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- PDB-2xi7: N-terminal endonuclease domain of La Crosse virus L-protein -

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Basic information

Entry
Database: PDB / ID: 2xi7
TitleN-terminal endonuclease domain of La Crosse virus L-protein
ComponentsRNA POLYMERASE L
KeywordsTRANSFERASE / ENDONUCLEASE
Function / homology
Function and homology information


host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / nucleotide binding ...host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
Restriction Endonuclease - #60 / RNA-directed RNA polymerase, orthobunyavirus / : / Virus, RNA-directed RNA polymerase L, thumb ring domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / : / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / Restriction Endonuclease ...Restriction Endonuclease - #60 / RNA-directed RNA polymerase, orthobunyavirus / : / Virus, RNA-directed RNA polymerase L, thumb ring domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / : / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / Restriction Endonuclease / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 2-4-DIOXO-4-PHENYLBUTANOIC ACID / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesBUNYAVIRUS LA CROSSE
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReguera, J. / Weber, F. / Cusack, S.
CitationJournal: Plos Pathog. / Year: 2010
Title: Bunyaviridae RNA Polymerases (L-Protein) Have an N-Terminal, Influenza-Like Endonuclease Domain, Essential for Viral CAP-Dependent Transcription.
Authors: Reguera, J. / Weber, F. / Cusack, S.
History
DepositionJun 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references / Non-polymer description / Version format compliance
Revision 1.2Dec 20, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA POLYMERASE L
B: RNA POLYMERASE L
C: RNA POLYMERASE L
D: RNA POLYMERASE L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,09916
Polymers86,8904
Non-polymers1,20812
Water8,017445
1
A: RNA POLYMERASE L
B: RNA POLYMERASE L
C: RNA POLYMERASE L
D: RNA POLYMERASE L
hetero molecules

A: RNA POLYMERASE L
B: RNA POLYMERASE L
C: RNA POLYMERASE L
D: RNA POLYMERASE L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,19732
Polymers173,7818
Non-polymers2,41624
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area18360 Å2
ΔGint-101.6 kcal/mol
Surface area68680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.590, 124.590, 294.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
RNA POLYMERASE L / LA CROSSE VIRUS L-PROTEIN


Mass: 21722.607 Da / Num. of mol.: 4 / Fragment: N-TERMINAL ENDONUCLEASE DOMAIN, RESIDUES 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BUNYAVIRUS LA CROSSE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5HC98
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-XI7 / 2-4-DIOXO-4-PHENYLBUTANOIC ACID


Mass: 192.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4 Å3/Da / Density % sol: 69.2 % / Description: NONE
Crystal growpH: 7.5
Details: 15-20 MG/ML PROTEIN IN 20 MM HEPES PH 7.5 150 MM NACL 5MM MNCL2 AND 2.5 MM BETA-MERCAPTO-ETHANOL AND A RESERVOIR COMPOSITION OF 3.4 M NA-FORMATE 0.1 M TRIS-HCL PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 69332 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XI5

2xi5


Resolution: 2.2→47.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.974 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2787 4 %RANDOM
Rwork0.188 ---
obs0.19 66523 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 64 445 6625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226432
X-RAY DIFFRACTIONr_bond_other_d0.0010.024327
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9798764
X-RAY DIFFRACTIONr_angle_other_deg0.932310538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5224.371350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.021151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7411547
X-RAY DIFFRACTIONr_chiral_restr0.0950.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217153
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021354
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_it0.9581.53744
X-RAY DIFFRACTIONr_mcbond_other0.2121.51465
X-RAY DIFFRACTIONr_mcangle_it1.88626181
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.88432688
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8834.52567
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
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 198 -
Rwork0.232 4836 -
obs--100 %

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