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- EMDB-60718: Cryo-EM structure of G1-ATPase dimer from Mycoplasma mobile glidi... -

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Basic information

Entry
Database: EMDB / ID: EMD-60718
TitleCryo-EM structure of G1-ATPase dimer from Mycoplasma mobile gliding machinery
Map data
Sample
  • Complex: G1-ATPase dimer from Mycoplasma mobile gliding machinery
    • Protein or peptide: x 8 types
  • Ligand: x 4 types
KeywordsATPase / Complex / kinase / Ring / HYDROLASE
Function / homology
Function and homology information


H+-transporting two-sector ATPase / phosphoglycerate kinase / phosphoglycerate kinase activity / : / proton-transporting ATP synthase activity, rotational mechanism / gluconeogenesis / glycolytic process / ADP binding / hydrolase activity / ATP hydrolysis activity ...H+-transporting two-sector ATPase / phosphoglycerate kinase / phosphoglycerate kinase activity / : / proton-transporting ATP synthase activity, rotational mechanism / gluconeogenesis / glycolytic process / ADP binding / hydrolase activity / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / ATP synthase, F1 complex, beta subunit / : / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit ...Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / ATP synthase, F1 complex, beta subunit / : / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phosphoglycerate kinase / Uncharacterized protein / ATP synthase beta chain / ATP synthase alpha chain / Expressed protein / Expressed protein
Similarity search - Component
Biological speciesMycoplasma mobile 163K (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsToyonaga T / Kato T / Kawamoto A / Miyata T / Kawakami K / Fujita J / Hamaguchi T / Namba K / Miyata M
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H01544 Japan
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Agency for Medical Research and Development (AMED)JP22am121003 Japan
Other government
CitationJournal: Sci Adv / Year: 2025
Title: Dimeric assembly of F-like ATPase for the gliding motility of .
Authors: Takuma Toyonaga / Takayuki Kato / Akihiro Kawamoto / Tomoko Miyata / Keisuke Kawakami / Junso Fujita / Tasuku Hamaguchi / Keiichi Namba / Makoto Miyata /
Abstract: Rotary ATPases, including FF-, VV-, and AA-ATPases, are molecular motors that exhibit rotational movements for energy conversion. In the gliding bacterium, , a dimeric F-like ATPase forms a chain ...Rotary ATPases, including FF-, VV-, and AA-ATPases, are molecular motors that exhibit rotational movements for energy conversion. In the gliding bacterium, , a dimeric F-like ATPase forms a chain structure within the cell, which is proposed to drive the gliding motility. However, the mechanisms of force generation and transmission remain unclear. We determined the electron cryomicroscopy (cryo-EM) structure of the dimeric F-like ATPase complex. The structure revealed an assembly distinct from those of dimeric FF-ATPases. The F-like ATPase unit associated by two subunits GliD and GliE was named G-ATPase as an R domain of rotary ATPases. G-β subunit, a homolog of the F-ATPase catalytic subunit, exhibited a specific N-terminal region that incorporates the glycolytic enzyme, phosphoglycerate kinase into the complex. Structural features of the ATPase displayed strong similarities to F-ATPase, suggesting a rotation based on the rotary catalytic mechanism. Overall, the cryo-EM structure provides insights into the mechanism through which G-ATPase drives the gliding motility.
History
DepositionJul 8, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60718.png

Downloads & links

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Map

FileDownload / File: emd_60718.map.gz / Format: CCP4 / Size: 561.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 528 pix.
= 459.36 Å		0.87 Å/pix.
x 528 pix.
= 459.36 Å		0.87 Å/pix.
x 528 pix.
= 459.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.8194501 - 3.9432313
Average (Standard dev.)0.0068840273 (±0.085754596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions528528528
Spacing528528528
CellA=B=C: 459.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_60718_additional_1.map
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Additional map: #1

Fileemd_60718_additional_2.map
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Half map: #2

Fileemd_60718_half_map_1.map
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Half map: #1

Fileemd_60718_half_map_2.map
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Sample components

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Entire : G1-ATPase dimer from Mycoplasma mobile gliding machinery

EntireName: G1-ATPase dimer from Mycoplasma mobile gliding machinery
Components
  • Complex: G1-ATPase dimer from Mycoplasma mobile gliding machinery
    • Protein or peptide: G1-ATPase subunit beta
    • Protein or peptide: G1-ATPase subunit alpha
    • Protein or peptide: G1-ATPase subunit gamma
    • Protein or peptide: Phosphoglycerate kinase
    • Protein or peptide: G1-ATPase subunit D
    • Protein or peptide: G1-ATPase subunit E
    • Protein or peptide: UNKNOWN HELIX
    • Protein or peptide: UNKNOWN HELIX
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION

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Supramolecule #1: G1-ATPase dimer from Mycoplasma mobile gliding machinery

SupramoleculeName: G1-ATPase dimer from Mycoplasma mobile gliding machinery
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521

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Macromolecule #1: G1-ATPase subunit beta

MacromoleculeName: G1-ATPase subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
Molecular weightTheoretical: 88.510383 KDa
SequenceString: MTTNNLTELE ILNIKKYLKT VNLNTLRAYA RRNVKDFSEK LIKVKVIEKI VEHDKKFDNI EDSIFVQISS QFGVNFETIL DGSFFLGQK AAKAMPKTFD TKIISETKSV QKFEEVKFAT SSKTEKIISE EKEILHLIEQ SKRDRDFIDN FSKILEEKNL T EEHQHMSC ...String:
MTTNNLTELE ILNIKKYLKT VNLNTLRAYA RRNVKDFSEK LIKVKVIEKI VEHDKKFDNI EDSIFVQISS QFGVNFETIL DGSFFLGQK AAKAMPKTFD TKIISETKSV QKFEEVKFAT SSKTEKIISE EKEILHLIEQ SKRDRDFIDN FSKILEEKNL T EEHQHMSC QVCYDHEKKH SDHNEKYATE HCDACVYHDF SDLDPEFVAS TYTEEEIIHN LLFKLYSVEQ LALFTIDQLN AL LFARGLG LEKNKVRAIK SLLTLQTSYE FMEKSQAALL PKVSFNPTNP LKPIEEKEFT IFGEIVEIRS QVYKIRIDKA EEE VLPKVI FYADVNGKEI QLEVADIFDK NLVSTFVLGN ETGLKIGTKV KSKNQSYAIK ISKRLLGRVI DPIGKILDDS IATP VHGNM YAPLEMQHDS EATRYVVSPK NAILETGIKV IDVLLPIPKG GKTGLLGGAG VGKTVIVQEL INAFIKFHDG VSVFA GIGE RIREGHELWK EAEALGFLNK TAFIFGQMNE SPGLRFRSGI SGVKVAEYFR NNLGKSVLLF MDNIFRYVQA GSEISS LLE KTPSAVGYQP TLFSEMGQLQ ERINSTKDGD ITSIQAMYIP ADDFTDPAAV AAFAHFDSTI ILSRQLAAEG VYPAIDP LE SNSKMLSIKY TSREHLDIAK KTVQTLEKTK TLEDIINILG FDALSEDDKK VVEVGRRLKW FLTQPFVVAE KFSGVPGK F VRLKDSLKGI KTILDGDLNH IPVSYFSFVG VVEEIIEKFN LDAKKEALKN ELEQNQKDLA SII

UniProtKB: ATP synthase beta chain

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Macromolecule #2: G1-ATPase subunit alpha

MacromoleculeName: G1-ATPase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
Molecular weightTheoretical: 58.794668 KDa
SequenceString: MKNLKITAIK DNLIFVEGEH QFSFLEIIKF SDKVEGVVLK ANDRSAIVAI LNEDKDLNLT VGSLAEATGE LYKIPIYDNY LGSIINVLG ESLVKQYERT NVALDKKYVF TEAQPIFTRS AVNEPLVTGI TVVDGVLPVG RGQKELIIGD RGTGKTAIAL N AMLAQENT ...String:
MKNLKITAIK DNLIFVEGEH QFSFLEIIKF SDKVEGVVLK ANDRSAIVAI LNEDKDLNLT VGSLAEATGE LYKIPIYDNY LGSIINVLG ESLVKQYERT NVALDKKYVF TEAQPIFTRS AVNEPLVTGI TVVDGVLPVG RGQKELIIGD RGTGKTAIAL N AMLAQENT DVINIFIAIG KKRDEIVEIY GTFKKHNILH KSIIVSAASD DAVAARYLAP YAGMAIAEFF QQIGKDVLVV MD DLTNHAD AYRELSLLAG IAPAREAYPG DIFYVHSSLL ERGGKYGPEF GGGSITILPI AQTLAGDISG YIPTNLISIT DGQ IYTSAK LFNEGTRPAI DVNLSVSRLG SAAQSKFMAF ASSGLKKIYT EYKYLKRLSS FSSKISNRDL ETLQKGKAFE SLID QAEYE VIDYETSAIL FLLLKKGFLN FYTEKTEALK VIIGVIKVFL AKDVLGRKMR AILVEHGIDS IVWNLYLNHM ILPLL KYHL LSELQYLATN REFIKKFKDI RNDGRILLAY ERKGYERGIA YDYK

UniProtKB: ATP synthase alpha chain

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Macromolecule #3: G1-ATPase subunit gamma

MacromoleculeName: G1-ATPase subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
Molecular weightTheoretical: 39.810602 KDa
SequenceString: MKRKDVEEKK QNLDFYHNYI DISKIKVLQK LNEEIASLNM LKLQKGESHY LLNRIINKWF PHNSNIYHEL HHENDRKELY ILIDPKKLD LFSEALLRKL SQTVKERIRP DKDFVITVGT NVDNIARQLN LNIIDHYDLD LFNQIDDFAN RIGELVDVGL N NKIFNYVS ...String:
MKRKDVEEKK QNLDFYHNYI DISKIKVLQK LNEEIASLNM LKLQKGESHY LLNRIINKWF PHNSNIYHEL HHENDRKELY ILIDPKKLD LFSEALLRKL SQTVKERIRP DKDFVITVGT NVDNIARQLN LNIIDHYDLD LFNQIDDFAN RIGELVDVGL N NKIFNYVS LLIAQSSTKN NGGLVQERIV PFNTKNIKVW NESNQDENGM PIVSEENEVE IMSYAKTLRN INFKKHTWLP NI NTFYEQF VKSVFKQELF EFKSISVIEE LKIELQLLDE KKKRLEEQKK ELILKWNRAR KEEATLQSTL LFSAFKVKNQ KST RDEILR LSKGKNRNGA

UniProtKB: Expressed protein

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Macromolecule #4: Phosphoglycerate kinase

MacromoleculeName: Phosphoglycerate kinase / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: phosphoglycerate kinase
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
Molecular weightTheoretical: 56.68075 KDa
SequenceString: MKKTLDQISL KNKKVIIRVD FNVPIVNGIV TSNKRIEAVI PTIKKVVNEG GKAILMSHLG RVKSEEDLKK KSLAPVVEIL VNLLGMPIT FVPATNGTEL EETINSMKSG EIVMMENTRF EDLNNDAESS NNPDLGMYWA SLGDVFINDA FGTVHRKHAS N VGISTYIA ...String:
MKKTLDQISL KNKKVIIRVD FNVPIVNGIV TSNKRIEAVI PTIKKVVNEG GKAILMSHLG RVKSEEDLKK KSLAPVVEIL VNLLGMPIT FVPATNGTEL EETINSMKSG EIVMMENTRF EDLNNDAESS NNPDLGMYWA SLGDVFINDA FGTVHRKHAS N VGISTYIA ESGIGYLVEK EIKNLDKALS RPERPIVAIL GGAKVSDKIG VLNNLLKYVD KIIIGGAMAY TFLAAQGIGI GK SLVEEDK IDLAREYLKN NLDKFVLPID YALAKDFEDV KPFYNLENTL EIPNGYMGLD IGPKSIEVFK KYIKDAKTIL WNG PLGVTE FKYFKEGTKA IAKAITELKG NVYTVVGGGD SVAIIEELGL DRRFSHVSTG GGATLEFLEG KELPGIQAIQ NEGE LGRTK EEIFSILTQN SEEVLHEHTA AFSTSEVEPA NEEFPSEYND SNSQTYFSNE VENDEDFLLN TNDFPTREAS FPNEV KTEE IILNENDDEF DIEDEELDSL PNDDIKF

UniProtKB: Phosphoglycerate kinase

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Macromolecule #5: G1-ATPase subunit D

MacromoleculeName: G1-ATPase subunit D / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
Molecular weightTheoretical: 33.753953 KDa
SequenceString: MKKTDKNQTG KEIMKKELLI KTNEQDINLA PKSQSTSKKL SNTWNYEELI NQTKEIDVNS KIVKTELEYV EEDSRLRKEK IELIQKNYD NLNAKPLVGV DLYESYSLVL NKSAWNYNEI IQRDTQLTIL DMALQVHLFL YEGKIIDIAH IQKIIKTFVL N VFAKIIKG ...String:
MKKTDKNQTG KEIMKKELLI KTNEQDINLA PKSQSTSKKL SNTWNYEELI NQTKEIDVNS KIVKTELEYV EEDSRLRKEK IELIQKNYD NLNAKPLVGV DLYESYSLVL NKSAWNYNEI IQRDTQLTIL DMALQVHLFL YEGKIIDIAH IQKIIKTFVL N VFAKIIKG VPIVLNPIII FDSVRFDKSK ILPVAVANPK LMPPLGVQDW DTIVDEDEEI KKIVSTFIKL LENALTVGHE VE FFQDTLL VRNVDGITSL YVSEKAAQVF NNSVIDQIMP EKPKYEALED PFSNKK

UniProtKB: Expressed protein

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Macromolecule #6: G1-ATPase subunit E

MacromoleculeName: G1-ATPase subunit E / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
Molecular weightTheoretical: 13.264168 KDa
SequenceString:
MTKNIFANKI ANQKAYFKRD IKTVHTFLGR VNYIQRASKF NDEKRVFRPL QIELSGTNEI VDIYLEATTY ISKKALDEIR QNSYIFLEA KWLPESNFLN NPLFEIQNIV IEN

UniProtKB: Uncharacterized protein

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Macromolecule #7: UNKNOWN HELIX

MacromoleculeName: UNKNOWN HELIX / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
Molecular weightTheoretical: 1.124378 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #8: UNKNOWN HELIX

MacromoleculeName: UNKNOWN HELIX / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
Molecular weightTheoretical: 783.958 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 10 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #12: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 12 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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

Concentration1 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
8.1 mMNa2HPO4disodium hydrogenphosphate
1.5 mMKH2PO4potassium dihydrogen phosphate
2.7 mMKClpotassium chloride
137.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride
0.1 %C32H58N2O7SCHAPS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: GRAPHENE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Details: Epoxidized graphene grid (EG-grid) was used.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7350 / Average exposure time: 3.3 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 633820
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
Software:
Namedetails
cryoSPARC (ver. 3.3.2)
RELION (ver. 4.0)Mask creation and post-processing were done in RELION 4.0.

Number images used: 142490
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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