[English] 日本語
Yorodumi
- EMDB-65918: Structure of HCMV UL33 in complex with human Gs protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65918
TitleStructure of HCMV UL33 in complex with human Gs protein
Map datasharpened full map, globally refined map (main map)
Sample
  • Complex: UL33-Gas-Gb1-Gg2-Nb35
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nanobody35
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBit fusion
    • Protein or peptide: G-protein coupled receptor homolog UL33,G-protein coupled receptor homolog UL33,G-protein coupled receptor homolog UL33, LgBit fusion
KeywordsHCMV / viral protein / viral-host interaction / GPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / intracellular transport / D1 dopamine receptor binding / vascular endothelial cell response to laminar fluid shear stress / activation of adenylate cyclase activity / renal water homeostasis / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway ...PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / intracellular transport / D1 dopamine receptor binding / vascular endothelial cell response to laminar fluid shear stress / activation of adenylate cyclase activity / renal water homeostasis / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of insulin secretion / cellular response to glucagon stimulus / adenylate cyclase activator activity / trans-Golgi network membrane / negative regulation of inflammatory response to antigenic stimulus / bone development / platelet aggregation / cognition / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / Adrenaline,noradrenaline inhibits insulin secretion / sensory perception of smell / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / sensory perception of taste / positive regulation of cold-induced thermogenesis / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / retina development in camera-type eye / G protein activity / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / GTP binding / protein-containing complex binding / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily ...G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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. / 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 G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama) / Human betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTsutsumi N / Suzuki S / Nishikawa K / Fujiyoshi Y
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K01965 Japan
CitationJournal: Commun Biol / Year: 2026
Title: Activation of cytomegalovirus-encoded G protein-coupled receptor UL33 by an innate N-terminal peptide.
Authors: Anna K Drzazga / Shota Suzuki / Caroline Wouters / Felix Faas / Kouki Nishikawa / Akiko Kamegawa / Yoshinori Fujiyoshi / Mette M Rosenkilde / Naotaka Tsutsumi /
Abstract: Human cytomegalovirus (HCMV) encodes the orphan G protein-coupled receptor (GPCR) UL33, which exhibits constitutive activity that disrupts host G protein signalling, facilitating efficient viral ...Human cytomegalovirus (HCMV) encodes the orphan G protein-coupled receptor (GPCR) UL33, which exhibits constitutive activity that disrupts host G protein signalling, facilitating efficient viral replication and pathogenesis. The cryo-electron microscopy (cryo-EM) structure of UL33 bound to the G subtype of G protein reveals the N-terminal peptide as a tethered ligand reminiscent of the protease-activated receptors and adhesion GPCRs. This self-agonism induces a non-canonical active state that facilitates promiscuous G protein coupling, a plausible viral strategy for fine-tuning host signalling. Structure-guided mutagenesis disrupting key interactions between the N-terminus and its binding pocket abolishes G protein-mediated signalling, confirming the role of the N-terminus as a self-agonist. Our findings elucidate the structural basis for this activation mechanism and highlight the strategies employed by HCMV to hijack host G protein signalling.
History
DepositionAug 20, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_65918.png

Downloads & links

-
Map

FileDownload / File: emd_65918.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened full map, globally refined map (main map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 256 pix.
= 252.8 Å		0.99 Å/pix.
x 256 pix.
= 252.8 Å		0.99 Å/pix.
x 256 pix.
= 252.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9875 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.50181097 - 0.9747996
Average (Standard dev.)0.00050280604 (±0.024951734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 252.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_65918_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_65918_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #3

Fileemd_65918_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sharpened full map, receptor local refined map

Fileemd_65918_additional_1.map
Annotationsharpened full map, receptor local refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_65918_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_65918_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : UL33-Gas-Gb1-Gg2-Nb35

EntireName: UL33-Gas-Gb1-Gg2-Nb35
Components
  • Complex: UL33-Gas-Gb1-Gg2-Nb35
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nanobody35
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBit fusion
    • Protein or peptide: G-protein coupled receptor homolog UL33,G-protein coupled receptor homolog UL33,G-protein coupled receptor homolog UL33, LgBit fusion

-
Supramolecule #1: UL33-Gas-Gb1-Gg2-Nb35

SupramoleculeName: UL33-Gas-Gb1-Gg2-Nb35 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cytomegalovirus GPCR UL33 complexed with heterotrimeric Gs protein with dominant negative mutations via HiBit tethering stabilized by nanobody35
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 180 KDa

-
Macromolecule #1: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.729947 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFCAIL

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

-
Macromolecule #2: Nanobody35

MacromoleculeName: Nanobody35 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.969623 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSSH HHHHHEPEAH HHHHH

-
Macromolecule #3: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.568238 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GCLGNSKTED QRNEEKAQRE ANKKIEKQLQ KDKQVYRATH RLLLLGAGES GKNTIVKQMR ILHVNGFNGE GGEEDPQAAR SNSDGEKAT KVQDIKNNLK EAIETIVAAM SNLVPPVELA NPENQFRVDY ILSVMNVPDF DFPPEFYEHA KALWEDEGVR A CYERSNEY ...String:
GCLGNSKTED QRNEEKAQRE ANKKIEKQLQ KDKQVYRATH RLLLLGAGES GKNTIVKQMR ILHVNGFNGE GGEEDPQAAR SNSDGEKAT KVQDIKNNLK EAIETIVAAM SNLVPPVELA NPENQFRVDY ILSVMNVPDF DFPPEFYEHA KALWEDEGVR A CYERSNEY QLIDCAQYFL DKIDVIKQAD YVPSDQDLLR CRVLTSGIFE TKFQVDKVNF HMFDVGAQRD ERRKWIQCFN DV TAIIFVV ASSSYNMVIR EDNQTNRLQA ALKLFDSIWN NKWLRDTSVI LFLNKQDLLA EKVLAGKSKI EDYFPEFARY TTP EDATPE PGEDPRVTRA KYFIRDEFLR ISTASGDGRH YCYPHFTCSV DTENIRRVFN DCRDIIQRMH LRQYELL

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

-
Macromolecule #4: 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,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta- ...Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBit fusion
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.039648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWNG SSGGGGSGGG GSSGVSGWRL FKKIS

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

-
Macromolecule #5: G-protein coupled receptor homolog UL33,G-protein coupled recepto...

MacromoleculeName: G-protein coupled receptor homolog UL33,G-protein coupled receptor homolog UL33,G-protein coupled receptor homolog UL33, LgBit fusion
type: protein_or_peptide / ID: 5
Details: G-protein coupled receptor homolog UL33, LgBit fusion,G-protein coupled receptor homolog UL33, LgBit fusion,G-protein coupled receptor homolog UL33, LgBit fusion,G-protein coupled receptor ...Details: G-protein coupled receptor homolog UL33, LgBit fusion,G-protein coupled receptor homolog UL33, LgBit fusion,G-protein coupled receptor homolog UL33, LgBit fusion,G-protein coupled receptor homolog UL33, LgBit fusion
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 68.188695 KDa
Recombinant expressionOrganism: Human betaherpesvirus 5
SequenceString: MDTIIHNSTR NNTPPHINDT CNMTGPLFAI RTTEAVLNTF IIFVGGPLNA IVLITQLLTN RVLGYSTPTI YMTNLYSTNF LTLTVLPFI VLSNQWLLPA GVASCKFLSV IYYSSCTVGF ATVALIAADR YRVLHKRTYA RQSYRSTYMI LLLTWLAGLI F SVPAAVYT ...String:
MDTIIHNSTR NNTPPHINDT CNMTGPLFAI RTTEAVLNTF IIFVGGPLNA IVLITQLLTN RVLGYSTPTI YMTNLYSTNF LTLTVLPFI VLSNQWLLPA GVASCKFLSV IYYSSCTVGF ATVALIAADR YRVLHKRTYA RQSYRSTYMI LLLTWLAGLI F SVPAAVYT TVVMHHDAND TNNTNGHATC VLYFVAEEVH TVLLSWKVLL TMVWGAAPVI MMTWFYAFFY STVQRTSQKQ RS RTLTFVS VLLISFVALQ TPYVSLMIFN SYATTAWPMQ CEHLTLRRTI GTLARVVPHL HCLINPILYA LLGHDFLQRM RQC FRGQLL DRRAFLRSQQ NQRATAETNL AAGNNSQSVA TSLDTNSKNY NQHAKRSVSF NFPSGTWKGG QKTASNDTST KIPH RLSQS HHNLSGVAAA EDQVDPRLID GKSRGSSGGG GSGGGGSSGV FTLEDFVGDW EQTAAYNLDQ VLEQGGVSSL LQNLA VSVT PIQRIVRSGE NALKIDIHVI IPYEGLSADQ MAQIEEVFKV VYPVDDHHFK VILPYGTLVI DGVTPNMLNY FGRPYE GIA VFDGKKITVT GTLWNGNKII DERLITPDGS MLFRVTINSG GGGSHHHHHH HH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration9 mg/mL
BufferpH: 7.2
Component:
ConcentrationName
10.0 mMHepes-Na
150.0 mMNaCl
0.001 % (w/v)LMNG
0.001 % (w/v)GDN
0.0001 % (w/v)CHS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
DetailsThe microscope model is the JEOL's "JEM-Z320FHC", a custom-built model of JEOL CRYO ARM 300.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 63291 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.4 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 1502019 / Details: initial particles that appeared to be protein
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6)
Details: CryoSPARC patch CTF estimation and global/local CTF refinements
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: CryoSPARC ab-initio reconstruction model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Details: CryoSPARC non-uniform refinement / Number images used: 54507
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6) / Details: CryoSPARC ab-initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6) / Details: CryoSPARC non-uniform refinement
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.6) / Details: CryoSPARC 3D classificaiotion
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChainDetails

7xt8

source_name: PDB, initial_model_type: experimental modelGs-Nb35

fold

source_name: Other, initial_model_type: in silico modelUL33
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 106.4
Output model

PDB-9wey:
Structure of HCMV UL33 in complex with human Gs protein

+
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