[English] 日本語
Yorodumi
- EMDB-24496: Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24496
TitleStructure of CX3CL1-US28-G11iN18-scFv16 in TL-state
Map dataFull sharpen map.
Sample
  • Complex: CX3CL1-US28-G11iN18-scFv16 complex
    • Complex: G11iN18 heterotrimer
      • Protein or peptide: Guanine nucleotide-binding protein subunit alpha-11
      • 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: scFv16
      • Protein or peptide: Antibody fragment scFv16
    • Complex: CX3CL1-US28
      • Protein or peptide: FractalkineCX3CL1
      • Protein or peptide: G-protein coupled receptor homolog US28
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


positive regulation by virus of host cell division / : / CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / regulation of melanocyte differentiation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process ...positive regulation by virus of host cell division / : / CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / regulation of melanocyte differentiation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / autocrine signaling / synapse pruning / negative regulation of neuron migration / positive regulation of microglial cell migration / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / negative regulation of microglial cell activation / positive regulation of transforming growth factor beta1 production / ion channel modulating, G protein-coupled receptor signaling pathway / regulation of lipopolysaccharide-mediated signaling pathway / Acetylcholine regulates insulin secretion / endothelin receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / developmental pigmentation / chemokine receptor activity / positive regulation of I-kappaB phosphorylation / cellular response to pH / microglial cell proliferation / PLC beta mediated events / phospholipase C-activating dopamine receptor signaling pathway / CCR chemokine receptor binding / leukocyte migration involved in inflammatory response / entrainment of circadian clock / cranial skeletal system development / positive regulation of actin filament bundle assembly / lymphocyte chemotaxis / phototransduction, visible light / integrin activation / eosinophil chemotaxis / angiogenesis involved in wound healing / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / negative regulation of cell-substrate adhesion / negative regulation of interleukin-1 beta production / positive regulation of cell-matrix adhesion / action potential / neuron remodeling / positive regulation of neuroblast proliferation / positive chemotaxis / chemoattractant activity / ligand-gated ion channel signaling pathway / monocyte chemotaxis / negative regulation of interleukin-6 production / negative regulation of apoptotic signaling pathway / negative regulation of tumor necrosis factor production / photoreceptor outer segment / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cellular response to interleukin-1 / enzyme regulator activity / extrinsic apoptotic signaling pathway in absence of ligand / virus-mediated perturbation of host defense response / cell chemotaxis / neutrophil chemotaxis / negative regulation of cell migration / positive regulation of release of sequestered calcium ion into cytosol / G protein activity / skeletal system development / cell projection / response to ischemia / G protein-coupled receptor binding / positive regulation of smooth muscle cell proliferation / microglial cell activation / regulation of synaptic plasticity / Olfactory Signaling Pathway / G-protein beta/gamma-subunit complex binding / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / defense response / 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 / positive regulation of insulin secretion / cell-cell adhesion / 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
Similarity search - Function
CX3C chemokine domain / G-protein alpha subunit, group Q / Chemokine receptor family / 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-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit ...CX3C chemokine domain / G-protein alpha subunit, group Q / Chemokine receptor family / 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-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 receptors family 1 signature. / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 alpha-11 / 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 / Fractalkine
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / Human betaherpesvirus 5 / Human cytomegalovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsTsutsumi N / Maeda S / Qu Q / Skiniotis G / Kobilka BK / Garcia KC
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125320 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Adv / Year: 2022
Title: Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins
Authors: Tsutsumi N / Maeda S / Qu Q / Voegele M / Jude KM / Suomivuori CM / Panova O / Waghray D / Kato HE / Velasco A / Dror RO / Skiniotis G / Kobilka BK / Garcia KC
History
DepositionJul 22, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateJan 26, 2022-
Current statusJan 26, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7rkf
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24496.png

Downloads & links

-
Map

FileDownload / File: emd_24496.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull sharpen map.
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.015
Minimum - Maximum-0.06689626 - 0.11834154
Average (Standard dev.)0.00016979901 (±0.0021678398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z255.000255.000255.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0670.1180.000

-
Supplemental data

-
Sample components

+
Entire : CX3CL1-US28-G11iN18-scFv16 complex

EntireName: CX3CL1-US28-G11iN18-scFv16 complex
Components
  • Complex: CX3CL1-US28-G11iN18-scFv16 complex
    • Complex: G11iN18 heterotrimer
      • Protein or peptide: Guanine nucleotide-binding protein subunit alpha-11
      • 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: scFv16
      • Protein or peptide: Antibody fragment scFv16
    • Complex: CX3CL1-US28
      • Protein or peptide: FractalkineCX3CL1
      • Protein or peptide: G-protein coupled receptor homolog US28
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

+
Supramolecule #1: CX3CL1-US28-G11iN18-scFv16 complex

SupramoleculeName: CX3CL1-US28-G11iN18-scFv16 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

+
Supramolecule #2: G11iN18 heterotrimer

SupramoleculeName: G11iN18 heterotrimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human) / Location in cell: Membrane
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 90 KDa

+
Supramolecule #3: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 30 KDa

+
Supramolecule #4: CX3CL1-US28

SupramoleculeName: CX3CL1-US28 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Human betaherpesvirus 5
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 50 KDa

+
Macromolecule #1: Guanine nucleotide-binding protein subunit alpha-11

MacromoleculeName: Guanine nucleotide-binding protein subunit alpha-11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.254125 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GCTLSAEDKA AVERSKMIEK QLRRDKRDAR RELKLLLLGT GESGKSTFIK QMRIIHGAGY SEEDKRGFTK LVYQNIFTAM QAMIRAMET LKILYKYEQN KANALLIREV DVEKVTTFEH QYVSAIKTLW EDPGIQECYD RRREYQLSDS AKYYLTDVDR I ATLGYLPT ...String:
GCTLSAEDKA AVERSKMIEK QLRRDKRDAR RELKLLLLGT GESGKSTFIK QMRIIHGAGY SEEDKRGFTK LVYQNIFTAM QAMIRAMET LKILYKYEQN KANALLIREV DVEKVTTFEH QYVSAIKTLW EDPGIQECYD RRREYQLSDS AKYYLTDVDR I ATLGYLPT QQDVLRVRVP TTGIIEYPFD LENIIFRMVD VGGQRSERRK WIHCFENVTS IMFLVALSEY DQVLVESDNE NR MEESKAL FRTIITYPWF QNSSVILFLN KKDLLEDKIL YSHLVDYFPE FDGPQRDAQA AREFILKMFV DLNPDSDKII YSH FTCATD TENIRFVFAA VKDTILQLNL KEYNLV

+
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

+
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

+
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

+
Macromolecule #5: Fractalkine

MacromoleculeName: Fractalkine / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.013487 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
(PCA)HHGVTKCNI TCSKMTSKIP VALLIHYQQN QASCGKRAII LETRQHRLFC ADPKEQWVKD AMQHLDRQAA ALTRNG GSG SGSAAALEVL FQ

+
Macromolecule #6: G-protein coupled receptor homolog US28

MacromoleculeName: G-protein coupled receptor homolog US28 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human cytomegalovirus / Strain: AD169
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

+
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 / Guanosine diphosphate

+
Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration25 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
0.05 % w/vOctyl beta-D-glucopyranoside
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 1 s blotting before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58679 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1330 / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 795403
CTF correctionSoftware: (Name: Gctf (ver. 1.06), RELION (ver. 3.1))
Details: Final per-particle CTF values were determined by Relion 3.1 CTF correction.
Startup modelType of model: OTHER / Details: Initial model created by Relion version 3.1.
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 126645

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7rkf:
Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state

+
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