[English] 日本語
Yorodumi
- PDB-7plr: Crystal structure of the N-terminal endonuclease domain of La Cro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7plr
TitleCrystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound Baloxavir
ComponentsRNA-directed RNA polymerase L
KeywordsTRANSFERASE / complex / inhibitor / 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-dependent 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-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
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 / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
Baloxavir acid / FORMIC ACID / : / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesBunyavirus La Crosse
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsFeracci, M. / Hernandez, S. / Vincentelli, R. / Ferron, F. / Reguera, J. / Canard, B. / Alvarez, K.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-ASTR-0010-01, PaNuVi France
CitationJournal: To Be Published
Title: Crystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound Baloxavir
Authors: Feracci, M. / Hernandez, S. / Vincentelli, R. / Ferron, F. / Reguera, J. / Canard, B. / Alvarez, K.
History
DepositionSep 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: RNA-directed RNA polymerase L
BBB: RNA-directed RNA polymerase L
DDD: RNA-directed RNA polymerase L
GGG: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,16622
Polymers86,8904
Non-polymers2,27618
Water1,13563
1
AAA: RNA-directed RNA polymerase L
hetero molecules


  • defined by author
  • Evidence: fluorescence resonance energy transfer
  • 22.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)22,5558
Polymers21,7231
Non-polymers8327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: RNA-directed RNA polymerase L
hetero molecules


  • defined by author
  • 21.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)21,8874
Polymers21,7231
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
DDD: RNA-directed RNA polymerase L
hetero molecules


  • defined by author
  • 22.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)22,3625
Polymers21,7231
Non-polymers6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
GGG: RNA-directed RNA polymerase L
hetero molecules


  • defined by author
  • 22.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)22,3625
Polymers21,7231
Non-polymers6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.738, 124.738, 295.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11DDD-322-

HOH

-
Components

-
Protein , 1 types, 4 molecules AAABBBDDDGGG

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


Mass: 21722.607 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bunyavirus La Crosse / Production host: Escherichia coli (E. coli)
References: UniProt: A5HC98, RNA-directed RNA polymerase, Hydrolases; Acting on ester bonds

-
Non-polymers , 5 types, 81 molecules

#2: Chemical ChemComp-E4Z / Baloxavir acid


Mass: 483.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H19F2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 3.4M Sodium Formate 0.1M Tris - HCl pH8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.64→108.03 Å / Num. obs: 40890 / % possible obs: 100 % / Redundancy: 39.8 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 20.1
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 39.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1987 / CC1/2: 0.912 / Rpim(I) all: 0.19 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia20.6.475-g7ac7bb6b-dials-2.2data reduction
DIALS2.2.10-g6dafd9427-releasedata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OA4

7oa4


Resolution: 2.64→108.026 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.181 / SU B: 9.949 / SU ML: 0.201 / Average fsc free: 0.9069 / Average fsc work: 0.9178 / Cross valid method: FREE R-VALUE / ESU R: 0.399 / ESU R Free: 0.277
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2539 2041 5.003 %
Rwork0.2136 38758 -
all0.216 --
obs-40799 100 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.557 Å2
Baniso -1Baniso -2Baniso -3
1-0.811 Å20.406 Å20 Å2
2--0.811 Å2-0 Å2
3----2.632 Å2
Refinement stepCycle: LAST / Resolution: 2.64→108.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 130 63 6325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136464
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176026
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.6498811
X-RAY DIFFRACTIONr_angle_other_deg1.0891.58413865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5035748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30722.778396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.438151103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7581545
X-RAY DIFFRACTIONr_chiral_restr0.0450.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021501
X-RAY DIFFRACTIONr_nbd_refined0.1850.21223
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1580.25480
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23148
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.23107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2150
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.219
X-RAY DIFFRACTIONr_nbd_other0.1260.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2750.213
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0560.21
X-RAY DIFFRACTIONr_mcbond_it1.6485.8242971
X-RAY DIFFRACTIONr_mcbond_other1.6485.8252972
X-RAY DIFFRACTIONr_mcangle_it2.6878.7293711
X-RAY DIFFRACTIONr_mcangle_other2.6868.7313712
X-RAY DIFFRACTIONr_scbond_it1.726.0343493
X-RAY DIFFRACTIONr_scbond_other1.7186.0333492
X-RAY DIFFRACTIONr_scangle_it2.8538.9995095
X-RAY DIFFRACTIONr_scangle_other2.8538.9995096
X-RAY DIFFRACTIONr_lrange_it4.60866.97079
X-RAY DIFFRACTIONr_lrange_other4.59866.8737074
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2.64-2.7090.3371450.31228210.31329660.8180.8350.289
2.709-2.7830.3371340.28427270.28728610.8590.8820.254
2.783-2.8630.3251230.27726750.27927980.8710.8830.247
2.863-2.9510.2861200.26926040.26927240.8950.8940.234
2.951-3.0480.2931420.25825150.2626570.8950.9070.224
3.048-3.1550.2971310.26624090.26825400.880.890.231
3.155-3.2740.2731330.23923650.24124980.9130.9220.208
3.274-3.4080.2841040.24322650.24523690.8880.920.213
3.408-3.5590.2731250.2421890.24223140.9040.9160.213
3.559-3.7320.2711190.21420760.21721950.9160.9310.189
3.732-3.9340.2241080.20520050.20621130.9410.9390.18
3.934-4.1720.233960.18519040.18720000.9340.9490.161
4.172-4.460.241920.17317940.17718860.9410.960.153
4.46-4.8170.19860.16416760.16517620.9670.9670.144
4.817-5.2750.2421020.17815300.18216320.9570.9650.156
5.275-5.8960.265780.19614180.19914960.9340.9580.172
5.896-6.8050.228610.19512720.19713330.9390.9530.173
6.805-8.3260.246540.17911020.18211560.9470.9610.163
8.326-11.740.182470.1538710.1559180.9750.9790.149
11.74-108.0260.263410.2885410.2865820.9520.9290.283

+
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://pdbjlc1.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