[English] 日本語
Yorodumi
- PDB-8twr: Influenza A virus (A/Aichi/2/1968(H3N2) nucleoprotein mutant - 2-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8twr
TitleInfluenza A virus (A/Aichi/2/1968(H3N2) nucleoprotein mutant - 2-7 deleted, P283S, R416A
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / nucleoprotein / influenza
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09 Å
AuthorsYoon, J. / Zhang, Y.M. / Grant, R.A. / Shoulders, M.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CAREER Award 1652390 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136354 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI168166 United States
CitationJournal: Sci Adv / Year: 2024
Title: The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure.
Authors: Yoon, J. / Zhang, Y.M. / Her, C. / Grant, R.A. / Ponomarenko, A.I. / Ackermann, B.E. / Hui, T. / Lin, Y.S. / Debelouchina, G.T. / Shoulders, M.D.
History
DepositionAug 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Nucleoprotein
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,9134
Polymers169,8903
Non-polymers231
Water00
1
A: Nucleoprotein
B: Nucleoprotein
hetero molecules

C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)169,9134
Polymers169,8903
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
Buried area6000 Å2
ΔGint-36 kcal/mol
Surface area60280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.420, 285.220, 116.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 21 through 451 or (resid 452...
21(chain B and (resid 21 through 453 or resid 459 through 499))
31chain C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNALAALA(chain A and (resid 21 through 451 or (resid 452...AB21 - 45115 - 445
12LYSLYSLYSLYS(chain A and (resid 21 through 451 or (resid 452...AB452446
13ASNASNLEULEU(chain A and (resid 21 through 451 or (resid 452...AB21 - 49915 - 493
14ASNASNLEULEU(chain A and (resid 21 through 451 or (resid 452...AB21 - 49915 - 493
15ASNASNLEULEU(chain A and (resid 21 through 451 or (resid 452...AB21 - 49915 - 493
16ASNASNLEULEU(chain A and (resid 21 through 451 or (resid 452...AB21 - 49915 - 493
21ASNASNPROPRO(chain B and (resid 21 through 453 or resid 459 through 499))BC21 - 45315 - 447
22GLNGLNLEULEU(chain B and (resid 21 through 453 or resid 459 through 499))BC459 - 499453 - 493
31ASNASNLEULEUchain CCA21 - 49915 - 493

-
Components

#1: Protein Nucleoprotein


Mass: 56630.102 Da / Num. of mol.: 3 / Mutation: P283S, R416A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Aichi/2/1968(H3N2))
Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: I6TAH8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 8.0, 1.01 M potassium sodium tartrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.09→48.92 Å / Num. obs: 50131 / % possible obs: 99.6 % / Redundancy: 8.532 % / Biso Wilson estimate: 81.083 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.151 / Χ2: 0.883 / Net I/σ(I): 12.76 / Num. measured all: 427717 / Scaling rejects: 1190
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.09-3.177.2321.3232.1425333366635030.691.42395.6
3.17-3.267.8991.093.1828264358035780.8321.16699.9
3.26-3.358.4160.8684.0629640352235220.8990.923100
3.35-3.469.2010.7264.9830796334733470.9330.769100
3.46-3.579.1490.5186.5730284331033100.9630.549100
3.57-3.699.0960.417.8428808316731670.9730.435100
3.69-3.839.0370.3029.4627880308530850.9850.32100
3.83-3.998.8920.22811.5226417297229710.9880.242100
3.99-4.178.790.17413.6524965284128400.9920.185100
4.17-4.378.5940.15114.4823418272527250.9930.161100
4.37-4.618.3140.13415.6921626260226010.9940.142100
4.61-4.897.4110.10816.8518224246324590.9950.11699.8
4.89-5.238.9960.1118.8920799231223120.9970.116100
5.23-5.649.0780.10519.7719754217621760.9960.112100
5.64-6.188.9840.12017942199719970.9960.106100
6.18-6.918.7130.08522.7615953183118310.9970.09100
6.91-7.988.3990.07225.9713439160016000.9980.077100
7.98-9.787.2090.05230.799985138913850.9980.05699.7
9.78-13.838.5030.04239.19260108910890.9990.045100
13.83-48.927.7880.04138.3949306526330.9990.04497.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.17.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→48.92 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 2005 4 %
Rwork0.2185 48076 -
obs0.2191 50081 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 286.14 Å2 / Biso mean: 97.4361 Å2 / Biso min: 50.35 Å2
Refinement stepCycle: final / Resolution: 3.09→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10737 0 1 0 10738
Biso mean--73.24 --
Num. residues----1363
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6777X-RAY DIFFRACTION3.205TORSIONAL
12B6777X-RAY DIFFRACTION3.205TORSIONAL
13C6777X-RAY DIFFRACTION3.205TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.09-3.170.44431350.39253226336195
3.17-3.250.34471440.319434183562100
3.25-3.350.35421400.298134103550100
3.35-3.460.29071420.285933853527100
3.46-3.580.27691420.260734283570100
3.58-3.730.22941380.239334263564100
3.73-3.890.24021440.226634163560100
3.89-4.10.24211430.215834313574100
4.1-4.360.22061420.216634243566100
4.36-4.690.22711460.202534613607100
4.69-5.160.20981430.196434513594100
5.16-5.910.24241480.212234733621100
5.91-7.440.21251470.20735043651100
7.44-48.920.18941510.176236233774100

+
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://pdbjlvh1.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