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- EMDB-15802: T5 Receptor Binding Protein pb5 in complex with its E. coli recep... -

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Entry
Database: EMDB / ID: EMD-15802
TitleT5 Receptor Binding Protein pb5 in complex with its E. coli receptor FhuA
Map data
Sample
  • Complex: Complex between T5 Receptor Binding Protein pb5 and its E. coli receptor FhuA, stabilized with detergent
    • Complex: E. coli receptor FhuA
      • Protein or peptide: FhuA iron-ferrichrome transporter
    • Complex: T5 Receptor Binding Protein pb5
      • Protein or peptide: pb5 bacteriophage T5 receptor binding protein
  • Ligand: DECYLAMINE-N,N-DIMETHYL-N-OXIDE
  • Ligand: [(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-4-[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-2-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-carboxy-5-oxidanyl-oxan-2-yl]oxymethyl]-5-[[(3R)-3-dodecanoyloxytetradecanoyl]amino]-4-(3-nonanoyloxypropanoyloxy)-6-[[(2R,3S,4R,5R,6R)-3-oxidanyl-4-[(3S)-3-oxidanyltetradecanoyl]oxy-5-[[(3R)-3-oxidanyltridecanoyl]amino]-6-phosphonatooxy-oxan-2-yl]methoxy]oxan-3-yl] phosphate
Keywordsbacteriophage / receptor / complex / RPB / VIRAL PROTEIN
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virus tail / virion binding / toxic substance binding / transmembrane transporter complex / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell ...siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virus tail / virion binding / toxic substance binding / transmembrane transporter complex / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / iron ion binding / protein domain specific binding / membrane
Similarity search - Function
TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily ...TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain
Similarity search - Domain/homology
Ferrichrome outer membrane transporter/phage receptor / Receptor-binding protein pb5
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia virus T5 / Escherichia phage T5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsDegroux S / Effantin G / Linares R / Schoehn G / Breyton C
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0027 France
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0023 France
CitationJournal: J Virol / Year: 2023
Title: Deciphering Bacteriophage T5 Host Recognition Mechanism and Infection Trigger.
Authors: Séraphine Degroux / Grégory Effantin / Romain Linares / Guy Schoehn / Cécile Breyton /
Abstract: Bacteriophages, viruses infecting bacteria, recognize their host with high specificity, binding to either saccharide motifs or proteins of the cell wall of their host. In the majority of ...Bacteriophages, viruses infecting bacteria, recognize their host with high specificity, binding to either saccharide motifs or proteins of the cell wall of their host. In the majority of bacteriophages, this host recognition is performed by receptor binding proteins (RBPs) located at the extremity of a tail. Interaction between the RBPs and the host is the trigger for bacteriophage infection, but the molecular details of the mechanisms are unknown for most bacteriophages. Here, we present the electron cryomicroscopy (cryo-EM) structure of bacteriophage T5 RBP in complex with its Escherichia coli receptor, the iron ferrichrome transporter FhuA. Monomeric RBP is located at the extremity of T5's long flexible tail, and its irreversible binding to FhuA commits T5 to infection. Analysis of the structure of RBP within the complex, comparison with its AlphaFold2-predicted structure, and its fit into a previously determined map of the T5 tail tip in complex with FhuA allow us to propose a mechanism of transmission of the RBP receptor binding to the straight fiber, initiating the cascade of events that commits T5 to DNA ejection. Tailed bacteriophages specifically recognize their bacterial host by interaction of their receptor binding protein(s) (RBPs) with saccharides and/or proteins located at the surface of their prey. This crucial interaction commits the virus to infection, but the molecular details of this mechanism are unknown for the majority of bacteriophages. We determined the structure of bacteriophage T5 RBP in complex with its E. coli receptor, FhuA, by cryo-EM. This first structure of an RBP bound to its protein receptor allowed us to propose a mechanism of transmission of host recognition to the rest of the phage, ultimately opening the capsid and perforating the cell wall and, thus, allowing safe channeling of the DNA into the host cytoplasm.
History
DepositionSep 9, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15802.png

Downloads & links

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Map

FileDownload / File: emd_15802.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.052 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0017797869 - 1.5113881
Average (Standard dev.)0.00016810768 (±0.010080138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 473.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15802_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15802_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15802_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between T5 Receptor Binding Protein pb5 and its E. coli r...

EntireName: Complex between T5 Receptor Binding Protein pb5 and its E. coli receptor FhuA, stabilized with detergent
Components
  • Complex: Complex between T5 Receptor Binding Protein pb5 and its E. coli receptor FhuA, stabilized with detergent
    • Complex: E. coli receptor FhuA
      • Protein or peptide: FhuA iron-ferrichrome transporter
    • Complex: T5 Receptor Binding Protein pb5
      • Protein or peptide: pb5 bacteriophage T5 receptor binding protein
  • Ligand: DECYLAMINE-N,N-DIMETHYL-N-OXIDE
  • Ligand: [(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-4-[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-2-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-carboxy-5-oxidanyl-oxan-2-yl]oxymethyl]-5-[[(3R)-3-dodecanoyloxytetradecanoyl]amino]-4-(3-nonanoyloxypropanoyloxy)-6-[[(2R,3S,4R,5R,6R)-3-oxidanyl-4-[(3S)-3-oxidanyltetradecanoyl]oxy-5-[[(3R)-3-oxidanyltridecanoyl]amino]-6-phosphonatooxy-oxan-2-yl]methoxy]oxan-3-yl] phosphate

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Supramolecule #1: Complex between T5 Receptor Binding Protein pb5 and its E. coli r...

SupramoleculeName: Complex between T5 Receptor Binding Protein pb5 and its E. coli receptor FhuA, stabilized with detergent
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: The FhuA-pb5 complex was formed by adding equimolar amounts of the two proteins, which results in 100% complex formation. FhuA-RBPpb5 complex is stabilized with 1.6% C10DAO at a protein ...Details: The FhuA-pb5 complex was formed by adding equimolar amounts of the two proteins, which results in 100% complex formation. FhuA-RBPpb5 complex is stabilized with 1.6% C10DAO at a protein concentration of 4.3 mg/mL
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 150 KDa

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Supramolecule #2: E. coli receptor FhuA

SupramoleculeName: E. coli receptor FhuA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia virus T5

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Supramolecule #3: T5 Receptor Binding Protein pb5

SupramoleculeName: T5 Receptor Binding Protein pb5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: FhuA iron-ferrichrome transporter

MacromoleculeName: FhuA iron-ferrichrome transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 79.876945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVEPKEDTIT VTAAPAPQES AWGPAATIAA RQSATGTKTD TPIQKVPQSI SVVTAEEMAL HQPKSVKEAL SYTPGVSVGT RGASNTYDH LIIRGFAAEG QSQNNYLNGL KLQGNFYNDA VIDPYMLERA EIMRGPVSVL YGKSSPGGLL NMVSKRPTTE P LKEVQFKA ...String:
AVEPKEDTIT VTAAPAPQES AWGPAATIAA RQSATGTKTD TPIQKVPQSI SVVTAEEMAL HQPKSVKEAL SYTPGVSVGT RGASNTYDH LIIRGFAAEG QSQNNYLNGL KLQGNFYNDA VIDPYMLERA EIMRGPVSVL YGKSSPGGLL NMVSKRPTTE P LKEVQFKA GTDSLFQTGF DFSDSLDDDG VYSYRLTGLA RSANAQQKGS EEQRYAIAPA FTWRPDDKTN FTFLSYFQNE PE TGYYGWL PKEGTVEPLP NGKRLPTDFN EGAKNNTYSR NEKMVGYSFD HEFNDTFTVR QNLRFAENKT SQNSVYGYGV CSD PANAYS KQCAALAPAD KGHYLARKYV VDDEKLQNFS VDTQLQSKFA TGDIDHTLLT GVDFMRMRND INAWFGYDDS VPLL NLYNP SHHHHHHGSV NTDFDFNAKD PANSGPYRIL NKQKQTGVYV QDQAQWDKVL VTLGGRYDWA DQESLNRVAG TTDKR DDKQ FTWRGGVNYL FDNGVTPYFS YSESFEPSSQ VGKDGNIFAP SKGKQYEVGV KYVPEDRPIV VTGAVYNLTK TNNLMA DPE GSFFSVEGGE IRARGVEIEA KAALSASVNV VGSYTYTDAE YTTDTTYKGN TPAQVPKHMA SLWADYTFFD GPLSGLT LG TGGRYTGSSY GDPANSFKVG SYTVVDALVR YDLARVGMAG SNVALHVNNL FDREYVASCF NTYGCFWGAE RQVVATAT F RF

UniProtKB: Ferrichrome outer membrane transporter/phage receptor

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Macromolecule #2: pb5 bacteriophage T5 receptor binding protein

MacromoleculeName: pb5 bacteriophage T5 receptor binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 68.782562 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSFFAGKLNN KSILSLRRGS GGDTNQHINP DSQTIFHSDM SHVIITETHS TGLRLDQGAG DYYWSEMPSR VTQLHNNDPN RVVLTEIEF SDGSRHMLSG MSMGVGAKAY GIINPQIMSQ GGLKTQITAS ADLSLDVGYF NTGTSGTIPQ KLRDGTGCQH M FGAFSGRR ...String:
MSFFAGKLNN KSILSLRRGS GGDTNQHINP DSQTIFHSDM SHVIITETHS TGLRLDQGAG DYYWSEMPSR VTQLHNNDPN RVVLTEIEF SDGSRHMLSG MSMGVGAKAY GIINPQIMSQ GGLKTQITAS ADLSLDVGYF NTGTSGTIPQ KLRDGTGCQH M FGAFSGRR GFASSAMYLG GAALYKSAWS GSGYVVADAG TLTIPSDYVR HPGARNFGFN AIYVRGRSCN RVLYGMEGPN YT TGGAVQG ASSSGALNFT YNPSNPESPK YSVGFARADP TNYAYWESMG DPNDSANGPI GIYSEHLGIY PSKITWYVTN LVY NGSGYN IDGGLFNGND IKLSPREFII KGVNVNNTSW KFINFIEKNF NVGNRADFRD VGCNLSKDSP STGISGIATF GLPT TESNN APSIKGGNVG GLHANVVSIY NFLPSASWYV SSNPPKIGNN YGDVWSENLL PLRLLGGSGS TILSGNIVFQ GNGSV HVGT VGLDLNSSRN GAIVCTMEFI DDTWLSAGGI GCFNPTEMLS QGAEYGDSRF RIGGNTINKK LHQILSLPAG EYVPFF TIK GTVVNACKLQ AAAYNPTPYW VSGLPGSVGQ TGYYTLTYYM RNDGNNNISI WLDSSMSNII GMKACLPNIK LIIQRLT

UniProtKB: Receptor-binding protein pb5

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Macromolecule #3: DECYLAMINE-N,N-DIMETHYL-N-OXIDE

MacromoleculeName: DECYLAMINE-N,N-DIMETHYL-N-OXIDE / type: ligand / ID: 3 / Number of copies: 1 / Formula: DDQ
Molecular weightTheoretical: 201.349 Da
Chemical component information

ChemComp-DDQ:
DECYLAMINE-N,N-DIMETHYL-N-OXIDE

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Macromolecule #4: [(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethy...

MacromoleculeName: [(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-4-[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-2-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-carboxy-5-oxidanyl-oxan-2-yl] ...Name: [(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-4-[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-2-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-carboxy-5-oxidanyl-oxan-2-yl]oxymethyl]-5-[[(3R)-3-dodecanoyloxytetradecanoyl]amino]-4-(3-nonanoyloxypropanoyloxy)-6-[[(2R,3S,4R,5R,6R)-3-oxidanyl-4-[(3S)-3-oxidanyltetradecanoyl]oxy-5-[[(3R)-3-oxidanyltridecanoyl]amino]-6-phosphonatooxy-oxan-2-yl]methoxy]oxan-3-yl] phosphate
type: ligand / ID: 4 / Number of copies: 1 / Formula: LU9
Molecular weightTheoretical: 1.996235 KDa
Chemical component information

ChemComp-LU9:
[(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-4-[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-2-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-carboxy-5-oxidanyl-oxan-2-yl]oxymethyl]-5-[[(3R)-3-dodecanoyloxytetradecanoyl]amino]-4-(3-nonanoyloxypropanoyloxy)-6-[[(2R,3S,4R,5R,6R)-3-oxidanyl-4-[(3S)-3-oxidanyltetradecanoyl]oxy-5-[[(3R)-3-oxidanyltridecanoyl]amino]-6-phosphonatooxy-oxan-2-yl]methoxy]oxan-3-yl] phosphate / toxin*YM

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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

Concentration1.11111111111111 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
1.6 %C10DAO
GridModel: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3.5 microliters of the FhuA-pb5 complex were deposited on a freshly glow discharged (25 mA, 30 sec) Cu/Rh 400 mesh Quantifoil R 2/1 EM grids and flash-frozen in nitrogen-cooled liquid ethane ...Details: 3.5 microliters of the FhuA-pb5 complex were deposited on a freshly glow discharged (25 mA, 30 sec) Cu/Rh 400 mesh Quantifoil R 2/1 EM grids and flash-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100% humidity, 293.15K, 2s blotting time, blot force 1)..
DetailsThe FhuA-pb5 complex was formed by adding equimolar amounts of the two proteins, which results in 100% complex formation. FhuA-RBPpb5 complex is stabilized with 1.6% C10DAO at a protein concentration of 4.3 mg/ml

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Detailscalibrated pixel size = 1.052
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Number grids imaged: 1 / #0 - Number real images: 8752 / #0 - Average electron dose: 60.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Number grids imaged: 1 / #1 - Number real images: 777 / #1 - Average electron dose: 60.0 e/Å2
#1 - Details: Unlike the first dataset, this one was acquired with a phase plate, close to focus (between -0.5 and -1.0 micrometer).
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 2191586
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 109350
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2grx


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe pb5 protein model was built de novo in the cryo-electron microscopy map. FhuA was adapted from the FhuA structure solved by X-ray crystallography (PDB 2GRX). The two structures were first refined separately using Coot (version 0.9.2) and Phenix (version 1.18.2-3874) softwares, then together. Structure validation was done using MolProbity.
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8b14:
T5 Receptor Binding Protein pb5 in complex with its E. coli receptor FhuA

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