T.A. / Barr, J.N.
History
DepositionFeb 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: NUCLEOCAPSID
B: NUCLEOCAPSID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3574
Polymers108,0572
Non-polymers3002
Water5,639313
1
A: NUCLEOCAPSID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1792
Polymers54,0281
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOCAPSID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1792
Polymers54,0281
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.380, 72.060, 101.230
Angle α, β, γ (deg.)90.00, 110.70, 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: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 1 - 482 / Label seq-ID: 1 - 482

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

NCS oper: (Code: given
Matrix: (-0.751, -0.005975, -0.6602), (0.005259, -1, 0.003067), (-0.6602, -0.001169, 0.751)
Vector: -0.3571, 27.14, 0.02075)

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Components

#1: Protein NUCLEOCAPSID


Mass: 54028.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS / Variant: BAGDAD 12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 PLYSS / References: UniProt: Q70UR4
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.4 Å3/Da / Density % sol: 48 %
Description: THE STRUCTURE WAS SOLVED FROM A LOW-RESOLUTION DATASET COLLECTED FROM A CRYSTAL CONTAINING A MERCURY DERIVATIVE. THE FINAL DATA BELONG TO A NATIVE CRYSTAL THAT DIFFRACTED TO HIGHER RESOLUTION.
Crystal growpH: 6.5
Details: 0.1 M BIS-TRIS PROPANE PH 6.5, 0.2 M NACL, 25% PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 25, 2011 / Details: TOROIDAL MIRROR
RadiationMonochromator: SINGLE BOUNCE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.1→48.79 Å / Num. obs: 56441 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→94.7 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.547 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23359 2857 5.1 %RANDOM
Rwork0.18394 ---
obs0.18639 53584 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.219 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20.61 Å2
2---1.34 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→94.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7463 0 20 313 7796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227863
X-RAY DIFFRACTIONr_bond_other_d0.0020.025434
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.94810641
X-RAY DIFFRACTIONr_angle_other_deg1.1673.00213356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75351004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71425.112356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.853151460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3531529
X-RAY DIFFRACTIONr_chiral_restr0.0850.21159
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021541
X-RAY DIFFRACTIONr_nbd_refined0.2120.21699
X-RAY DIFFRACTIONr_nbd_other0.1560.25021
X-RAY DIFFRACTIONr_nbtor_refined0.1770.23794
X-RAY DIFFRACTIONr_nbtor_other0.0840.23653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1350.279
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_it0.5021.54794
X-RAY DIFFRACTIONr_mcbond_other0.1141.51947
X-RAY DIFFRACTIONr_mcangle_it0.92427748
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3733069
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1944.52862
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2814medium positional0.220.5
2B2814medium positional0.220.5
1A3651loose positional0.375
2B3651loose positional0.375
1A2814medium thermal0.362
2B2814medium thermal0.362
1A3651loose thermal0.4110
2B3651loose thermal0.4110
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 215 -
Rwork0.24 3997 -
obs--96.63 %
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)
12.1199-0.0372-0.45611.6906-0.04231.58840.02520.13830.0555-0.11760.04750.1367-0.0884-0.2655-0.07270.10430.0029-0.04410.06860.03890.048-30.628114.53315.6956
26.3980.0201-2.2735.2710.8942.7076-0.55810.183-1.55330.28360.03060.28990.5828-0.17530.52750.232-0.02480.15010.015-0.02360.6414-20.397257.020714.0916
31.31030.0594-0.03791.4255-0.02662.00920.0368-0.06890.1521-0.0276-0.0223-0.1631-0.05620.2793-0.01460.0379-0.01240.02380.0436-0.01270.091612.381512.388931.9511
41.52650.36470.26186.64350.76542.8542-0.15-0.02620.30990.02430.04260.1422-0.10590.14410.10740.12890.001-0.08050.01570.02480.19585.1682-29.715724.2933
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 183
2X-RAY DIFFRACTION1A296 - 483
3X-RAY DIFFRACTION2A184 - 295
4X-RAY DIFFRACTION3B2 - 183
5X-RAY DIFFRACTION3B296 - 483
6X-RAY DIFFRACTION4B184 - 295

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