[English] 日本語
Yorodumi
- EMDB-36888: Cryo-EM structure of Kaposi's Sarcoma-Associated Herpesvirus-G Pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36888
TitleCryo-EM structure of Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1
Map data
Sample
  • Complex: Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1 and Gi protein
    • Protein or peptide: G protein-coupled receptor
    • Protein or peptide: Growth-regulated alpha protein
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein subunit gamma
KeywordsKaposi's Sarcoma Herpesvirus GPCR / KSHV-GPCR / chemokine / VIRAL PROTEIN
Function / homology
Function and homology information


CXCR chemokine receptor binding / C-C chemokine receptor activity / C-C chemokine binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / G protein-coupled serotonin receptor binding / enzyme activator activity / neutrophil chemotaxis ...CXCR chemokine receptor binding / C-C chemokine receptor activity / C-C chemokine binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / G protein-coupled serotonin receptor binding / enzyme activator activity / neutrophil chemotaxis / calcium-mediated signaling / growth factor activity / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / specific granule lumen / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / antimicrobial humoral immune response mediated by antimicrobial peptide / GPER1 signaling / chemotaxis / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / tertiary granule lumen / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / nervous system development / cell cortex / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / actin cytoskeleton organization / G alpha (s) signalling events / G alpha (q) signalling events / cellular response to lipopolysaccharide / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / intracellular signal transduction / inflammatory response / immune response / G protein-coupled receptor signaling pathway / cell cycle / negative regulation of cell population proliferation / cell division / lysosomal membrane / signaling receptor binding / GTPase activity / centrosome / synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / G-protein alpha subunit, group I ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein subunit gamma / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Growth-regulated alpha protein / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / G protein-coupled receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Human gammaherpesvirus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsLiu YZ / Liu AJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of Kaposi's Sarcoma Herpesvirus GPCR (KSHV-GPCR)in complex with CXCL1
Authors: Liu YZ / Liu AJ
History
DepositionJul 20, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36888.png

Downloads & links

-
Map

FileDownload / File: emd_36888.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.4423473 - 4.1872015
Average (Standard dev.)-0.0019661942 (±0.09202834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_36888_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_36888_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Recepto...

EntireName: Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1 and Gi protein
Components
  • Complex: Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1 and Gi protein
    • Protein or peptide: G protein-coupled receptor
    • Protein or peptide: Growth-regulated alpha protein
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein subunit gamma

-
Supramolecule #1: Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Recepto...

SupramoleculeName: Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1 and Gi protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: G protein-coupled receptor

MacromoleculeName: G protein-coupled receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human gammaherpesvirus 8
Molecular weightTheoretical: 37.881773 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DFLTIFLDDD ESWNETLNMS GYDYSGNFSL EVSVCEMTTV VPYTWNVGIL SLIFLINVLG NGLVTYIFCK HRSRAGAIDI LLLGICLNS LCLSISLLAE VLMFLFPNII STGLCRLEIF FYYLYVYLDI FSVVCVSLVR YLLVAYSTRS WPKKQSLGWV L TSAALLIA ...String:
DFLTIFLDDD ESWNETLNMS GYDYSGNFSL EVSVCEMTTV VPYTWNVGIL SLIFLINVLG NGLVTYIFCK HRSRAGAIDI LLLGICLNS LCLSISLLAE VLMFLFPNII STGLCRLEIF FYYLYVYLDI FSVVCVSLVR YLLVAYSTRS WPKKQSLGWV L TSAALLIA LVLSGDACRH RSRVVDPVSK QAMCYENAGN MTADWRLHVR TVSVTAGFLL PLALLILFYA LTWCVVRRTK LQ ARRKVRG VIVAVVLLFF VFCFPYHVLN LLDTLLRRRW IRDSCYTRGL INVGLAVTSL LQALYSAVVP LIYSCLGSLF RQR MYGLFQ SLRQSFM

UniProtKB: G protein-coupled receptor

-
Macromolecule #2: Growth-regulated alpha protein

MacromoleculeName: Growth-regulated alpha protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.727939 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASVATELRCQ CLQTLQGIHP KNIQSVNVKS PGPHCAQTEV IATLKNGRKA CLNPASPIVK KII

UniProtKB: Growth-regulated alpha protein

-
Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.956383 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSAS QDGKLIIWDS YTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT GYLSCCRFLD DNQIVTSSGD T TCALWDIE ...String:
DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSAS QDGKLIIWDS YTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT GYLSCCRFLD DNQIVTSSGD T TCALWDIE TGQQTTTFTG HTGDVMSLSL APDTRLFVSG ACDASAKLWD VREGMCRQTF TGHESDINAI CFFPNGNAFA TG SDDATCR LFDLRADQEL MTYSHDNIIC GITSVSFSKS GRLLLAGYDD FNCNVWDALK ADRAGVLAGH DNRVSCLGVT DDG MAVATG SWDSFLKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

-
Macromolecule #4: Guanine nucleotide-binding protein G(I) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(I) subunit alpha-1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.914406 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LSAEDKAAVE RSKMIDRNLR EDGEKAAREV KLLLLGAGES GKSTIVKQMK IIHEAGYSEE ECKQYKAVVY SNTIQSIIAI IRAMGRLKI DFGDAARADD ARQLFVLAGS AEEGFMTAEL AGVIKRLWKD GGVQACFSRS REYQLNDSAA YYLNDLDRIS Q GSYIPTQQ ...String:
LSAEDKAAVE RSKMIDRNLR EDGEKAAREV KLLLLGAGES GKSTIVKQMK IIHEAGYSEE ECKQYKAVVY SNTIQSIIAI IRAMGRLKI DFGDAARADD ARQLFVLAGS AEEGFMTAEL AGVIKRLWKD GGVQACFSRS REYQLNDSAA YYLNDLDRIS Q GSYIPTQQ DVLRTRVKTT GIVETHFTFK DLHFKMFDVG GQRSERKKWI HCFEGVTAII FCVALSDYDL VLAEDEEMNR MH ESMKLFD SICNNKWFTD TSIILFLNKK DLFEEKIKKS PLTICYPEYA GSNTYEEAAA YIQCQFEDLN KRKDTKEIYT HFT CATDTK NVQFVFDAVT DVIIKNNLKD CGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

-
Macromolecule #5: Guanine nucleotide-binding protein subunit gamma

MacromoleculeName: Guanine nucleotide-binding protein subunit gamma / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.00197 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
IAQARKLVEQ LKMEANIDRI KVSKAAADLM AYCEAHAKED PLLTPVPASE NPFR

UniProtKB: Guanine nucleotide-binding protein subunit gamma

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridMaterial: GOLD
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6lfo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107180
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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