[English] 日本語
Yorodumi
- PDB-4o46: 14-3-3-gamma in complex with influenza NS1 C-terminal tail phosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o46
Title14-3-3-gamma in complex with influenza NS1 C-terminal tail phosphorylated at S228
Components
  • 14-3-3 protein gamma
  • Nonstructural protein 1
  • Unidentified polymer
KeywordsVIRAL PROTEIN / influenza / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / protein kinase C inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / Regulation of localization of FOXO transcription factors / protein serine/threonine kinase inhibitor activity ...symbiont-mediated suppression of host mRNA processing / positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / protein kinase C inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / Regulation of localization of FOXO transcription factors / protein serine/threonine kinase inhibitor activity / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / insulin-like growth factor receptor binding / negative regulation of TORC1 signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein kinase C binding / protein sequestering activity / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / receptor tyrosine kinase binding / regulation of synaptic plasticity / positive regulation of T cell activation / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / presynapse / regulation of protein localization / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / mitochondrial matrix / symbiont-mediated suppression of host gene expression / protein domain specific binding / focal adhesion / host cell nucleus / signal transduction / RNA binding / extracellular exosome / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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) / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein ...Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / S15/NS1, RNA-binding / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein gamma / Non-structural protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus H3N2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsQin, S. / Liu, Y. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2014
Title: Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1.
Authors: Qin, S. / Liu, Y. / Tempel, W. / Eram, M.S. / Bian, C. / Liu, K. / Senisterra, G. / Crombet, L. / Vedadi, M. / Min, J.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
C: 14-3-3 protein gamma
D: 14-3-3 protein gamma
E: 14-3-3 protein gamma
F: 14-3-3 protein gamma
G: Nonstructural protein 1
H: Nonstructural protein 1
I: Nonstructural protein 1
J: Nonstructural protein 1
K: Nonstructural protein 1
L: Nonstructural protein 1
M: Unidentified polymer
N: Unidentified polymer
O: Unidentified polymer
V: Unidentified polymer


Theoretical massNumber of molelcules
Total (without water)196,44473
Polymers196,44416
Non-polymers057
Water00
1
A: 14-3-3 protein gamma
G: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)31,36712
Polymers31,3672
Non-polymers010
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-7 kcal/mol
Surface area12250 Å2
MethodPISA
2
B: 14-3-3 protein gamma
H: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)31,36720
Polymers31,3672
Non-polymers018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-6 kcal/mol
Surface area12410 Å2
MethodPISA
3
C: 14-3-3 protein gamma
I: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)31,36716
Polymers31,3672
Non-polymers014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-8 kcal/mol
Surface area12260 Å2
MethodPISA
4
D: 14-3-3 protein gamma
J: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)31,36711
Polymers31,3672
Non-polymers09
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-8 kcal/mol
Surface area12410 Å2
MethodPISA
5
E: 14-3-3 protein gamma
K: Nonstructural protein 1
M: Unidentified polymer
N: Unidentified polymer
O: Unidentified polymer
V: Unidentified polymer


Theoretical massNumber of molelcules
Total (without water)39,60911
Polymers39,6096
Non-polymers05
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-9 kcal/mol
Surface area12370 Å2
MethodPISA
6
F: 14-3-3 protein gamma
L: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)31,3673
Polymers31,3672
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.829, 121.829, 314.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Components

#1: Protein
14-3-3 protein gamma / Protein kinase C inhibitor protein 1 / KCIP-1 / 14-3-3 protein gamma / N-terminally processed


Mass: 29494.809 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: P61981
#2: Protein/peptide
Nonstructural protein 1


Mass: 1872.202 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Influenza A virus H3N2 / References: UniProt: Q9YP60
#3: Protein/peptide
Unidentified polymer


Mass: 2060.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 57 / Source method: obtained synthetically
Has protein modificationY
Sequence detailsTHE AUTHORS STATE THAT THE UNIDENTIFIED POLYMER IN CHAINS M, N, O, AND V IS LIKELY PART OF ...THE AUTHORS STATE THAT THE UNIDENTIFIED POLYMER IN CHAINS M, N, O, AND V IS LIKELY PART OF DISORDERED 14-3-3-GAMMA.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 291 K
Details: 20% PEG3350, 0.2 M magnesium nitrate, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→113.59 Å / Num. all: 53464 / Num. obs: 53464 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 71.39 Å2 / Rsym value: 0.14 / Net I/σ(I): 21.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-3.0615.10.920.811522676540.92100
3.06-3.24150.5451.410916072620.545100
3.24-3.47150.3332.310276868480.333100
3.47-3.74150.2213.49576764040.221100
3.74-4.114.90.1375.58799359030.137100
4.1-4.5914.80.09387961253660.093100
4.59-5.2914.70.089.37081148080.08100
5.29-6.4814.50.0868.75938840880.086100
6.48-9.1714.20.04116.64574932310.041100
9.17-38.52612.90.02820.32444919000.02898.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.12data extraction
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3uzd

3uzd


Resolution: 2.9→38.53 Å / Cor.coef. Fo:Fc: 0.8997 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 0.01 / SU R Cruickshank DPI: 0.682 / Cross valid method: THROUGHOUT / σ(F): 0
Details: coot was used for interactive model building. refmac was used during intermediate refinement steps. Model geometry was assessed on the molprobity server. disjoint helices have been modeled ...Details: coot was used for interactive model building. refmac was used during intermediate refinement steps. Model geometry was assessed on the molprobity server. disjoint helices have been modeled into weak density. They have not been assigned specific amino acid sequences, and their direction is uncertain. additional uninterpreted density remains in that area of the electron density map. Attempts to locate additional 14-3-3-g molecules or larger fragments thereof by molecular replacement failed.
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 1510 2.83 %THIN SHELLS (SFTOOLS)
Rwork0.2255 ---
obs0.2262 53371 100 %-
Displacement parametersBiso max: 215.11 Å2 / Biso mean: 69.7905 Å2 / Biso min: 18.32 Å2
Baniso -1Baniso -2Baniso -3
1--5.5067 Å20 Å20 Å2
2---5.5067 Å20 Å2
3---11.0135 Å2
Refine analyzeLuzzati coordinate error obs: 0.494 Å
Refinement stepCycle: LAST / Resolution: 2.9→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10854 0 57 0 10911
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3699SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes277HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1635HARMONIC5
X-RAY DIFFRACTIONt_it10998HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1536SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12794SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10998HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg14930HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion2.02
X-RAY DIFFRACTIONt_other_torsion18.7
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2764 129 3.33 %
Rwork0.2555 3743 -
all0.2562 3872 -
obs--100 %
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)
11.54610.3873-0.26422.39140.04092.15410-0.2505-0.02640.6583-0.01540.21940.3417-0.24120.01540.0901-0.0331-0.0011-0.2263-0.0577-0.142-10.662332.8536-26.1691
20.82160.33210.44912.15511.1222.21530.10560.1795-0.18320.1160.0039-0.12440.2535-0.0928-0.1094-0.06510.0249-0.1247-0.1396-0.0748-0.0013-10.137125.7826-58.0392
31.3620.13180.12993.04210.20181.6072-0.179-0.14470.08260.21770.1648-0.3919-0.31060.25730.0142-0.0348-0.0007-0.0717-0.1725-0.0903-0.061914.484661.5555-29.5978
41.32020.3607-0.59361.88380.18332.2958-0.02460.52380.0266-0.40820.2659-0.1118-0.64720.4185-0.24130.09-0.14940.0284-0.0975-0.0873-0.16114.758159.7083-67.2424
55.0461-3.9239-1.09795.55231.62781.8595-0.24390.3172-0.14680.695-0.09330.27370.40440.03150.33720.0951-0.01510.0967-0.3373-0.0066-0.1834-38.242277.6745-57.7331
63.87140.6653-1.56150.4201-0.69541.9115-0.04490.12280.1074-0.02890.2030.36950.1196-0.5645-0.1581-0.1996-0.16380.304-0.4578-0.19920.4536-74.747173.4749-55.4519
70-0.7968-0.63480.5454-1.35140.28130.00670.0233-0.01650.0103-0.00360.0050.00520.0173-0.00310.0745-0.0250.0171-0.00430.0244-0.0715-41.203379.3187-13.8204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 236
2X-RAY DIFFRACTION2{ B|* }B2 - 235
3X-RAY DIFFRACTION3{ C|* }C1 - 235
4X-RAY DIFFRACTION4{ D|* }D1 - 235
5X-RAY DIFFRACTION5{ E|* }E2 - 237
6X-RAY DIFFRACTION6{ F|* }F2 - 235
7X-RAY DIFFRACTION7{ M|* }M6 - 25

+
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