[English] 日本語
Yorodumi
- PDB-4miw: High-resolution structure of the N-terminal endonuclease domain o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4miw
TitleHigh-resolution structure of the N-terminal endonuclease domain of the Lassa virus L polymerase
ComponentsRNA-directed RNA polymerase L
KeywordsViral Protein / Transferase / beta sheet / helix / Endoribonuclease type II / endonuclease
Function / homology
Function and homology information


virion component => GO:0044423 / negative stranded viral RNA replication / cap snatching / host cell cytoplasm / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding
Similarity search - Function
Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsWallat, G.D. / Huang, Q. / Wang, W. / Dong, H. / Ly, H. / Liang, Y. / Dong, C.
CitationJournal: Plos One / Year: 2014
Title: High-resolution structure of the N-terminal endonuclease domain of the lassa virus L polymerase in complex with magnesium ions.
Authors: Wallat, G.D. / Huang, Q. / Wang, W. / Dong, H. / Ly, H. / Liang, Y. / Dong, C.
History
DepositionSep 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / 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 / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,3603
Polymers20,3111
Non-polymers492
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.720, 57.720, 134.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein RNA-directed RNA polymerase L / Protein L


Mass: 20311.367 Da / Num. of mol.: 1 / Fragment: L-N terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus / Strain: josah / Gene: L / Plasmid: pHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GWS2, RNA-directed RNA polymerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Tris-Hcl, pH8-9.5, 250 mM MgSO4 and 10% PEG10000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 8-9

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 6, 2011 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.72→53.05 Å / Num. obs: 22935 / % possible obs: 97.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9.3 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.06 / Net I/σ(I): 23.7
Reflection shellResolution: 1.72→1.8 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.57 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
PHASESphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JSB

3jsb


Resolution: 1.72→40.814 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.96 / SU ML: 0.14 / σ(F): 0 / Phase error: 16.95 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rfree0.1783 1233 5.1 %
Rwork0.1654 --
obs0.1661 24166 96.66 %
all-23100 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.864 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å20 Å2
2--3.46 Å20 Å2
3----6.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.02 Å0.03 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.025 Å
Refinement stepCycle: LAST / Resolution: 1.72→40.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 2 158 1532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011410
X-RAY DIFFRACTIONf_angle_d1.121907
X-RAY DIFFRACTIONf_dihedral_angle_d11.961544
X-RAY DIFFRACTIONf_chiral_restr0.063220
X-RAY DIFFRACTIONf_plane_restr0.005246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.78890.25781210.19552354X-RAY DIFFRACTION91
1.7889-1.87030.20911410.17662484X-RAY DIFFRACTION96
1.8703-1.96890.18571430.16262482X-RAY DIFFRACTION97
1.9689-2.09230.18041280.15092523X-RAY DIFFRACTION97
2.0923-2.25380.17661510.14732511X-RAY DIFFRACTION97
2.2538-2.48060.17861450.14612542X-RAY DIFFRACTION97
2.4806-2.83950.16551240.15972596X-RAY DIFFRACTION98
2.8395-3.57710.18661400.15972640X-RAY DIFFRACTION98
3.5771-40.82570.1691400.18072801X-RAY DIFFRACTION98
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)
12.9071-0.61192.20572.9433-1.25297.8607-0.2586-0.53940.26720.13720.0483-0.3589-0.49770.57940.15810.22840.1431-0.0430.3973-0.0790.2762-12.0826-7.080731.4294
23.3793-0.6707-0.4762.2252-1.26954.65760.03110.1328-0.2471-0.2583-0.05280.04140.453-0.0818-0.08450.12530.0557-0.00150.13490.01440.1588-14.8635-15.048123.8717
32.7785-0.1409-1.79680.7854-0.32314.1549-0.1174-0.2175-0.27790.13410.0474-0.0239-0.1342-0.1041-0.06710.08230.0515-0.00920.1243-0.01560.1426-5.1977-16.693523.8613
47.58534.9288-0.33653.8860.62291.0406-0.00940.22810.4131-0.1612-0.03580.37180.0337-0.4874-0.04120.0720.004-0.01440.1608-0.00510.1107-6.0711-19.79719.1184
50.8026-0.15440.86240.5315-0.20992.74820.04950.0402-0.2896-0.17090.22120.16130.484-0.02590.02380.1357-0.0631-0.03220.1036-0.01860.1278-4.1616-28.94951.7887
61.0357-0.15060.94490.8109-0.4544.5638-0.06350.1252-0.0479-0.0520.03020.0101-0.20080.26180.03320.0561-0.0341-0.00360.1165-0.01090.08673.6863-20.45958.6091
71.50520.24251.20881.40230.11624.25080.04010.3261-0.3107-0.0921-0.0259-0.11910.58960.4826-0.06690.07410.01770.02250.1326-0.03340.11879.1262-27.4189.0493
86.9606-2.70292.03553.0484-1.46552.5594-0.1378-0.27580.6802-0.07260.3769-0.0259-0.2388-0.06240.16230.20710.0077-0.10030.1224-0.07030.22422.4588-10.198423.7213
94.1402-0.01820.92041.2411-0.10231.5592-0.3758-0.86830.04540.33760.1329-0.0397-0.2731-0.14970.1260.14240.1545-0.19950.3719-0.10530.1345-3.1108-11.342235.4628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 58 )
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 89 )
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 108 )
7X-RAY DIFFRACTION7chain 'A' and (resid 109 through 144 )
8X-RAY DIFFRACTION8chain 'A' and (resid 145 through 153 )
9X-RAY DIFFRACTION9chain 'A' and (resid 154 through 170 )

+
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