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- EMDB-14570: E.coli gyrase holocomplex with 217 bp DNA and albicidin -

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Basic information

Entry
Database: EMDB / ID: EMD-14570
TitleE.coli gyrase holocomplex with 217 bp DNA and albicidin
Map dataGyrase-Mu217-albicidin
Sample
  • Complex: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA and albicidin stabilised by ADPNP
    • Complex: Escherichia coli gyrase holocomplex
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: 217 bp phage Mu SGS DNA
      • DNA: DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3')
      • DNA: DNA (5'-D(P*AP*GP*AP*AP*TP*CP*AP*GP*GP*CP*AP*TP*AP*A)-3')
      • DNA: DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3')
      • DNA: DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: albicidin
  • Ligand: water
Keywordstype II topoisomerase / antibiotic / albicidin / DNA gyrase / ISOMERASE
Function / homology
Function and homology information


negative regulation of DNA-templated DNA replication / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus ...negative regulation of DNA-templated DNA replication / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / membrane / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA gyrase subunit A / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria) / Escherichia phage Mu (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsGhilarov D / Heddle JGH / Suessmuth R
Funding support United Kingdom, Poland, 2 items
OrganizationGrant numberCountry
Wellcome Trust221868/Z/20/Z United Kingdom
Polish National Science Centre2020/39/B/NZ1/02898 Poland
CitationJournal: Nat Catal / Year: 2023
Title: Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin.
Authors: Elizabeth Michalczyk / Kay Hommernick / Iraj Behroz / Marcel Kulike / Zuzanna Pakosz-Stępień / Lukasz Mazurek / Maria Seidel / Maria Kunert / Karine Santos / Holger von Moeller / Bernhard ...Authors: Elizabeth Michalczyk / Kay Hommernick / Iraj Behroz / Marcel Kulike / Zuzanna Pakosz-Stępień / Lukasz Mazurek / Maria Seidel / Maria Kunert / Karine Santos / Holger von Moeller / Bernhard Loll / John B Weston / Andi Mainz / Jonathan G Heddle / Roderich D Süssmuth / Dmitry Ghilarov /
Abstract: The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is ...The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.
History
DepositionMar 21, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14570.png

Downloads & links

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Map

FileDownload / File: emd_14570.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGyrase-Mu217-albicidin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.6414513 - 1.2093315
Average (Standard dev.)0.0011467556 (±0.02808097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Gyrase-Mu217-albicidin 2.61 A (core)

Fileemd_14570_additional_1.map
AnnotationGyrase-Mu217-albicidin 2.61 A (core)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map A

Fileemd_14570_half_map_1.map
Annotationhalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map B

Fileemd_14570_half_map_2.map
Annotationhalf-map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA ...

EntireName: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA and albicidin stabilised by ADPNP
Components
  • Complex: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA and albicidin stabilised by ADPNP
    • Complex: Escherichia coli gyrase holocomplex
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: 217 bp phage Mu SGS DNA
      • DNA: DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3')
      • DNA: DNA (5'-D(P*AP*GP*AP*AP*TP*CP*AP*GP*GP*CP*AP*TP*AP*A)-3')
      • DNA: DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3')
      • DNA: DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: albicidin
  • Ligand: water

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Supramolecule #1: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA ...

SupramoleculeName: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA and albicidin stabilised by ADPNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Escherichia coli gyrase holocomplex

SupramoleculeName: Escherichia coli gyrase holocomplex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)

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Supramolecule #3: 217 bp phage Mu SGS DNA

SupramoleculeName: 217 bp phage Mu SGS DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Escherichia phage Mu (virus)

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Macromolecule #1: DNA gyrase subunit A

MacromoleculeName: DNA gyrase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain: K12
Molecular weightTheoretical: 97.854305 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTI VRMAQPFSLR YMLVDGQGNF GSIDGDSAAA MR(PTR)TEIRLAK IAHELMADLE KETVDFVDNY DGTEKIP DV MPTKIPNLLV ...String:
SSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTI VRMAQPFSLR YMLVDGQGNF GSIDGDSAAA MR(PTR)TEIRLAK IAHELMADLE KETVDFVDNY DGTEKIP DV MPTKIPNLLV NGSSGIAVGM ATNIPPHNLT EVINGCLAYI DDEDISIEGL MEHIPGPDFP TAAIINGRRG IEEAYRTG R GKVYIRARAE VEVDAKTGRE TIIVHEIPYQ VNKARLIEKI AELVKEKRVE GISALRDESD KDGMRIVIEV KRDAVGEVV LNNLYSQTQL QVSFGINMVA LHHGQPKIMN LKDIIAAFVR HRREVVTRRT IFELRKARDR AHILEALAVA LANIDPIIEL IRHAPTPAE AKTALVANPW QLGNVAAMLE RAGDDAARPE WLEPEFGVRD GLYYLTEQQA QAILDLRLQK LTGLEHEKLL D EYKELLDQ IAELLRILGS ADRLMEVIRE ELELVREQFG DKRRTEITAN SADINLEDLI TQEDVVVTLS HQGYVKYQPL SE YEAQRRG GKGKSAARIK EEDFIDRLLV ANTHDHILCF SSRGRVYSMK VYQLPEATRG ARGRPIVNLL PLEQDERITA ILP VTEFEE GVKVFMATAN GTVKKTVLTE FNRLRTAGKV AIKLVDGDEL IGVDLTSGED EVMLFSAEGK VVRFKESSVR AMGC NTTGV RGIRLGEGDK VVSLIVPRGD GAILTATQNG YGKRTAVAEY PTKSRATKGV ISIKVTERNG LVVGAVQVDD CDQIM MITD AGTLVRTRVS EISIVGRNTQ GVILIRTAED ENVVGLQRVA EPVDEEDLDT IDGSAAEGDD EIAPEVDVDD EPEEEL EVL FQ

UniProtKB: DNA gyrase subunit A

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Macromolecule #2: DNA gyrase subunit B

MacromoleculeName: DNA gyrase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain: K12
Molecular weightTheoretical: 90.891734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPSNSYDSSS IKVLKGLDAV RKRPGMYIGD TDDGTGLHHM VFEVVDNAID EALAGHCKEI IVTIHADNSV SVQDDGRGIP TGIHPEEGV SAAEVIMTVL HAGGKFDDNS YKVSGGLHGV GVSVVNALSQ KLELVIQREG KIHRQIYEHG VPQAPLAVTG E TEKTGTMV ...String:
GPSNSYDSSS IKVLKGLDAV RKRPGMYIGD TDDGTGLHHM VFEVVDNAID EALAGHCKEI IVTIHADNSV SVQDDGRGIP TGIHPEEGV SAAEVIMTVL HAGGKFDDNS YKVSGGLHGV GVSVVNALSQ KLELVIQREG KIHRQIYEHG VPQAPLAVTG E TEKTGTMV RFWPSLETFT NVTEFEYEIL AKRLRELSFL NSGVSIRLRD KRDGKEDHFH YEGGIKAFVE YLNKNKTPIH PN IFYFSTE KDGIGVEVAL QWNDGFQENI YCFTNNIPQR DGGTHLAGFR AAMTRTLNAY MDKEGYSKKA KVSATGDDAR EGL IAVVSV KVPDPKFSSQ TKDKLVSSEV KSAVEQQMNE LLAEYLLENP TDAKIVVGKI IDAARAREAA RRAREMTRRK GALD LAGLP GKLADCQERD PALSELYLVE GDSAGGSAKQ GRNRKNQAIL PLKGKILNVE KARFDKMLSS QEVATLITAL GCGIG RDEY NPDKLRYHSI IIMTDADVDG SHIRTLLLTF FYRQMPEIVE RGHVYIAQPP LYKVKKGKQE QYIKDDEAMD QYQISI ALD GATLHTNASA PALAGEALEK LVSEYNATQK MINRMERRYP KAMLKELIYQ PTLTEADLSD EQTVTRWVNA LVSELND KE QHGSQWKFDV HTNAEQNLFE PIVRVRTHGV DTDYPLDHEF ITGGEYRRIC TLGEKLRGLL EEDAFIERGE RRQPVASF E QALDWLVKES RRGLSIQRYK GLGEMNPEQL WETTMDPESR RMLRVTVKDA IAADQLFTTL MGDAVEPRRA FIEENALKA ANIDIENLYF Q

UniProtKB: DNA gyrase subunit B

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Macromolecule #3: DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 4.335827 KDa
SequenceString:
(DA)(DA)(DA)(DT)(DC)(DT)(DG)(DT)(DG)(DC) (DG)(DG)(DG)(DT)

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Macromolecule #4: DNA (5'-D(P*AP*GP*AP*AP*TP*CP*AP*GP*GP*CP*AP*TP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*GP*AP*AP*TP*CP*AP*GP*GP*CP*AP*TP*AP*A)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 4.321856 KDa
SequenceString:
(DA)(DG)(DA)(DA)(DT)(DC)(DA)(DG)(DG)(DC) (DA)(DT)(DA)(DA)

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Macromolecule #5: DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3')

MacromoleculeName: DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3')
type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 5.444558 KDa
SequenceString:
(DA)(DA)(DT)(DC)(DA)(DC)(DC)(DC)(DG)(DC) (DA)(DC)(DA)(DG)(DA)(DT)(DT)(DT)

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Macromolecule #6: DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3')

MacromoleculeName: DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3')
type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 5.487561 KDa
SequenceString:
(DG)(DA)(DT)(DT)(DT)(DT)(DA)(DT)(DG)(DC) (DC)(DT)(DG)(DA)(DT)(DT)(DC)(DT)

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: albicidin

MacromoleculeName: albicidin / type: ligand / ID: 8 / Number of copies: 1 / Formula: BWH
Molecular weightTheoretical: 842.806 Da
Chemical component information

ChemComp-BWH:
albicidin

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 10 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration12 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 mM / Component - Name: HEPES
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2040353
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23435
FSC plot (resolution estimation)

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