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- EMDB-40953: Cryo-EM structure of DENV2 NS5 in complex with human STAT2 with t... -

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Basic information

Entry
Database: EMDB / ID: EMD-40953
TitleCryo-EM structure of DENV2 NS5 in complex with human STAT2 with the N-terminal domain of STAT2 disordered
Map data
Sample
  • Complex: Complex of DENV2 NS5 with human STAT2
    • Protein or peptide: Signal transducer and activator of transcription 2
    • Protein or peptide: Non-structural protein 5
  • Ligand: ZINC ION
KeywordsComplex / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


ISGF3 complex / negative regulation of type I interferon-mediated signaling pathway / regulation of mitochondrial fission / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / cell surface receptor signaling pathway via JAK-STAT / host cell mitochondrion / Regulation of IFNA/IFNB signaling ...ISGF3 complex / negative regulation of type I interferon-mediated signaling pathway / regulation of mitochondrial fission / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / cell surface receptor signaling pathway via JAK-STAT / host cell mitochondrion / Regulation of IFNA/IFNB signaling / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / regulation of protein phosphorylation / defense response / response to peptide hormone / RNA polymerase II transcription regulator complex / : / viral capsid / Interferon alpha/beta signaling / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / regulation of cell population proliferation / clathrin-dependent endocytosis of virus by host cell / defense response to virus / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Potential therapeutics for SARS / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / induction by virus of host autophagy / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / chromatin / virion attachment to host cell / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / : / Signal transducer and activator of transcription, linker domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain ...Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / : / Signal transducer and activator of transcription, linker domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / : / p53-like transcription factor, DNA-binding / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Signal transducer and activator of transcription 2 / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Dengue virus type 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsBiswal M / Lu J / Song J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of DENV2 NS5 in complex with human STAT2 with the N-terminal domain of STAT2 disordered
Authors: Biswal M / Lu J / Song J
History
DepositionJun 1, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40953.png

Downloads & links

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Map

FileDownload / File: emd_40953.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-1.3289365 - 2.148532
Average (Standard dev.)-0.000006111587 (±0.024543539)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 444.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_40953_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_40953_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_40953_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of DENV2 NS5 with human STAT2

EntireName: Complex of DENV2 NS5 with human STAT2
Components
  • Complex: Complex of DENV2 NS5 with human STAT2
    • Protein or peptide: Signal transducer and activator of transcription 2
    • Protein or peptide: Non-structural protein 5
  • Ligand: ZINC ION

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Supramolecule #1: Complex of DENV2 NS5 with human STAT2

SupramoleculeName: Complex of DENV2 NS5 with human STAT2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Signal transducer and activator of transcription 2

MacromoleculeName: Signal transducer and activator of transcription 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.025031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAQWEMLQNL DSPFQDQLHQ LYSHSLLPVD IRQYLAVWIE DQNWQEAALG SDDSKATMLF FHFLDQLNYE CGRCSQDPES LLLQHNLRK FCRDIQPFSQ DPTQLAEMIF NLLLEEKRIL IQAQRAQLEQ GEPVLETPVE SQQHEIESRI LDLRAMMEKL V KSISQLKD ...String:
MAQWEMLQNL DSPFQDQLHQ LYSHSLLPVD IRQYLAVWIE DQNWQEAALG SDDSKATMLF FHFLDQLNYE CGRCSQDPES LLLQHNLRK FCRDIQPFSQ DPTQLAEMIF NLLLEEKRIL IQAQRAQLEQ GEPVLETPVE SQQHEIESRI LDLRAMMEKL V KSISQLKD QQDVFCFRYK IQAKGKTPSL DPHQTKEQKI LQETLNELDK RRKEVLDASK ALLGRLTTLI ELLLPKLEEW KA QQQKACI RAPIDHGLEQ LETWFTAGAK LLFHLRQLLK ELKGLSCLVS YQDDPLTKGV DLRNAQVTEL LQRLLHRAFV VET QPCMPQ TPHRPLILKT GSKFTVRTRL LVRLQEGNES LTVEVSIDRN PPQLQGFRKF NILTSNQKTL TPEKGQSQGL IWDF GYLTL VEQRSGGSGK GSNKGPLGVT EELHIISFTV KYTYQGLKQE LKTDTLPVVI ISNMNQLSIA WASVLWFNLL SPNLQ NQQF FSNPPKAPWS LLGPALSWQF SSYVGRGLNS DQLSMLRNKL FGQNCRTEDP LLSWADFTKR ESPPGKLPFW TWLDKI LEL VHDHLKDLWN DGRIMGFVSR SQERRLLKKT MSGTFLLRFS ESSEGGITCS WVEHQDDDKV LIYSVQPYTK EVLQSLP LT EIIRHYQLLT EENIPENPLR FLYPRIPRDE AFGCYYQEKV NLQERRKYLK HRLIVVSNRQ VDELQQPLEL KPEPELES L ELELGLVPEP ELSLDLEPLL KAGLDLGPEL ESVLESTLEP VIEPTLCMVS QTVPEPDQGP VSQPVPEPDL PCDLRHLNT EPMEIFRNCV KIEEIMPNGD PLLAGQNTVD EVYVSRPSHF YTDGPLMPSD F

UniProtKB: Signal transducer and activator of transcription 2

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Macromolecule #2: Non-structural protein 5

MacromoleculeName: Non-structural protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus type 2
Molecular weightTheoretical: 103.264656 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GTGNTGETLG EKWKNRLNAL GKSEFQIYKK SGIQEVDRTL AKEGIKRGET DHHAVSRGSA KLRWFVERNL VTPEGKVVDL GCGRGGWSY YCGGLKNVKE VKGLTKGGPG HEEPIPMSTY GWNLVRLQSG VDVFFTPPEK CDTLLCDIGE SSPNPTVEAG R TLRVLNLV ...String:
GTGNTGETLG EKWKNRLNAL GKSEFQIYKK SGIQEVDRTL AKEGIKRGET DHHAVSRGSA KLRWFVERNL VTPEGKVVDL GCGRGGWSY YCGGLKNVKE VKGLTKGGPG HEEPIPMSTY GWNLVRLQSG VDVFFTPPEK CDTLLCDIGE SSPNPTVEAG R TLRVLNLV ENWLNNNTQF CIKVLNPYMP SVIEKMEALQ RKYGGALVRN PLSRNSTHEM YWVSNASGNI VSSVNMISRM LI NRFTMRH KKATYEPDVD LGSGTRNIGI ESETPNLDII GKRIEKIKQE HETSWHYDQD HPYKTWAYHG SYETKQTGSA SSM VNGVVR LLTKPWDIIP MVTQMAMTDT TPFGQQRVFK EKVDTRTQEP KEGTKKLMKI TAEWLWKELG KKKTPRMCTR EEFT RKVRS NAALGAIFTD ENKWKSAREA VEDSGFWELV DKERNLHLEG KCETCVYNMM GKREKKLGEF GKAKGSRAIW YMWLG ARFL EFEALGFLNE DHWFSRENSL SGVEGEGLHK LGYILRDVSK KEGGAMYADD TAGWDTRITL EDLKNEEMVT NHMEGE HKK LAEAIFKLTY QNKVVRVQRP TPRGTVMDII SRRDQRGSGQ VVTYGLNTFT NMEAQLIRQM EGEGVFKSIQ HLTVTEE IA VKNWLVRVGR ERLSRMAISG DDCVVKPLDD RFASALTALN DMGKVRKDIQ QWEPSRGWND WTQVPFCSHH FHELIMKD G RVLVVPCRNQ DELIGRARIS QGAGWSLRET ACLGKSYAQM WSLMYFHRRD LRLAANAICS AVPSHWVPTS RTTWSIHAT HEWMTTEDML TVWNRVWIQE NPWMEDKTPV ESWEEIPYLG KREDQWCGSL IGLTSRATWA KNIQTAINQV RSLIGNEEYT DYMPSMKRF RREEEEAGVL W

UniProtKB: Genome polyprotein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86928

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