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- EMDB-4577: Structure of fatty acid synthase complex with bound gamma subunit... -

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Basic information

Entry
Database: EMDB / ID: EMD-4577
TitleStructure of fatty acid synthase complex with bound gamma subunit from Saccharomyces cerevisiae at 2.8 angstrom
Map dataSharpened map
Sample
  • Complex: Fatty acid synthase holoenzyme complex at 2.8 angstrom resolution
    • Protein or peptide: Fatty acid synthase subunit alpha
    • Protein or peptide: Fatty acid synthase subunit beta
    • Protein or peptide: Translation machinery-associated protein 17
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine
  • Ligand: FLAVIN MONONUCLEOTIDE
Function / homology
Function and homology information


: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase ...: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / proteasome regulatory particle assembly / holo-[acyl-carrier-protein] synthase activity / fatty acid synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / long-chain fatty acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / protein-macromolecule adaptor activity / magnesium ion binding / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Translation machinery-associated protein 17 / : / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain ...Translation machinery-associated protein 17 / : / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Fatty acid synthase / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / MaoC-like dehydratase domain / MaoC like domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / HotDog domain superfamily / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site. / Thiolase-like / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Fatty acid synthase subunit beta / Fatty acid synthase subunit alpha / Translation machinery-associated protein 17
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSingh K / Graf B / Linden A / Sautner V / Urlaub H / Tittmann K / Stark H / Chari A
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research FoundationSFB860-TP A5 Germany
CitationJournal: Cell / Year: 2020
Title: Discovery of a Regulatory Subunit of the Yeast Fatty Acid Synthase.
Authors: Kashish Singh / Benjamin Graf / Andreas Linden / Viktor Sautner / Henning Urlaub / Kai Tittmann / Holger Stark / Ashwin Chari /
Abstract: Fatty acid synthases (FASs) are central to metabolism but are also of biotechnological interest for the production of fine chemicals and biofuels from renewable resources. During fatty acid ...Fatty acid synthases (FASs) are central to metabolism but are also of biotechnological interest for the production of fine chemicals and biofuels from renewable resources. During fatty acid synthesis, the growing fatty acid chain is thought to be shuttled by the dynamic acyl carrier protein domain to several enzyme active sites. Here, we report the discovery of a γ subunit of the 2.6 megadalton α-βS. cerevisiae FAS, which is shown by high-resolution structures to stabilize a rotated FAS conformation and rearrange ACP domains from equatorial to axial positions. The γ subunit spans the length of the FAS inner cavity, impeding reductase activities of FAS, regulating NADPH turnover by kinetic hysteresis at the ketoreductase, and suppressing off-pathway reactions at the enoylreductase. The γ subunit delineates the functional compartment within FAS. As a scaffold, it may be exploited to incorporate natural and designed enzymatic activities that are not present in natural FAS.
History
DepositionJan 31, 2019-
Header (metadata) releaseFeb 27, 2019-
Map releaseMar 18, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ql5
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4577.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.057575833 - 0.14180543
Average (Standard dev.)0.0000703127 (±0.009491231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.200339.200339.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0580.1420.000

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Supplemental data

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Additional map: unsharpened map

Fileemd_4577_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map 2

Fileemd_4577_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map 1

Fileemd_4577_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Fatty acid synthase holoenzyme complex at 2.8 angstrom resolution

EntireName: Fatty acid synthase holoenzyme complex at 2.8 angstrom resolution
Components
  • Complex: Fatty acid synthase holoenzyme complex at 2.8 angstrom resolution
    • Protein or peptide: Fatty acid synthase subunit alpha
    • Protein or peptide: Fatty acid synthase subunit beta
    • Protein or peptide: Translation machinery-associated protein 17
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine
  • Ligand: FLAVIN MONONUCLEOTIDE

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Supramolecule #1: Fatty acid synthase holoenzyme complex at 2.8 angstrom resolution

SupramoleculeName: Fatty acid synthase holoenzyme complex at 2.8 angstrom resolution
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Strain: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
Molecular weightExperimental: 2.6 MDa

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Macromolecule #1: Fatty acid synthase subunit alpha

MacromoleculeName: Fatty acid synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: fatty-acyl-CoA synthase system
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 207.184422 KDa
SequenceString: MKPEVEQELA HILLTELLAY QFASPVRWIE TQDVFLKDFN TERVVEIGPS PTLAGMAQRT LKNKYESYDA ALSLHREILC YSKDAKEIY YTPDPSELAA KEEPAKEEAP APTPAASAPA PAAAAPAPVA AAAPAAAAAE IADEPVKASL LLHVLVAHKL K KSLDSIPM ...String:
MKPEVEQELA HILLTELLAY QFASPVRWIE TQDVFLKDFN TERVVEIGPS PTLAGMAQRT LKNKYESYDA ALSLHREILC YSKDAKEIY YTPDPSELAA KEEPAKEEAP APTPAASAPA PAAAAPAPVA AAAPAAAAAE IADEPVKASL LLHVLVAHKL K KSLDSIPM SKTIKDLVGG KSTVQNEILG DLGKEFGTTP EKPEETPLEE LAETFQDTFS GALGKQSSSL LSRLISSKMP GG FTITVAR KYLQTRWGLP SGRQDGVLLV ALSNEPAARL GSEADAKAFL DSMAQKYASI VGVDLSSAAS ASGAAGAGAA AGA AMIDAG ALEEITKDHK VLARQQLQVL ARYLKMDLDN GERKFLKEKD TVAELQAQLD YLNAELGEFF VNGVATSFSR KKAR TFDSS WNWAKQSLLS LYFEIIHGVL KNVDREVVSE AINIMNRSND ALIKFMEYHI SNTDETKGEN YQLVKTLGEQ LIENC KQVL DVDPVYKDVA KPTGPKTAID KNGNITYSEE PREKVRKLSQ YVQEMALGGP ITKESQPTIE EDLTRVYKAI SAQADK QDI SSSTRVEFEK LYSDLMKFLE SSKEIDPSQT TQLAGMDVED ALDKDSTKEV ASLPNKSTIS KTVSSTIPRE TIPFLHL RK KTPAGDWKYD RQLSSLFLDG LEKAAFNGVT FKDKYVLITG AGKGSIGAEV LQGLLQGGAK VVVTTSRFSK QVTDYYQS I YAKYGAKGST LIVVPFNQGS KQDVEALIEF IYDTEKNGGL GWDLDAIIPF AAIPEQGIEL EHIDSKSEFA HRIMLTNIL RMMGCVKKQK SARGIETRPA QVILPMSPNH GTFGGDGMYS ESKLSLETLF NRWHSESWAN QLTVCGAIIG WTRGTGLMSA NNIIAEGIE KMGVRTFSQK EMAFNLLGLL TPEVVELCQK SPVMADLNGG LQFVPELKEF TAKLRKELVE TSEVRKAVSI E TALEHKVV NGNSADAAYA QVEIQPRANI QLDFPELKPY KQVKQIAPAE LEGLLDLERV IVVTGFAEVG PWGSARTRWE ME AFGEFSL EGCVEMAWIM GFISYHNGNL KGRPYTGWVD SKTKEPVDDK DVKAKYETSI LEHSGIRLIE PELFNGYNPE KKE MIQEVI VEEDLEPFEA SKETAEQFKH QHGDKVDIFE IPETGEYSVK LLKGATLYIP KALRFDRLVA GQIPTGWNAK TYGI SDDII SQVDPITLFV LVSVVEAFIA SGITDPYEMY KYVHVSEVGN CSGSGMGGVS ALRGMFKDRF KDEPVQNDIL QESFI NTMS AWVNMLLISS SGPIKTPVGA CATSVESVDI GVETILSGKA RICIVGGYDD FQEEGSFEFG NMKATSNTLE EFEHGR TPA EMSRPATTTR NGFMEAQGAG IQIIMQADLA LKMGVPIYGI VAMAATATDK IGRSVPAPGK GILTTAREHH SSVKYAS PN LNMKYRKRQL VTREAQIKDW VENELEALKL EAEEIPSEDQ NEFLLERTRE IHNEAESQLR AAQQQWGNDF YKRDPRIA P LRGALATYGL TIDDLGVASF HGTSTKANDK NESATINEMM KHLGRSEGNP VIGVFQKFLT GHPKGAAGAW MMNGALQIL NSGIIPGNRN ADNVDKILEQ FEYVLYPSKT LKTDGVRAVS ITSFGFGQKG GQAIVVHPDY LYGAITEDRY NEYVAKVSAR EKSAYKFFH NGMIYNKLFV SKEHAPYTDE LEEDVYLDPL ARVSKDKKSG SLTFNSKNIQ SKDSYINANT IETAKMIENM T KEKVSNGG VGVDVELITS INVENDTFIE RNFTPQEIEY CSAQPSVQSS FAGTWSAKEA VFKSLGVKSL GGGAALKDIE IV RVNKNAP AVELHGNAKK AAEEAGVTDV KVSISHDDLQ AVAVAVSTKK

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Macromolecule #2: Fatty acid synthase subunit beta

MacromoleculeName: Fatty acid synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: fatty-acyl-CoA synthase system
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 227.785141 KDa
SequenceString: STRPLTLSHG SLEHVLLVPT ASFFIASQLQ EQFNKILPEP TEGFAADDEP TTPAELVGKF LGYVSSLVEP SKVGQFDQVL NLCLTEFEN CYLEGNDIHA LAAKLLQEND TTLVKTKELI KNYITARIMA KRPFDKKSNS ALFRAVGEGN AQLVAIFGGQ G NTDDYFEE ...String:
STRPLTLSHG SLEHVLLVPT ASFFIASQLQ EQFNKILPEP TEGFAADDEP TTPAELVGKF LGYVSSLVEP SKVGQFDQVL NLCLTEFEN CYLEGNDIHA LAAKLLQEND TTLVKTKELI KNYITARIMA KRPFDKKSNS ALFRAVGEGN AQLVAIFGGQ G NTDDYFEE LRDLYQTYHV LVGDLIKFSA ETLSELIRTT LDAEKVFTQG LNILEWLENP SNTPDKDYLL SIPISCPLIG VI QLAHYVV TAKLLGFTPG ELRSYLKGAT GHSQGLVTAV AIAETDSWES FFVSVRKAIT VLFFIGVRCY EAYPNTSLPP SIL EDSLEN NEGVPSPMLS ISNLTQEQVQ DYVNKTNSHL PAGKQVEISL VNGAKNLVVS GPPQSLYGLN LTLRKAKAPS GLDQ SRIPF SERKLKFSNR FLPVASPFHS HLLVPASDLI NKDLVKNNVS FNAKDIQIPV YDTFDGSDLR VLSGSISERI VDCII RLPV KWETTTQFKA THILDFGPGG ASGLGVLTHR NKDGTGVRVI VAGTLDINPD DDYGFKQEIF DVTSNGLKKN PNWLEE YHP KLIKNKSGKI FVETKFSKLI GRPPLLVPGM TPCTVSPDFV AATTNAGYTI ELAGGGYFSA AGMTAAIDSV VSQIEKG ST FGINLIYVNP FMLQWGIPLI KELRSKGYPI QFLTIGAGVP SLEVASEYIE TLGLKYLGLK PGSIDAISQV INIAKAHP N FPIALQWTGG RGGGHHSFED AHTPMLQMYS KIRRHPNIML IFGSGFGSAD DTYPYLTGEW STKFDYPPMP FDGFLFGSR VMIAKEVKTS PDAKKCIAAC TGVPDDKWEQ TYKKPTGGIV TVRSEMGEPI HKIATRGVML WKEFDETIFN LPKNKLVPTL EAKRDYIIS RLNADFQKPW FATVNGQARD LATMTYEEVA KRLVELMFIR STNSWFDVTW RTFTGDFLRR VEERFTKSKT L SLIQSYSL LDKPDEAIEK VFNAYPAARE QFLNAQDIDH FLSMCQNPMQ KPVPFVPVLD RRFEIFFKKD SLWQSEHLEA VV DQDVQRT CILHGPVAAQ FTKVIDEPIK SIMDGIHDGH IKKLLHQYYG DDESKIPAVE YFGGESPVDV QSDSEDSAVF KAT SSTDEE SWFKALAGSE INWRHASFLC SFITQDKMFV SNPIRKVFKP SQGMVVEISN GNTSSKTVVT LSEPVQGELK PTVI LKLLK ENIIQMEMIE NRTMDGKPVS LPLLYNFNPD NGFAPISEVM EDRNQRIKEM YWKLWIDEPF NLDFDPRDVI KGKDF EITA KEVYDFTHAV GNNCEDFVSR PDRTMLAPMD FAIVVGWRAI IKAIFPNTVD GDLLKLVHLS NGYKMIPGAK PLQVGD VVS TTAVIESVVN QPTGKIVDVV GTLSRNGKPV MEVTSSFFYR GNYTDFENTF QKTVEPVYQM HIKTSKDIAV LRSKEWF QL DDEDFDLLNK TLTFETETEV TFKNANIFSS VKCFGPIKVE LPTKETVEIG IVDYEAGASH GNPVVDFLKR NGSTLEQK V NLENPIPIAV LDSYTPSTNE PYARVSGDLN PIHVSRHFAS YANLPGTITH GMFSSASVRA LIENWAADSV SSRVRGYTC QFVDMVLPNT ALKTSIQHVG MINGRKLIKF ETRNEDDVVV LTGEAEIEQP VTTFVFTGQG SQEQGMGMDL YKTSKAAQDV WNRADNHFK DTYGFSILDI VINNPVNLTI HFGGEKGKRI RENYSAMIFE TIVDGKLKTE KIFKEINEHS TSYTFRSEKG L LSATQFTQ PALTLMEKAA FEDLKSKGLI PADATFAGHS LGEYAALASL ADVMSIESLV EVVFYRGMTM QVAVPRDELG RS NYGMIAI NPGRVAASFS QEALQYVVER VGKRTGWLVE IVNYNVENQQ YVAAGDLRAL DTVTNVLNFI KLQKIDIIEL QKS LSLEEV EGHLFEIIDE ASKKSAVKPR PLKLERGFAC IPLVGISVPF HSTYLMNGVK PFKSFLKKNI IKENVKVARL AGKY IPNLT AKPFQVTKEY FQDVYDLTGS EPIKEIIDNW EKYEQ

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Macromolecule #3: Translation machinery-associated protein 17

MacromoleculeName: Translation machinery-associated protein 17 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 16.558117 KDa
SequenceString:
SAGGIRRPIQ IEEFKTAISG MSDMELAQIK TEIENSINHL QRSNARLGKY IAKLEGADDR LEADDSDDLE NIDSGDLALY KDSVRENEI VLNNYNERVD ALEQETVYRK TGHGKSKHEV EAKDNTNKGP DVDMDNSNVD VVTPNSIFI

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Macromolecule #4: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 4 / Number of copies: 6 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE / Phosphopantetheine

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Macromolecule #5: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 6 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

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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

Concentration0.5 mg/mL
BufferpH: 6.5
Component:
ConcentrationName
50.0 mMBisTris pH 6.5
50.0 mMPotassium acetate
10.0 mMMagnesium acetate
10.0 mMDithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 132000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 5441 / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 856940
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 110597
FSC plot (resolution estimation)

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