[English] 日本語
Yorodumi
- PDB-2kkz: Solution NMR structure of the monomeric W187R mutant of A/Udorn N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kkz
TitleSolution NMR structure of the monomeric W187R mutant of A/Udorn NS1 effector domain. Northeast Structural Genomics target OR8C[W187R].
ComponentsNon-structural protein NS1
KeywordsANTIVIRAL PROTEIN / Influenza A / Effector Domain / solution NMR structure / W187R mutant / Cytoplasm / Host-virus interaction / Interferon antiviral system evasion / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / signaling receptor inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression ...symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / signaling receptor inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / signaling receptor binding / host cell nucleus / RNA binding / identical protein binding
Similarity search - Function
Influenza virus non-structural protein, effector domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1 / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsAramini, J.M. / Ma, L. / Lee, H. / Zhao, L. / Cunningham, K. / Ciccosanti, C. / Janjua, H. / Fang, Y. / Xiao, R. / Krug, R.M. ...Aramini, J.M. / Ma, L. / Lee, H. / Zhao, L. / Cunningham, K. / Ciccosanti, C. / Janjua, H. / Fang, Y. / Xiao, R. / Krug, R.M. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the monomeric W187R mutant of A/Udorn NS1 effector domain. Northeast Structural Genomics target OR8C[W187R].
Authors: Aramini, J.M. / Ma, L. / Lee, H. / Zhao, L. / Cunningham, K. / Ciccosanti, C. / Janjua, H. / Fang, Y. / Xiao, R. / Krug, R.M. / Montelione, G.T.
History
DepositionJun 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein NS1


Theoretical massNumber of molelcules
Total (without water)15,9351
Polymers15,9351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Non-structural protein NS1


Mass: 15935.354 Da / Num. of mol.: 1 / Fragment: sequence database residues 85-215 / Mutation: W187R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: Udorn/1972 / Gene: NS, NS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q6XSU2, UniProt: P03495*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CO
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D simultaneous CN NOESY
11013D 1H-13C NOESY aromatic
11113D (H)CCH-COSY
11222D 1H-13C HSQC high resolution (L/V methyl stereoassignment)
11322D 1H-15N hetNOE
11421D 1H-15N T1 and T2
11513D (H)CCH-TOCSY
11613D CCH-TOCSY
NMR detailsText: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 98.3%, SIDE CHAIN, 95.9%, AROMATICS, 97.8%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 80%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 84 TO 217, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 87-163,169-202: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 0.9. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 88.4%, ADDITIONALLY ALLOWED, 11.6%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.43/-1.38, ALL, -0.30/-1.77. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 17.12/-1.41 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 84-217): RECALL, 0.968, PRECISION, 0.911, F-MEASURE, 0.939, DP-SCORE, 0.740. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 13. (G) AGREEMENT WITH RESIDUAL DIPOLAR COUPLINGS (20 MODELS): CORRELATION COEFFICIENT (R): 0.992 (0.001); Q RMS: 0.125 (0.008). THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 84-86,164-168,203-END.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.71 mM [U-100% 13C; U-100% 15N] OR8w187r, 20 mM sodium phosphate, 100 mM sodium chloride, 50 mM arginine, 50 mM glutamic acid, 1 % glycerol, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
21.2 mM [U-5% 13C; U-100% 15N] OR8w187r, 20 mM sodium phosphate, 100 mM sodium chloride, 50 mM arginine, 50 mM glutamic acid, 1 % glycerol, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.71 mMOR8w187r-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
50 mMarginine-41
50 mMglutamic acid-51
1 %glycerol-61
50 uMDSS-71
1.2 mMOR8w187r-8[U-5% 13C; U-100% 15N]2
20 mMsodium phosphate-92
100 mMsodium chloride-102
50 mMarginine-112
50 mMglutamic acid-122
1 %glycerol-132
50 uMDSS-142
Sample conditionsIonic strength: 0.1 / pH: 6.9 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospindata analysis
Sparky3.112Goddarddata analysis
Sparky3.112Goddardpeak picking
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
PSVS1.3Bhattacharya and Montelionestructure validation
MolProbity3.15Richardsonstructure quality analysis
PdbStat5.1Tejero and Montelionepdb processing
TALOSplusCornilescu, Delaglio and Baxrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2251 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 203 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (18.5 ...Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2251 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 203 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (18.5 CONSTRAINTS PER RESIDUE, 5.5 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 84 TO 217 BY PSVS 1.3). IN ADDITION, 75 RESOLVED N-H RESIDUAL DIPOLAR COUPLINGS FOR ORDERED RESIDUES WERE INCLUDED IN ALL STRUCTURE CALCULATIONS. STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19 AND USING A NEUTRAL HISTIDINE TAUTOMER (ND1H FORM) AT RESIDUE 169.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5.3 ° / Maximum upper distance constraint violation: 0.33 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

+
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