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- EMDB-66864: Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state -

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Basic information

Entry
Database: EMDB / ID: EMD-66864
TitleStructure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state
Map dataSharpened map for refinement.
Sample
  • Complex: CX3CL1.44-US28-GqiN18-scFv16
    • Complex: Gq heterotrimer
      • 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)/G(S)/G(O) subunit gamma-2
    • Complex: CX3CL1.44-US28
      • Protein or peptide: G-protein coupled receptor homolog US28
      • Protein or peptide: N-terminal fragment of the engineered fractalkine CX3CL1.44
    • Complex: scFv16
      • Protein or peptide: Antibody fragment scFv16
  • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: CHOLESTEROL
KeywordsMEMBRANE PROTEIN / GPCR / intermediate state / GDP / engineered chemokine / HCMV / viral protein / viral-host interaction
Function / homology
Function and homology information


positive regulation of gonadotropin secretion / phospholipase C-activating tachykinin receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / regulation of platelet activation / PLC beta mediated events / phospholipase C-activating serotonin receptor signaling pathway / entrainment of circadian clock / sensory perception of itch ...positive regulation of gonadotropin secretion / phospholipase C-activating tachykinin receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / regulation of platelet activation / PLC beta mediated events / phospholipase C-activating serotonin receptor signaling pathway / entrainment of circadian clock / sensory perception of itch / positive regulation of membrane depolarization / phototransduction, visible light / C-C chemokine binding / C-C chemokine receptor activity / regulation of canonical Wnt signaling pathway / symbiont-mediated transformation of host cell / glutamate receptor signaling pathway / postsynaptic cytosol / photoreceptor outer segment / hormone-mediated signaling pathway / cellular response to acidic pH / symbiont-mediated perturbation of host defense response / GTPase activator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / mast cell degranulation / calcium-mediated signaling / cell chemotaxis / neuropeptide signaling pathway / response to prostaglandin E / G protein-coupled receptor binding / blood coagulation / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / glucose homeostasis / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / nuclear membrane / G-protein beta-subunit binding / extracellular vesicle / positive regulation of cytosolic calcium ion concentration / Thrombin signalling through proteinase activated receptors (PARs) / adenylate cyclase-activating G protein-coupled receptor signaling pathway / signaling receptor complex adaptor activity / GTPase binding / G protein activity / Ca2+ pathway / 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 / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic side of plasma membrane / Ras protein signal transduction / Extra-nuclear estrogen signaling / protein stabilization / immune response / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / GTP binding / synapse / host cell plasma membrane / protein-containing complex binding / Golgi apparatus / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
G-protein alpha subunit, group Q / Chemokine receptor family / : / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. ...G-protein alpha subunit, group Q / Chemokine receptor family / : / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / 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 / Guanine nucleotide-binding protein, beta subunit / G protein beta WD-40 repeat protein / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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(q) subunit alpha / 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 / G protein-coupled receptor homolog US28
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / Human betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJude KM / Garcia KC / Tsutsumi N
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K01965 Japan
CitationJournal: To Be Published
Title: Structural basis of a stepwise Gq activation by a chemokine receptor US28
Authors: Jude KM / Garcia KC / Tsutsumi N
History
DepositionOct 31, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_66864.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map for refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 300 pix.
= 305.4 Å
1.02 Å/pix.
x 300 pix.
= 305.4 Å
1.02 Å/pix.
x 300 pix.
= 305.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.018 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.9111277 - 1.425036
Average (Standard dev.)-0.00009725899 (±0.025524773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 305.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66864_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: Unsharpened map.

Fileemd_66864_additional_1.map
AnnotationUnsharpened map.
Projections & Slices
AxesZYX

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Additional map: deepEMhancer sharpened map.

Fileemd_66864_additional_2.map
AnnotationdeepEMhancer sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map B.

Fileemd_66864_half_map_1.map
AnnotationHalf map B.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: Half map A.

Fileemd_66864_half_map_2.map
AnnotationHalf map A.
Projections & Slices
AxesZYX

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Sample components

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Entire : CX3CL1.44-US28-GqiN18-scFv16

EntireName: CX3CL1.44-US28-GqiN18-scFv16
Components
  • Complex: CX3CL1.44-US28-GqiN18-scFv16
    • Complex: Gq heterotrimer
      • 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)/G(S)/G(O) subunit gamma-2
    • Complex: CX3CL1.44-US28
      • Protein or peptide: G-protein coupled receptor homolog US28
      • Protein or peptide: N-terminal fragment of the engineered fractalkine CX3CL1.44
    • Complex: scFv16
      • Protein or peptide: Antibody fragment scFv16
  • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: CHOLESTEROL

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Supramolecule #1: CX3CL1.44-US28-GqiN18-scFv16

SupramoleculeName: CX3CL1.44-US28-GqiN18-scFv16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: Gq heterotrimer

SupramoleculeName: Gq heterotrimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Supramolecule #3: CX3CL1.44-US28

SupramoleculeName: CX3CL1.44-US28 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Details: Complex between chemokine analog CX3CL1.44 and HCMV GPCR US28
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Details: GPCR/G protein complex-stabilizing antibody fragment scFv16
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 30 KDa

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

MacromoleculeName: Guanine nucleotide-binding protein G(q) subunit alpha / type: protein_or_peptide / ID: 1
Details: engineered G protein G(q) subunit alpha with G(i1) subunit alpha N-terminal region
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: 41.249934 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GCTLSAEDKA AVERSKMIER QLRRDKRDAR RELKLLLLGT GESGKSTFIK QMRIIHGSGY SDEDKRGFTK LVYQNIFTAM QAMIRAMDT LKIPYKYEHN KAHAQLVREV DVEKVSAFEN PYVDAIKSLW NDPGIQECYD RRREYQLSDS TKYYLNDLDR V ADPAYLPT ...String:
GCTLSAEDKA AVERSKMIER QLRRDKRDAR RELKLLLLGT GESGKSTFIK QMRIIHGSGY SDEDKRGFTK LVYQNIFTAM QAMIRAMDT LKIPYKYEHN KAHAQLVREV DVEKVSAFEN PYVDAIKSLW NDPGIQECYD RRREYQLSDS TKYYLNDLDR V ADPAYLPT QQDVLRVRVP TTGIIEYPFD LQSVIFRMVD VGGQRSERRK WIHCFENVTS IMFLVALSEY DQVLVESDNE NR MEESKAL FRTIITYPWF QNSSVILFLN KKDLLEEKIM YSHLVDYFPE YDGPQRDAQA AREFILKMFV DLNPDSDKII YSH FTCATD TENIRFVFAA VKDTILQLNL KEYNLV

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

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Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.728152 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 WDSFLKIWN

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

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.432554 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFC

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

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Macromolecule #4: Antibody fragment scFv16

MacromoleculeName: Antibody fragment scFv16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.340482 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KGSLEVLFQ

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Macromolecule #5: G-protein coupled receptor homolog US28

MacromoleculeName: G-protein coupled receptor homolog US28 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 42.041098 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDAMT PTTTTAELTT EFDYDEDATP CVFTDVLNQS KPVTLFLYGV VFLFGSIGNF LVIFTITWRR RIQCSGDVYF INLAAADLL FVCTLPLWMQ YLLDHNSLAS VPCTLLTACF YVAMFASLCF ITEIALDRYY AIVYMRYRPV KQACLFSIFW W IFAVIIAI ...String:
DYKDDDDAMT PTTTTAELTT EFDYDEDATP CVFTDVLNQS KPVTLFLYGV VFLFGSIGNF LVIFTITWRR RIQCSGDVYF INLAAADLL FVCTLPLWMQ YLLDHNSLAS VPCTLLTACF YVAMFASLCF ITEIALDRYY AIVYMRYRPV KQACLFSIFW W IFAVIIAI PHFMVVTKKD NQCMTDYDYL EVSYPIILNV ELMLGAFVIP LSVISYCYYR ISRIVAVSQS RHKGRIVRVL IA VVLVFII FWLPYHLTLF VDTLKLLKWI SSSCEFERSL KRALILTESL AFCHCCLNPL LYVFVGTKFR QELHCLLAEF RQR LFSRDV SWYHSMSFSR RSSPSRRETS SDTLSDEVCR VSQIIP

UniProtKB: G protein-coupled receptor homolog US28

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Macromolecule #6: N-terminal fragment of the engineered fractalkine CX3CL1.44

MacromoleculeName: N-terminal fragment of the engineered fractalkine CX3CL1.44
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.072578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VRPHINNCNI TCSKMTSKIP VALLIHYQQN QASCGKRAII LETRQHRLFC ADPKEQWVKD AMQHLDRQAA ALTRNGGSGS GSAAALEVL FQ

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Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #8: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 8 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

Concentration20 mg/mL
BufferpH: 7.2
Component:
ConcentrationName
10.0 mMHepes-sodium salt
150.0 mMSodium chloride
0.001 % w/vLauryl Maltose Neopentyl Glycol
0.001 % w/vGlyco-diosgenin
0.0001 % w/vCholesterol Hydrogen Succinate
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289 K / Instrument: LEICA EM GP / Details: 3 s blotting before plunging.
Detailschemokine-GPCR complex coupled to Gq heterotrimer

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 11773 / Average exposure time: 2.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 57624 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8400483 / 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 reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 193867
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 local refinement
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9xh2:
Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state

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