[English] 日本語
Yorodumi
- PDB-6u28: Crystal structure of 1918 NS1-ED W187A in complex with the p85-be... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u28
TitleCrystal structure of 1918 NS1-ED W187A in complex with the p85-beta-iSH2 domain of human PI3K
Components
  • Non-structural protein 1
  • Phosphatidylinositol 3-kinase regulatory subunit beta
KeywordsVIRAL PROTEIN / 1918 influenza A virus / NS1 / PI3K
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / protein serine/threonine kinase inhibitor activity / RHOF GTPase cycle / regulation of stress fiber assembly / RHOD GTPase cycle ...symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / protein serine/threonine kinase inhibitor activity / RHOF GTPase cycle / regulation of stress fiber assembly / RHOD GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / RND2 GTPase cycle / PI3K/AKT activation / RND3 GTPase cycle / negative regulation of MAPK cascade / Signaling by ALK / RHOB GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / phosphatidylinositol phosphate biosynthetic process / CDC42 GTPase cycle / RHOU GTPase cycle / T cell differentiation / RET signaling / positive regulation of cell adhesion / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of protein localization to plasma membrane / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Tie2 Signaling / GPVI-mediated activation cascade / RAC1 GTPase cycle / Interleukin-7 signaling / phosphotyrosine residue binding / response to endoplasmic reticulum stress / Downstream signal transduction / B cell differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / regulation of autophagy / Regulation of signaling by CBL / Signaling by SCF-KIT / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / cellular response to insulin stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / Signaling by ALK fusions and activated point mutants / protein transport / Downstream TCR signaling / insulin receptor signaling pathway / PIP3 activates AKT signaling / DAP12 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / G alpha (q) signalling events / protein phosphatase binding / host cell cytoplasm / Extra-nuclear estrogen signaling / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / protein heterodimerization activity / focal adhesion / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / 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) / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain ...Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / 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) / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit beta / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCho, J.H. / Zhao, B. / Savage, N. / Li, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM127723 01A1 United States
National Institute of Food and Agriculture (NIFA, United States)1020344 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses.
Authors: Cho, J.H. / Zhao, B. / Shi, J. / Savage, N. / Shen, Q. / Byrnes, J. / Yang, L. / Hwang, W. / Li, P.
History
DepositionAug 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _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
C: Phosphatidylinositol 3-kinase regulatory subunit beta
B: Non-structural protein 1
D: Phosphatidylinositol 3-kinase regulatory subunit beta


Theoretical massNumber of molelcules
Total (without water)72,4634
Polymers72,4634
Non-polymers00
Water00
1
A: Non-structural protein 1
C: Phosphatidylinositol 3-kinase regulatory subunit beta


Theoretical massNumber of molelcules
Total (without water)36,2312
Polymers36,2312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-8 kcal/mol
Surface area15040 Å2
MethodPISA
2
B: Non-structural protein 1
D: Phosphatidylinositol 3-kinase regulatory subunit beta


Theoretical massNumber of molelcules
Total (without water)36,2312
Polymers36,2312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-8 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.190, 92.390, 66.940
Angle α, β, γ (deg.)90.000, 105.170, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 16337.927 Da / Num. of mol.: 2 / Fragment: effector domain / Mutation: W187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)
Strain: A/Brevig Mission/1/1918 H1N1 / Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: Q99AU3
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit beta / PtdIns-3-kinase regulatory subunit beta / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit beta / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit beta / PtdIns-3-kinase regulatory subunit p85-beta


Mass: 19893.389 Da / Num. of mol.: 2 / Mutation: C501S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00459

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.1 / Details: tris 20 mM, trehalose 0.7 M, sodium chloride 80 mM

-
Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→64.61 Å / Num. obs: 15268 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 67.87 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.111 / Rrim(I) all: 0.211 / Net I/σ(I): 6.1 / Num. measured all: 53699 / Scaling rejects: 104
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.95-3.133.50.938864624550.5980.5871.111.3100
8.85-64.613.30.12519305920.9450.080.1491399.2

-
Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OX7

6ox7


Resolution: 2.95→34.145 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.47
RfactorNum. reflection% reflection
Rfree0.2395 701 4.61 %
Rwork0.2225 --
obs0.2233 15214 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.18 Å2 / Biso mean: 74.0454 Å2 / Biso min: 36.34 Å2
Refinement stepCycle: final / Resolution: 2.95→34.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4219 0 0 0 4219
Num. residues----519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.9503-3.17790.30881370.31782892
3.1779-3.49740.29381450.27192858
3.4974-4.00290.27341280.22742902
4.0029-5.04060.21781550.19352909
5.0406-34.1450.20431360.20092952
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)
10.06180.1745-0.20830.7006-0.5910.5445-0.1707-0.7407-0.50460.4328-0.2556-0.0339-0.15950.6275-0.00190.64710.0705-0.02520.49650.05540.492124.56621.453715.0104
20.8492-0.4979-0.2961.0735-0.4770.7928-0.3212-0.02540.85360.31050.2720.2149-0.6211-0.2075-0.00230.62330.1245-0.06240.4311-0.04450.538818.607339.70569.6145
31.0192-0.15690.30870.3874-0.51420.7974-0.22510.1046-0.0390.0442-0.05970.00280.02220.7075-0.00020.44980.0722-0.02770.44130.00110.486927.071325.27838.4362
40.99760.7463-0.53492.1398-0.07241.1173-0.2974-0.10340.2478-0.00360.1829-0.2273-0.3040.3648-0.00010.5128-0.0003-0.0090.4301-0.04560.527826.233232.36356.3605
5-0.01650.0186-0.00940.06410.0412-0.0108-0.2685-0.1378-0.66920.77710.44570.5709-0.20070.17440.00061.3519-0.2385-0.11261.6916-0.05671.037536.680739.45427.9024
60.2764-0.6001-0.39550.98210.03520.9992-0.2407-0.6031-0.34870.36780.46830.38820.2237-0.09390.01160.79360.15190.03170.6533-0.02330.568826.2772.064223.1158
70.52640.51430.09620.7949-0.40080.49720.2189-0.1292-0.42820.3199-0.02910.5529-0.11430.182601.09880.3432-0.03510.8049-0.11150.70641.7016-17.49526.1572
80.80160.66090.49291.3988-0.81072.0302-0.10990.06350.20250.56270.0553-0.0805-0.1225-0.33910.00030.51880.0930.01370.4738-0.04910.451614.23418.85915.7217
90.33210.4226-0.3350.9267-0.15040.50850.30220.9472-0.4476-0.4842-0.062-0.6236-0.02290.16660.00050.41580.04350.03750.6038-0.09410.562615.48977.3079-10.5836
101.9223-1.07510.43880.598-0.28660.1169-0.01380.2015-0.401-0.00110.05770.9314-0.0626-0.27450.00020.5528-0.03020.05620.6318-0.02930.7035-3.66415.2714-5.3868
110.3559-0.2125-0.22580.11520.11060.15420.12980.2049-0.4476-0.01820.1156-0.2630.38790.077800.42350.11950.0140.5765-0.04560.500412.0711.63-5.9498
120.8564-0.3367-0.79481.0833-0.01210.8480.0158-0.05940.09940.3643-0.25350.04350.61410.1309-00.54950.05110.0120.5218-0.00670.4379.02214.4392-5.4754
130.9829-0.36510.84410.8938-0.3171.0003-0.0424-0.2343-0.41120.44740.02480.21360.339-0.36220.00010.4608-0.0123-0.00710.40570.03470.44024.74672.02880.9384
140.1572-0.0627-0.00280.0538-0.11140.3393-0.14110.2383-1.12590.34290.5983-1.0211.2858-0.20080.01170.78970.04430.05060.48290.00690.795216.111-4.0163-1.4274
151.3955-0.0175-0.36510.02990.13531.01280.1730.36870.4614-0.07950.0405-0.20310.05630.04020.00020.58310.0117-0.01210.63610.00130.517340.97015.8633-20.5082
160.8956-0.3142-1.21520.59760.72871.1665-0.03430.2024-0.0192-0.18440.2246-0.10510.02420.21110.00160.44-0.00150.02930.5814-0.05690.472235.295810.4162-16.982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 86 through 99 )A86 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 126 )A100 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 151 )A127 - 151
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 201 )A152 - 201
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 212 )A202 - 212
6X-RAY DIFFRACTION6chain 'C' and (resid 433 through 489 )C433 - 489
7X-RAY DIFFRACTION7chain 'C' and (resid 490 through 561 )C490 - 561
8X-RAY DIFFRACTION8chain 'C' and (resid 562 through 597 )C562 - 597
9X-RAY DIFFRACTION9chain 'B' and (resid 86 through 99 )B86 - 99
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 126 )B100 - 126
11X-RAY DIFFRACTION11chain 'B' and (resid 127 through 137 )B127 - 137
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 162 )B138 - 162
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 195 )B163 - 195
14X-RAY DIFFRACTION14chain 'B' and (resid 196 through 204 )B196 - 204
15X-RAY DIFFRACTION15chain 'D' and (resid 433 through 525 )D433 - 525
16X-RAY DIFFRACTION16chain 'D' and (resid 526 through 597 )D526 - 597

+
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