[English] 日本語
Yorodumi
- EMDB-35909: Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35909
TitleCryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with bedaquiline(BDQ)
Map data
Sample
  • Complex: Mycobacterium tuberculosis ATP synthase in complex with bedaquiline(BDQ)
    • Protein or peptide: x 8 types
  • Ligand: x 4 types
KeywordsATP synthase / Mycobacterium tuberculosis / cryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / peptidoglycan-based cell wall / ADP binding / hydrolase activity ...proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / peptidoglycan-based cell wall / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site ...ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / 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
ATP synthase subunit b / ATP synthase subunit c / ATP synthase subunit a / Multifunctional fusion protein / ATP synthase subunit beta / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase epsilon chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsZhang Y / Lai Y / Liu F / Rao Z / Gong H
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: Nature / Year: 2024
Title: Inhibition of M. tuberculosis and human ATP synthase by BDQ and TBAJ-587.
Authors: Yuying Zhang / Yuezheng Lai / Shan Zhou / Ting Ran / Yue Zhang / Ziqing Zhao / Ziyan Feng / Long Yu / Jinxu Xu / Kun Shi / Jianyun Wang / Yu Pang / Liang Li / Hongming Chen / Luke W Guddat / ...Authors: Yuying Zhang / Yuezheng Lai / Shan Zhou / Ting Ran / Yue Zhang / Ziqing Zhao / Ziyan Feng / Long Yu / Jinxu Xu / Kun Shi / Jianyun Wang / Yu Pang / Liang Li / Hongming Chen / Luke W Guddat / Yan Gao / Fengjiang Liu / Zihe Rao / Hongri Gong /
Abstract: Bedaquiline (BDQ), a first-in-class diarylquinoline anti-tuberculosis drug, and its analogue, TBAJ-587, prevent the growth and proliferation of Mycobacterium tuberculosis by inhibiting ATP synthase. ...Bedaquiline (BDQ), a first-in-class diarylquinoline anti-tuberculosis drug, and its analogue, TBAJ-587, prevent the growth and proliferation of Mycobacterium tuberculosis by inhibiting ATP synthase. However, BDQ also inhibits human ATP synthase. At present, how these compounds interact with either M. tuberculosis ATP synthase or human ATP synthase is unclear. Here we present cryogenic electron microscopy structures of M. tuberculosis ATP synthase with and without BDQ and TBAJ-587 bound, and human ATP synthase bound to BDQ. The two inhibitors interact with subunit a and the c-ring at the leading site, c-only sites and lagging site in M. tuberculosis ATP synthase, showing that BDQ and TBAJ-587 have similar modes of action. The quinolinyl and dimethylamino units of the compounds make extensive contacts with the protein. The structure of human ATP synthase in complex with BDQ reveals that the BDQ-binding site is similar to that observed for the leading site in M. tuberculosis ATP synthase, and that the quinolinyl unit also interacts extensively with the human enzyme. This study will improve researchers' understanding of the similarities and differences between human ATP synthase and M. tuberculosis ATP synthase in terms of the mode of BDQ binding, and will allow the rational design of novel diarylquinolines as anti-tuberculosis drugs.
History
DepositionApr 11, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35909.png

Downloads & links

-
Map

FileDownload / File: emd_35909.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.6
Minimum - Maximum-22.616346 - 42.036003000000001
Average (Standard dev.)0.009829542 (±1.1153575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Mycobacterium tuberculosis ATP synthase in complex with bedaquili...

EntireName: Mycobacterium tuberculosis ATP synthase in complex with bedaquiline(BDQ)
Components
  • Complex: Mycobacterium tuberculosis ATP synthase in complex with bedaquiline(BDQ)
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: Multifunctional fusion protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: Bedaquiline

+
Supramolecule #1: Mycobacterium tuberculosis ATP synthase in complex with bedaquili...

SupramoleculeName: Mycobacterium tuberculosis ATP synthase in complex with bedaquiline(BDQ)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

+
Macromolecule #1: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 27.488436 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTETILAAQI EVGEHHTATW LGMTVNTDTV LSTAIAGLIV IALAFYLRAK VTSTDVPGGV QLFFEAITIQ MRNQVESAIG MRIAPFVLP LAVTIFVFIL ISNWLAVLPV QYTDKHGHTT ELLKSAAADI NYVLALALFV FVCYHTAGIW RRGIVGHPIK L LKGHVTLL ...String:
MTETILAAQI EVGEHHTATW LGMTVNTDTV LSTAIAGLIV IALAFYLRAK VTSTDVPGGV QLFFEAITIQ MRNQVESAIG MRIAPFVLP LAVTIFVFIL ISNWLAVLPV QYTDKHGHTT ELLKSAAADI NYVLALALFV FVCYHTAGIW RRGIVGHPIK L LKGHVTLL APINLVEEVA KPISLSLRLF GNIFAGGILV ALIALFPPYI MWAPNAIWKA FDLFVGAIQA FIFALLTILY FS QAMELEE EHH

UniProtKB: ATP synthase subunit a

+
Macromolecule #2: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 59.35807 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MAELTIPADD IQSAIEEYVS SFTADTSREE VGTVVDAGDG IAHVEGLPSV MTQELLEFPG GILGVALNLD EHSVGAVILG DFENIEEGQ QVKRTGEVLS VPVGDGFLGR VVNPLGQPID GRGDVDSDTR RALELQAPSV VHRQGVKEPL QTGIKAIDAM T PIGRGQRQ ...String:
MAELTIPADD IQSAIEEYVS SFTADTSREE VGTVVDAGDG IAHVEGLPSV MTQELLEFPG GILGVALNLD EHSVGAVILG DFENIEEGQ QVKRTGEVLS VPVGDGFLGR VVNPLGQPID GRGDVDSDTR RALELQAPSV VHRQGVKEPL QTGIKAIDAM T PIGRGQRQ LIIGDRKTGK TAVCVDTILN QRQNWESGDP KKQVRCVYVA IGQKGTTIAA VRRTLEEGGA MDYTTIVAAA AS ESAGFKW LAPYTGSAIA QHWMYEGKHV LIIFDDLTKQ AEAYRAISLL LRRPPGREAY PGDVFYLHSR LLERCAKLSD DLG GGSLTG LPIIETKAND ISAYIPTNVI SITDGQCFLE TDLFNQGVRP AINVGVSVSR VGGAAQIKAM KEVAGSLRLD LSQY RELEA FAAFASDLDA ASKAQLERGA RLVELLKQPQ SQPMPVEEQV VSIFLGTGGH LDSVPVEDVR RFETELLDHM RASEE EILT EIRDSQKLTE EAADKLTEVI KNFKKGFAAT GGGSVVPDEH VEALDEDKLA KEAVKVKKPA PKKKK

UniProtKB: ATP synthase subunit alpha

+
Macromolecule #3: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 53.150934 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTTTAEKTDR PGKPGSSDTS GRVVRVTGPV VDVEFPRGSI PELFNALHAE ITFESLAKTL TLEVAQHLGD NLVRTISLQP TDGLVRGVE VIDTGRSISV PVGEGVKGHV FNALGDCLDE PGYGEKFEHW SIHRKPPAFE ELEPRTEMLE TGLKVVDLLT P YVRGGKIA ...String:
MTTTAEKTDR PGKPGSSDTS GRVVRVTGPV VDVEFPRGSI PELFNALHAE ITFESLAKTL TLEVAQHLGD NLVRTISLQP TDGLVRGVE VIDTGRSISV PVGEGVKGHV FNALGDCLDE PGYGEKFEHW SIHRKPPAFE ELEPRTEMLE TGLKVVDLLT P YVRGGKIA LFGGAGVGKT VLIQEMINRI ARNFGGTSVF AGVGERTREG NDLWVELAEA NVLKDTALVF GQMDEPPGTR MR VALSALT MAEWFRDEQG QDVLLFIDNI FRFTQAGSEV STLLGRMPSA VGYQPTLADE MGELQERITS TRGRSITSMQ AVY VPADDY TDPAPATTFA HLDATTELSR AVFSKGIFPA VDPLASSSTI LDPSVVGDEH YRVAQEVIRI LQRYKDLQDI IAIL GIDEL SEEDKQLVNR ARRIERFLSQ NMMAAEQFTG QPGSTVPVKE TIEAFDRLCK GDFDHVPEQA FFLIGGLDDL AKKAE SLGA KL

UniProtKB: ATP synthase subunit beta

+
Macromolecule #4: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 33.929332 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIARAQARL ESARPYAFEI TRMLTTLAAE AALDHPLLVE RPEPKRAGVL VVSSDRGLC GAYNANIFRR SEELFSLLRE AGKQPVLYVV GRKAQNYYSF RNWNITESWM GFSEQPTYEN AAEIASTLVD A FLLGTDNG ...String:
MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIARAQARL ESARPYAFEI TRMLTTLAAE AALDHPLLVE RPEPKRAGVL VVSSDRGLC GAYNANIFRR SEELFSLLRE AGKQPVLYVV GRKAQNYYSF RNWNITESWM GFSEQPTYEN AAEIASTLVD A FLLGTDNG EDQRSDSGEG VDELHIVYTE FKSMLSQSAE AHRIAPMVVE YVEEDIGPRT LYSFEPDATM LFESLLPRYL TT RVYAALL ESAASELASR QRAMKSATDN ADDLIKALTL MANRERQAQI TQEISEIVGG ANALAEAR

UniProtKB: ATP synthase gamma chain

+
Macromolecule #5: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 13.149744 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MAELNVEIVA VDRNIWSGTA KFLFTRTTVG EIGILPRHIP LVAQLVDDAM VRVEREGEKD LRIAVDGGFL SVTEEGVSIL AESAEFESE IDEAAAKQDS ESDDPRIAAR GRARLRAVGA ID

UniProtKB: ATP synthase epsilon chain

+
Macromolecule #6: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 6 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.058423 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MDPTIAAGAL IGGGLIMAGG AIGAGIGDGV AGNALISGVA RQPEAQGRLF TPFFITVGLV EAAYFINLAF MALFVFATPV K

UniProtKB: ATP synthase subunit c

+
Macromolecule #7: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 18.345771 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MGEVSAIVLA ASQAAEEGGE SSNFLIPNGT FFVVLAIFLV VLAVIGTFVV PPILKVLRER DAMVAKTLAD NKKSDEQFAA AQADYDEAM TEARVQASSL RDNARADGRK VIEDARVRAE QQVASTLQTA HEQLKRERDA VELDLRAHVG TMSATLASRI L GVDLTASA ATR

UniProtKB: ATP synthase subunit b

+
Macromolecule #8: Multifunctional fusion protein

MacromoleculeName: Multifunctional fusion protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 48.866648 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MSTFIGQLFG FAVIVYLVWR FIVPLVGRLM SARQDTVRQQ LADAAAAADR LAEASQAHTK ALEDAKSEAH RVVEEARTDA ERIAEQLEA QADVEAERIK MQGARQVDLI RAQLTRQLRL ELGHESVRQA RELVRNHVAD QAQQSATVDR FLDQLDAMAP A TADVDYPL ...String:
MSTFIGQLFG FAVIVYLVWR FIVPLVGRLM SARQDTVRQQ LADAAAAADR LAEASQAHTK ALEDAKSEAH RVVEEARTDA ERIAEQLEA QADVEAERIK MQGARQVDLI RAQLTRQLRL ELGHESVRQA RELVRNHVAD QAQQSATVDR FLDQLDAMAP A TADVDYPL LAKMRSASRR ALTSLVDWFG TMAQDLDHQG LTTLAGELVS VARLLDREAV VTRYLTVPAE DATPRIRLIE RL VSGKVGA PTLEVLRTAV SKRWSANSDL IDAIEHVSRQ ALLELAERAG QVDEVEDQLF RFSRILDVQP RLAILLGDCA VPA EGRVRL LRKVLERADS TVNPVVVALL SHTVELLRGQ AVEEAVLFLA EVAVARRGEI VAQVGAAAEL SDAQRTRLTE VLSR IYGHP VTVQLHIDAA LLGGLSIAVG DEVIDGTLSS RLAAAEARLP D

UniProtKB: Multifunctional fusion protein

+
Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
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

+
Macromolecule #12: Bedaquiline

MacromoleculeName: Bedaquiline / type: ligand / ID: 12 / Number of copies: 7 / Formula: BQ1
Molecular weightTheoretical: 555.505 Da
Chemical component information

ChemComp-BQ1:
Bedaquiline / antibiotic*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96592
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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