[English] 日本語
Yorodumi
- PDB-5ize: Hantaan virus L protein cap-snatching endonuclease -

+
Open data


ID or keywords:

Loading...

-
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 / RNA-dependent RNA polymerase activity / nucleotide binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more