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- PDB-5ize: Hantaan virus L protein cap-snatching endonuclease -

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Basic information

Entry
Database: PDB / ID: 5ize
TitleHantaan virus L protein cap-snatching endonuclease
ComponentsRNA-directed RNA polymerase L
KeywordsTRANSFERASE / In complex with manganese metal ions
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / endonuclease activity / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, hantavirus / RNA-directed RNA polymerase, hantavirus, N-terminal / : / RNA dependent RNA polymerase / Cap-snatching endonuclease / : / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
MANGANESE (III) ION / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesHantaan virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsReguera, J. / Cusack, S.
Funding support France, Belgium, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV8-0019 France
European Research Council322586 Belgium
CitationJournal: Plos Pathog. / Year: 2016
Title: Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases.
Authors: Reguera, J. / Gerlach, P. / Rosenthal, M. / Gaudon, S. / Coscia, F. / Gunther, S. / Cusack, S.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_contact_author / pdbx_entry_details
Item: _pdbx_contact_author.country / _pdbx_contact_author.phone

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4638
Polymers41,1332
Non-polymers3306
Water4,864270
1
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7314
Polymers20,5671
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7314
Polymers20,5671
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.200, 76.150, 63.720
Angle α, β, γ (deg.)90.00, 103.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 0 - 170 / Label seq-ID: 1 - 171

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

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 20566.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Manganese ions (MN3) / Source: (gene. exp.) Hantaan virus / Strain: 76-118 / Production host: Escherichia coli (E. coli) / References: UniProt: P23456, RNA-directed RNA polymerase
#2: Chemical
ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Mn / Details: Manganese ions (MN3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 316 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Hepes 0.1 M pH7, 20% PEG 6K, 1 M LiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Type: OTHER / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.7→48 Å / Num. obs: 41154 / % possible obs: 97.8 % / Redundancy: 3.02 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.99
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 1.03

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→48 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.931 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21595 1991 4.8 %RANDOM
Rwork0.1659 ---
obs0.16821 39163 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å20.01 Å2
2---0.03 Å20 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.7→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 3 270 3085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192867
X-RAY DIFFRACTIONr_bond_other_d0.0030.022797
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9643871
X-RAY DIFFRACTIONr_angle_other_deg1.08936471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.56524.766128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60515536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1471512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213147
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02617
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_it2.4392.7361393
X-RAY DIFFRACTIONr_mcbond_other2.4242.7351392
X-RAY DIFFRACTIONr_mcangle_it3.0114.0981736
X-RAY DIFFRACTIONr_mcangle_other3.014.11737
X-RAY DIFFRACTIONr_scbond_it3.1393.2381474
X-RAY DIFFRACTIONr_scbond_other3.1383.2411475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6394.6472136
X-RAY DIFFRACTIONr_long_range_B_refined4.3323.313385
X-RAY DIFFRACTIONr_long_range_B_other3.94822.5763273
X-RAY DIFFRACTIONr_rigid_bond_restr3.58735664
X-RAY DIFFRACTIONr_sphericity_free26.2155104
X-RAY DIFFRACTIONr_sphericity_bonded9.35555787
Refine LS restraints NCS

Ens-ID: 1 / Number: 20768 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.704→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 162 -
Rwork0.357 2838 -
obs--97.53 %

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