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- EMDB-26738: Integrin alphaM/beta2 ectodomain in complex with adenylate cyclas... -

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Basic information

Entry
Database: EMDB / ID: EMD-26738
TitleIntegrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5 Fab
Map dataComposite map of global and local sharpened maps
Sample
  • Complex: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
    • Protein or peptide: Integrin alpha-M
    • Protein or peptide: Integrin beta
    • Protein or peptide: Bifunctional hemolysin-adenylate cyclase
    • Protein or peptide: M1F5 fab heavy chain
    • Protein or peptide: M1F5 fab light chain
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


cellular extravasation / ectodermal cell differentiation / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning ...cellular extravasation / ectodermal cell differentiation / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / cytolysis / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / leukocyte migration involved in inflammatory response / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / complement receptor mediated signaling pathway / heterotypic cell-cell adhesion / integrin complex / cargo receptor activity / cell adhesion mediated by integrin / phagocytosis, engulfment / leukocyte cell-cell adhesion / amyloid-beta clearance / plasma membrane raft / tertiary granule membrane / positive regulation of protein targeting to membrane / endothelial cell migration / Integrin cell surface interactions / specific granule membrane / phagocytosis / response to mechanical stimulus / forebrain development / heat shock protein binding / cell adhesion molecule binding / receptor-mediated endocytosis / cell-matrix adhesion / positive regulation of superoxide anion generation / response to ischemia / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / integrin binding / response to estradiol / amyloid-beta binding / toxin activity / Interleukin-4 and Interleukin-13 signaling / cell adhesion / membrane raft / external side of plasma membrane / innate immune response / calcium ion binding / Neutrophil degranulation / protein-containing complex binding / cell surface / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
RTX, pore-forming domain / N-terminal domain in RTX protein / RTX toxin determinant A / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) ...RTX, pore-forming domain / N-terminal domain in RTX protein / RTX toxin determinant A / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Integrin beta / Bifunctional hemolysin-adenylate cyclase / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human) / Bordetella pertussis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGoldsmith JA / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI155453 United States
CitationJournal: Cell Rep / Year: 2022
Title: Structural basis for non-canonical integrin engagement by Bordetella adenylate cyclase toxin.
Authors: Jory A Goldsmith / Andrea M DiVenere / Jennifer A Maynard / Jason S McLellan /
Abstract: Integrins are ubiquitous cell-surface heterodimers that are exploited by pathogens and toxins, including leukotoxins that target β integrins on phagocytes. The Bordetella adenylate cyclase toxin ...Integrins are ubiquitous cell-surface heterodimers that are exploited by pathogens and toxins, including leukotoxins that target β integrins on phagocytes. The Bordetella adenylate cyclase toxin (ACT) uses the αβ integrin as a receptor, but the structural basis for integrin binding and neutralization by antibodies is poorly understood. Here, we use cryoelectron microscopy to determine a 2.7 Å resolution structure of an ACT fragment bound to αβ. This structure reveals that ACT interacts with the headpiece and calf-2 of the α subunit in a non-canonical manner specific to bent, inactive αβ. Neutralizing antibody epitopes map to ACT residues involved in α binding, providing the basis for antibody-mediated attachment inhibition. Furthermore, binding to αβ positions the essential ACT acylation sites, which are conserved among toxins exported by type I secretion systems, at the cell membrane. These findings reveal a structural mechanism for integrin-mediated attachment and explain antibody-mediated neutralization of ACT intoxication.
History
DepositionApr 25, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26738.png

Downloads & links

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Map

FileDownload / File: emd_26738.map.gz / Format: CCP4 / Size: 147.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of global and local sharpened maps
Voxel sizeX=Y=Z: 1.073 Å
Density
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-9.475574 - 271.23026
Average (Standard dev.)0.014895657 (±1.3623712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions338338338
Spacing338338338
CellA=B=C: 362.67398 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ternary complex of integrin alphaM/beta2 ectodomain with adenylat...

EntireName: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
Components
  • Complex: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
    • Protein or peptide: Integrin alpha-M
    • Protein or peptide: Integrin beta
    • Protein or peptide: Bifunctional hemolysin-adenylate cyclase
    • Protein or peptide: M1F5 fab heavy chain
    • Protein or peptide: M1F5 fab light chain
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of integrin alphaM/beta2 ectodomain with adenylat...

SupramoleculeName: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Integrin alpha-M

MacromoleculeName: Integrin alpha-M / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 128.455289 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FNLDTENAMT FQENARGFGQ SVVQLQGSRV VVGAPQEIVA ANQRGSLYQC DYSTGSCEPI RLQVPVEAVN MSLGLSLAAT TSPPQLLAC GPTVHQTCSE NTYVKGLCFL FGSNLRQQPQ KFPEALRGCP QEDSDIAFLI DGSGSIIPHD FRRMKEFVST V MEQLKKSK ...String:
FNLDTENAMT FQENARGFGQ SVVQLQGSRV VVGAPQEIVA ANQRGSLYQC DYSTGSCEPI RLQVPVEAVN MSLGLSLAAT TSPPQLLAC GPTVHQTCSE NTYVKGLCFL FGSNLRQQPQ KFPEALRGCP QEDSDIAFLI DGSGSIIPHD FRRMKEFVST V MEQLKKSK TLFSLMQYSE EFRIHFTFKE FQNNPNPRSL VKPITQLLGR THTATGIRKV VRELFNITNG ARKNAFKILV VI TDGEKFG DPLGYEDVIP EADREGVIRY VIGVGDAFRS EKSRQELNTI ASKPPRDHVF QVNNFEALKT IQNQLREKIF AIE GTQTGS SSSFEHEMSQ EGFSAAITSN GPLLSTVGSY DWAGGVFLYT SKEKSTFINM TRVDSDMNDA YLGYAAAIIL RNRV QSLVL GAPRYQHIGL VAMFRQNTGM WESNANVKGT QIGAYFGASL CSVDVDSNGS TDLVLIGAPH YYEQTRGGQV SVCPL PRGR ARWQCDAVLY GEQGQPWGRF GAALTVLGDV NGDKLTDVAI GAPGEEDNRG AVYLFHGTSG SGISPSHSQR IAGSKL SPR LQYFGQSLSG GQDLTMDGLV DLTVGAQGHV LLLRSQPVLR VKAIMEFNPR EVARNVFECN DQVVKGKEAG EVRVCLH VQ KSTRDRLREG QIQSVVTYDL ALDSGRPHSR AVFNETKNST RRQTQVLGLT QTCETLKLQL PNCIEDPVSP IVLRLNFS L VGTPLSAFGN LRPVLAEDAQ RLFTALFPFE KNCGNDNICQ DDLSITFSFM SLDCLVVGGP REFNVTVTVR NDGEDSYRT QVTFFFPLDL SYRKVSTLQN QRSQRSWRLA CESASSTEVS GALKSTSCSI NHPIFPENSE VTFNITFDVD SKASLGNKLL LKANVTSEN NMPRTNKTEF QLELPVKYAV YMVVTSHGVS TKYLNFTASE NTSRVMQHQY QVSNLGQRSL PISLVFLVPV R LNQTVIWD RPQVTFSENL SSTCHTKERL PSHSDFLAEL RKAPVVNCSI AVCQRIQCDI PFFGIQEEFN ATLKGNLSFD WY IKTSHNH LLIVSTAEIL FNDSVFTLLP GQGAFVRSQT ETKVEPFEVP NGCGGLEVLF QGPGENAQCE KELQALEKEN AQL EWELQA LEKELAQWSH PQFEKGGGSG GGGSGGSAWS HPQFEK

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Macromolecule #2: Integrin beta

MacromoleculeName: Integrin beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.784938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QECTKFKVSS CRECIESGPG CTWCQKLNFT GPGDPDSIRC DTRPQLLMRG CAADDIMDPT SLAETQEDHN GGQKQLSPQK VTLYLRPGQ AAAFNVTFRR AKGYPIDLYY LMDLSYSMLD DLRNVKKLGG DLLRALNEIT ESGRIGFGSF VDKTVLPFVN T HPDKLRNP ...String:
QECTKFKVSS CRECIESGPG CTWCQKLNFT GPGDPDSIRC DTRPQLLMRG CAADDIMDPT SLAETQEDHN GGQKQLSPQK VTLYLRPGQ AAAFNVTFRR AKGYPIDLYY LMDLSYSMLD DLRNVKKLGG DLLRALNEIT ESGRIGFGSF VDKTVLPFVN T HPDKLRNP CPNKEKECQP PFAFRHVLKL TNNSNQFQTE VGKQLISGNL DAPEGGLDAM MQVAACPEEI GWRNVTRLLV FA TDDGFHF AGDGKLGAIL TPNDGRCHLE DNLYKRSNEF DYPSVGQLAH KLAENNIQPI FAVTSRMVKT YEKLTEIIPK SAV GELSED SSNVVHLIKN AYNKLSSRVF LDHNALPDTL KVTYDSFCSN GVTHRNQPRG DCDGVQINVP ITFQVKVTAT ECIQ EQSFV IRALGFTDIV TVQVLPQCEC RCRDQSRDRS LCHGKGFLEC GICRCDTGYI GKNCECQTQG RSSQELEGSC RKDNN SIIC SGLGDCVCGQ CLCHTSDVPG KLIYGQYCEC DTINCERYNG QVCGGPGRGL CFCGKCRCHP GFEGSACQCE RTTEGC LNP RRVECSGRGR CRCNVCECHS GYQLPLCQEC PGCPSPCGKY ISCAECLKFE KGPFGKNCSA ACPGLQLSNN PVKGRTC KE RDSEGCWVAY TLEQQDGMDR YLIYVDESRE CVAGPDGCGL EVLFQGPGKN AQCKKKLQAL KKKNAQLKWK LQALKKKL A QGGHHHHHH

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Macromolecule #3: Bifunctional hemolysin-adenylate cyclase

MacromoleculeName: Bifunctional hemolysin-adenylate cyclase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 100.286688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGSANSDGL RKMLADLQAG WNASSVIGVQ TTEISKSALE LAAITGNADN LKSVDVFVDR FVQGERVAGQ PVVLDVAAGG IDIASRKGE RPALTFITPL AAPGEEQRRR TKTGKSEFTT FVEIVGKQDR WRIRDGAADT TIDLAKVVSQ LVDANGVLKH S IKLDVIGG ...String:
GPGSANSDGL RKMLADLQAG WNASSVIGVQ TTEISKSALE LAAITGNADN LKSVDVFVDR FVQGERVAGQ PVVLDVAAGG IDIASRKGE RPALTFITPL AAPGEEQRRR TKTGKSEFTT FVEIVGKQDR WRIRDGAADT TIDLAKVVSQ LVDANGVLKH S IKLDVIGG DGDDVVLANA SRIHYDGGAG TNTVSYAALG RQDSITVSAD GERFNVRKQL NNANVYREGV ATQTTAYGKR TE NVQYRHV ELARVGQLVE VDTLEHVQHI IGGAGNDSIT GNAHDNFLAG GSGDDRLDGG AGNDTLVGGE GQNTVIGGAG DDV FLQDLG VWSNQLDGGA GVDTVKYNVH QPSEERLERM GDTGIHADLQ KGTVEKWPAL NLFSVDHVKN IENLHGSRLN DRIA GDDQD NELWGHDGND TIRGRGGDDI LRGGLGLDTL YGEDGNDIFL QDDETVSDDI DGGAGLDTVD YSAMIHPGRI VAPHE YGFG IEADLSREWV RKASALGVDY YDNVRNVENV IGTSMKDVLI GDAQANTLMG QGGDDTVRGG DGDDLLFGGD GNDMLY GDA GNDTLYGGLG DDTLEGGAGN DWFGQTQARE HDVLRGGDGV DTVDYSQTGA HAGIAAGRIG LGILADLGAG RVDKLGE AG SSAYDTVSGI ENVVGTELAD RITGDAQANV LRGAGGADVL AGGEGDDVLL GGDGDDQLSG DAGRDRLYGE AGDDWFFQ D AANAGNLLDG GDGRDTVDFS GPGRGLDAGA KGVFLSLGKG FASLMDEPET SNVLRNIENA VGSARDDVLI GDAGANVLN GLAGNDVLSG GAGDDVLLGD EGSDLLSGDA GNDDLFGGQG DDTYLFGVGY GHDTIYESGG GHDTIRINAG ADQLWFARQG NDLEIRILG TDDALTVHDW YRDADHRVEI IHAANQAVDQ AGIEKLVEAM AQYPDPGAAA AAPPAARVPD TLMQSLAVNW R

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Macromolecule #4: M1F5 fab heavy chain

MacromoleculeName: M1F5 fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.665729 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLKQSGPE LVKPGASVRM SCKGSGYSFT FHNIHWVKQR PGQGLEWIGW IYPGDGNTKY NEKFKGKTTL TVDKSSNTAY MLLSSLTSE DSAIYFCAYG NYYFDQWGQG TTLTVSSRST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String:
QVQLKQSGPE LVKPGASVRM SCKGSGYSFT FHNIHWVKQR PGQGLEWIGW IYPGDGNTKY NEKFKGKTTL TVDKSSNTAY MLLSSLTSE DSAIYFCAYG NYYFDQWGQG TTLTVSSRST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKGLEVLFQ

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Macromolecule #5: M1F5 fab light chain

MacromoleculeName: M1F5 fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.360854 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IQMMQSTSSL SASLGDRVTI SCSASQGITN YLNWYQQKPD GTVKLLIYYT SSLHSGVPSR FSGSGSGTDY SLTISNLEPE DIATYYCQQ YSNLPWTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
IQMMQSTSSL SASLGDRVTI SCSASQGITN YLNWYQQKPD GTVKLLIYYT SSLHSGVPSR FSGSGSGTDY SLTISNLEPE DIATYYCQQ YSNLPWTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 33 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 11 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3k6s

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 347508

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