[English] 日本語
Yorodumi
- PDB-6zlc: Non-specific dsRNA recognition by wildtype H7N1 RNA-binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zlc
TitleNon-specific dsRNA recognition by wildtype H7N1 RNA-binding domain
Components
  • Non-structural protein 1
  • RNA (5'-R(*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*U)-3')
KeywordsVIRAL PROTEIN / INFLUENZA A VIRUS / RNA BINDING DOMAIN / RNA-PROTEIN COMPLEX
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / host cell nucleus / RNA binding
Similarity search - Function
Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding
Similarity search - Domain/homology
NITRATE ION / RNA / RNA (> 10) / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCoste, F. / Wacquiez, A. / Marc, D. / Castaing, B.
CitationJournal: Viruses / Year: 2020
Title: Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1.
Authors: Wacquiez, A. / Coste, F. / Kut, E. / Gaudon, V. / Trapp, S. / Castaing, B. / Marc, D.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
C: RNA (5'-R(*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*U)-3')
D: RNA (5'-R(*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,15410
Polymers29,7144
Non-polymers4406
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-62 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.596, 103.596, 102.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Non-structural protein 1 / NS1


Mass: 8817.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/turkey/Italy/977/1999(H7N1))
Strain: A/turkey/Italy/977/1999(H7N1) / Gene: ns1, NS, NS1 / Variant: A/turkey/Italy/977/1999(H7N1) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1PST0
#2: RNA chain RNA (5'-R(*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*U)-3')


Mass: 6039.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.61 Å3/Da / Density % sol: 73.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200mM ammonium nitrate, 2M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.3→46.33 Å / Num. obs: 25358 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 62.02 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.8
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2431 / CC1/2: 0.55 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZKO

2zko


Resolution: 2.3→46.33 Å / SU ML: 0.3394 / Cross valid method: FREE R-VALUE / Phase error: 22.7724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 1233 4.87 %
Rwork0.191 24069 -
obs0.1923 25302 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 798 26 56 2045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422088
X-RAY DIFFRACTIONf_angle_d0.66682986
X-RAY DIFFRACTIONf_chiral_restr0.0319368
X-RAY DIFFRACTIONf_plane_restr0.0036245
X-RAY DIFFRACTIONf_dihedral_angle_d4.69251177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.33771470.3122602X-RAY DIFFRACTION99.93
2.39-2.50.34091560.29312592X-RAY DIFFRACTION99.96
2.5-2.630.32691630.27422611X-RAY DIFFRACTION100
2.63-2.80.30371480.26412628X-RAY DIFFRACTION100
2.8-3.010.27411090.26522669X-RAY DIFFRACTION100
3.01-3.320.28891140.22812682X-RAY DIFFRACTION100
3.32-3.80.19971350.17612683X-RAY DIFFRACTION100
3.8-4.780.17551360.14072715X-RAY DIFFRACTION100
4.78-46.330.171250.1662887X-RAY DIFFRACTION99.77
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)
18.68204049493-5.606253175515.200388095514.07682051937-4.948634289748.505832831311.135398636491.92899850350.520727375759-0.889736303223-2.59575463549-0.131286024123-0.6229340646672.114740551811.005469065820.9553566964740.0865255257039-0.07648788184391.3728006250.01434005850670.91100993371635.930736982311.1894648568-1.47726253921
22.423079500130.16704492082-0.02326796941496.12485243648-3.374661906551.99987346320.03207575599240.2116809142-0.0599944638974-0.532487960983-0.166626206691-0.05360472691490.1776877934780.007692405824010.1263691438950.5831694793620.01885204337840.01748650857290.574092183648-0.04945501387140.38838279699841.3387263392-9.25852070359-2.76324336802
35.03384301052-5.23140357093-4.966940672145.470032424275.227934391975.051093270310.4933702922341.4075127727-1.03251800202-0.424755190014-0.428536111611-0.1119405364410.590436114754-0.6002830548820.05412663589381.097458254680.03064718388080.04739478597380.859671808593-0.140352840290.74506015453941.2689057314-26.2064568915-4.06978321724
41.40455233759-0.3998458841570.7139295371763.43148456198-3.669765251744.306968559220.003196447750390.260485851111-0.15559633011-0.183734970720.3935060145630.899717913090.239986745509-0.234365043273-0.3537115197390.574034385004-0.01470590647560.01637981318610.568353290919-0.07675393161620.50593260200732.4419847681-11.6633963516-1.11798095223
53.6921628144-2.87188458752-1.443690572219.86093962814-2.405542829728.87923521061-0.3481025121180.626912678427-0.156951923996-0.0352203297923-0.24923662889-0.722002604053-0.4710819758171.050568135080.5444317770980.546756550598-0.02649858519030.04652989652970.4545483183960.012448368320.42740726922447.5213902694-4.42865503323-4.6128986254
61.843985001840.596196906091.32311585215.690044235461.270241713573.971783467180.113583414012-0.0117077864954-0.352311720155-0.492585230702-0.44808192648-0.1801759040440.09923720839660.07360383491990.3002456978820.6018114139960.01193441602170.09504744056960.5821455745170.006485840230.53371755904846.1479340428-17.75597264796.31651512094
71.45559220427-1.0245846311-0.1243045038487.82378438038-2.245104561652.94011334080.0177132398883-0.113547357484-0.06094270684230.469737990988-0.2437965133210.0902743630171-0.3212345293890.1749634619410.2470322933990.601876436881-0.08039155207460.01752826138250.585614863488-0.0473333043720.43195799646241.4894479856-11.16732114511.9892677626
87.26812006318-0.5457457104714.141781737527.56879294532-3.523616688956.297752389050.1009510565780.515553321954-0.552429651623-0.668328993288-0.206671137556-0.5541839729230.6004636472571.53181435570.1421488851050.5956464064060.1140519137340.110685696090.483635528425-0.02013354327410.59691199499251.889432201-21.15515196712.28546496985
94.168724682214.71198925051-2.219255939737.919015860780.5879270870116.19549876783-0.440211882259-0.720673725321-1.218511854910.432748248061-0.0001676581343881.701451183941.129619341520.2281541436380.5276066595440.8475312810750.005057977895760.1421672813550.5448679936850.08514106736661.0731741813631.8623989062-29.527533898717.8407288663
102.284916721170.948530566744-0.3831364417196.2778712342-1.51431781266.75315367535-0.1544429360570.139733855550.527904845630.373785467636-0.06686403743131.005009949070.141045076854-0.3514558299730.1602113959580.679355719918-0.07037247008460.04395030638630.649308227612-0.09835740353690.85073283199323.8829672139-16.83622016487.75442260484
114.01815953694-0.877945049515-0.59016824193.88815881418-3.296782760734.902817928210.164890904133-0.226368711615-0.3349133162450.372926209883-0.1006187460431.16887064344-0.419283184411-0.261873906279-0.159031462410.7180206650890.07037809218460.1102833862650.607000128856-0.1175831530480.82650644600126.45955881271.3893652120111.5160561353
124.9010793656-2.971371696470.2833118655623.92341537618-1.632958369085.694234737070.02563427614840.0281518591330.00181796810560.559937539087-0.08663383468390.826480753666-0.2404901049380.170911227828-0.1130699779290.622170314992-0.1002118626130.07595986548540.488500076869-0.0286952671760.71697795216725.5969154699-3.368217578239.83303173178
134.64534211882-1.12123485863-1.512244655253.04432197282-1.970396655933.543107782740.380406932148-0.13630101174-0.4469164974940.389265145205-0.2554214423460.5171383612520.214226396897-0.16679371403-0.1383152657650.938601156155-0.1954133602020.07917784418990.625795472976-6.58582189361E-60.91097722863327.010029455-28.083924471411.0217203484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 2 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 29 )
4X-RAY DIFFRACTION4chain 'A' and (resid 30 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 73 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 50 )
8X-RAY DIFFRACTION8chain 'B' and (resid 51 through 72 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 5 )
10X-RAY DIFFRACTION10chain 'C' and (resid 6 through 10 )
11X-RAY DIFFRACTION11chain 'C' and (resid 11 through 19 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 10 )
13X-RAY DIFFRACTION13chain 'D' and (resid 11 through 19 )

+
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