[English] 日本語
Yorodumi
- PDB-4i1t: Crystal structure of the cap-snatching endonuclease from Pichinde... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i1t
TitleCrystal structure of the cap-snatching endonuclease from Pichinde virus
ComponentsRNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / Arenavirus / Pichinde virus / viral transcription / cap-snatching / endonuclease / L protein / RNA-dependent RNA polymerase / PD-(D/E)XK nuclease fold / cap-snatching RNA endonuclease
Function / homology
Function and homology information


virion component => GO:0044423 / cap snatching / host cell cytoplasm / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding
Similarity search - Function
RNA-directed RNA polymerase L, helical domain / Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / de novo design (two linked rop proteins) / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Alpha-Beta Plaits ...RNA-directed RNA polymerase L, helical domain / Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / de novo design (two linked rop proteins) / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesPichinde virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsBussetta, C. / Choi, K.H.
CitationJournal: To be Published
Title: Crystal structure of the cap-snatching endonuclease from Pichinde virus, a new world arenavirus
Authors: Bussetta, C. / Ye, M. / Shrestha, L. / Bujalowski, P.J. / White, M.A. / Choi, K.H.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)25,1411
Polymers25,1411
Non-polymers00
Water0
1
A: RNA-directed RNA polymerase L

A: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)50,2822
Polymers50,2822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area1670 Å2
ΔGint-10 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.962, 142.962, 46.835
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

-
Components

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


Mass: 25140.799 Da / Num. of mol.: 1
Fragment: cap-snatching endonuclease domain (residues 1-194)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichinde virus / Strain: AN3739 / Gene: L / Plasmid: pJexpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q915A5, RNA-directed RNA polymerase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 6M ammonium nitrate, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 9, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 7360 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Rmerge(I) obs: 0.088 / Χ2: 1.896 / Net I/σ(I): 29.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.8-2.853.90.623.773501.48797.8
2.85-2.94.60.882.133481.67498.9
2.9-2.965.20.8042.093661.46100
2.96-3.025.90.82.433461.51100
3.02-3.086.40.6094.033581.97399.7
3.08-3.157.90.55.973621.795100
3.15-3.239.50.4028.383611.749100
3.23-3.329.70.311.93591.872100
3.32-3.429.80.26913.73611.961100
3.42-3.539.90.21916.93502.093100
3.53-3.6510.50.18420.123741.971100
3.65-3.8110.15124.473591.973100
3.8-3.97110.12928.883712.182100
3.97-4.1824.70.13642.563651.856100
4.18-4.4427.60.10857.073672.03100
4.44-4.7928.10.08569.023751.878100
4.79-5.2728.80.08569.033791.923100
5.27-6.0328.60.09365.073791.886100
6.03-7.5928.20.06583.243911.751100
7.59-5024.50.03997.814391.971100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å46.8 Å
Translation4 Å46.8 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.11data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JSB
Resolution: 2.8→46.795 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2944 339 4.65 %RANDOM
Rwork0.2361 ---
obs0.2387 7286 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.042 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso max: 185.25 Å2 / Biso mean: 78.3406 Å2 / Biso min: 24.96 Å2
Baniso -1Baniso -2Baniso -3
1-6.7793 Å20 Å2-0 Å2
2--6.7793 Å20 Å2
3----13.5585 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 0 0 1386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091411
X-RAY DIFFRACTIONf_angle_d1.2081907
X-RAY DIFFRACTIONf_chiral_restr0.073220
X-RAY DIFFRACTIONf_plane_restr0.005237
X-RAY DIFFRACTIONf_dihedral_angle_d17.223543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.8001-3.52770.34021830.256334735303347
3.5277-46.80180.27451560.2293360037563600
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.5227-2.49550.43013.3863-0.59952.0962-0.24470.14390.96-0.45140.02520.2786-0.2925-0.4684-0.00460.21680.04320.07120.78030.00790.451-1.182351.882510.7352
23.74110.812-1.83681.30330.14242.40170.01310.55180.1024-0.48790.1750.843-0.1678-1.05310.01260.13890.27990.03280.6888-0.01780.394720.926355.16080.9836
31.6564-0.1682-0.92170.92820.45872.3489-0.6320.9031-0.7456-0.8310.22020.11761.0736-0.15530.00450.42230.13560.13330.5871-0.13270.500124.98943.7097-3.4033
41.7572-1.1973-0.80931.6333-1.18783.5546-0.1001-0.8494-0.66780.03910.40270.48591.5649-0.34040.0554-0.0691-0.00310.06870.59330.05720.4698.614343.24112.0863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:50)A1 - 50
2X-RAY DIFFRACTION2(chain A and resid 51:106)A51 - 106
3X-RAY DIFFRACTION3(chain A and resid 107:133)A107 - 133
4X-RAY DIFFRACTION4(chain A and resid 134:169)A134 - 169

+
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