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- EMDB-52338: TTLL11 bound to microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-52338
TitleTTLL11 bound to microtubule
Map data
Sample
  • Complex: Complex of TTLL11 and two tubulin dimers
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Tubulin polyglutamylase TTLL11
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: TAXOL
KeywordsTTLL11 / polyglutamylase / tubulin / microtubule / LIGASE
Function / homology
Function and homology information


tubulin-glutamic acid ligase activity / protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / microtubule severing / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / odontoblast differentiation / Post-chaperonin tubulin folding pathway / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane ...tubulin-glutamic acid ligase activity / protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / microtubule severing / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / odontoblast differentiation / Post-chaperonin tubulin folding pathway / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / haloalkane dehalogenase / haloalkane dehalogenase activity / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / Kinesins / GTPase activating protein binding / COPI-independent Golgi-to-ER retrograde traffic / Assembly and cell surface presentation of NMDA receptors / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / regulation of synapse organization / nuclear envelope lumen / Recycling pathway of L1 / MHC class I protein binding / RHOH GTPase cycle / RHO GTPases activate IQGAPs / microtubule-based process / Hedgehog 'off' state / intercellular bridge / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / spindle assembly / cytoplasmic microtubule / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / cellular response to interleukin-4 / tubulin binding / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / PKR-mediated signaling / protein modification process / structural constituent of cytoskeleton / response to toxic substance / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / HCMV Early Events / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / cell body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Potential therapeutics for SARS / microtubule / cytoskeleton / cilium / ciliary basal body / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / ATP binding / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. ...Haloalkane dehalogenase, subfamily 2 / : / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Tubulin beta chain / Haloalkane dehalogenase / Tubulin alpha-1B chain / Tubulin polyglutamylase TTLL11
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBarinka C / Campbell J / Desfosses A / Gutsche I
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science Foundation23-07149S Czech Republic
CitationJournal: Sci Adv / Year: 2025
Title: Mechanistic insights into TTLL11 polyglutamylase-mediated primary tubulin chain elongation.
Authors: Jana Campbell / Miroslava Vosahlikova / Samar Ismail / Margareta Volnikova / Lucia Motlova / Julia Kudlacova / Kseniya Ustinova / Ivan Snajdr / Zora Novakova / Miroslav Basta / Irina Gutsche ...Authors: Jana Campbell / Miroslava Vosahlikova / Samar Ismail / Margareta Volnikova / Lucia Motlova / Julia Kudlacova / Kseniya Ustinova / Ivan Snajdr / Zora Novakova / Miroslav Basta / Irina Gutsche / Marie-Jo Moutin / Ambroise Desfosses / Cyril Barinka /
Abstract: Microtubules (MTs) undergo diverse posttranslational modifications that regulate their structural and functional properties. Among these, polyglutamylation-a dominant and conserved modification ...Microtubules (MTs) undergo diverse posttranslational modifications that regulate their structural and functional properties. Among these, polyglutamylation-a dominant and conserved modification targeting unstructured tubulin C-terminal tails-plays a pivotal role in defining the tubulin code. Here, we describe a mechanism by which tubulin tyrosine ligase-like 11 (TTLL11) expands and diversifies the code. Cryo-electron microscopy revealed a unique bipartite MT recognition strategy wherein TTLL11 binding and catalytic domains engage adjacent MT protofilaments. Biochemical and cellular assays identified previously uncharacterized polyglutamylation patterns, showing that TTLL11 directly extends the primary polypeptide chains of α- and β-tubulin in vitro, challenging the prevailing paradigms emphasizing lateral branching. Moreover, cell-based and in vivo data suggest a cross-talk between polyglutamylation and the detyrosination/tyrosination cycle likely linked to the TTLL11-mediated elongation of the primary α-tubulin chain. These findings unveil an unrecognized layer of complexity within the tubulin code and offer mechanistic insights into the molecular basis of functional specialization of MT cytoskeleton.
History
DepositionDec 16, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52338.png

Downloads & links

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Map

FileDownload / File: emd_52338.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 480 pix.
= 647.52 Å		1.35 Å/pix.
x 480 pix.
= 647.52 Å		1.35 Å/pix.
x 480 pix.
= 647.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.349 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0956
Minimum - Maximum-0.0285344 - 2.275384
Average (Standard dev.)0.0013154492 (±0.021378549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 647.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52338_msk_1.map
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Half map: #2

Fileemd_52338_half_map_1.map
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Half map: #1

Fileemd_52338_half_map_2.map
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Sample components

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Entire : Complex of TTLL11 and two tubulin dimers

EntireName: Complex of TTLL11 and two tubulin dimers
Components
  • Complex: Complex of TTLL11 and two tubulin dimers
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Tubulin polyglutamylase TTLL11
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: TAXOL

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Supramolecule #1: Complex of TTLL11 and two tubulin dimers

SupramoleculeName: Complex of TTLL11 and two tubulin dimers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1
Details: Native tubulin isolated from HEK 293T cells, unaligned regions are intrinsicly disordered
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.204445 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2
Details: The C-terminal part of tubulin is intrinsicaly disordered thus not visible in the structure.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.717629 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQVFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMAVT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEED FGEEAEEEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: Tubulin polyglutamylase TTLL11

MacromoleculeName: Tubulin polyglutamylase TTLL11 / type: protein_or_peptide / ID: 3
Details: The original protein contains N-terminal Halo tag on a flexible linker so it is not visible in the map or included in the model. TTLL11 containes several instriscally disordered regions that ...Details: The original protein contains N-terminal Halo tag on a flexible linker so it is not visible in the map or included in the model. TTLL11 containes several instriscally disordered regions that are left out from the model.
Number of copies: 1 / Enantiomer: LEVO
EC number: Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.410188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGSGGSDY KDDDDKGSGS GEIGTGFPFD PHYVEVLGER MHYVDVGPRD GTPVLFLHG NPTSSYVWRN IIPHVAPTHR CIAPDLIGMG KSDKPDLGYF FDDHVRFMDA FIEALGLEEV VLVIHDWGSA L GFHWAKRN ...String:
MASAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGSGGSDY KDDDDKGSGS GEIGTGFPFD PHYVEVLGER MHYVDVGPRD GTPVLFLHG NPTSSYVWRN IIPHVAPTHR CIAPDLIGMG KSDKPDLGYF FDDHVRFMDA FIEALGLEEV VLVIHDWGSA L GFHWAKRN PERVKGIAFM EFIRPIPTWD EWPEFARETF QAFRTTDVGR KLIIDQNVFI EGTLPMGVVR PLTEVEMDHY RE PFLNPVD REPLWRFPNE LPIAGEPANI VALVEEYMDW LHQSPVPKLL FWGTPGVLIP PAEAARLAKS LPNCKAVDIG PGL NLLQED NPDLIGSEIA RWLSTLEISG EPTTEDLYFQ SDNAIASEFC RYPAQWRPLE SSRHNQTSLY KKAGSENLYF QSGG GENGS QRPVTVDSSK ARTSLDALKI SIRQLKWKEF PFGRRLPCDI YWHGVSFHDN DIFSGQVNKF PGMTEMVRKI TLSRA VRTM QNLFPEEYNF YPRSWILPDE FQLFVAQVQM VKDDDPSWKP TFIVKPDGGC QGDGIYLIKD PSDIRLAGTL QSRPAV VQE YICKPLLIDK LKFDIRLYVL LKSLDPLEIY IAKDGLSRFC TEPYQEPTPK NLHRIFMHLT NYSLNIHSGN FIHSDSA ST GSKRTFSSIL CRLSSKGVDI KKVWSDIISV VIKTVIALTP ELKVFYQSDI PTGRPGPTCF QILGFDILLM KNLKPILL G VNANPSMRIE HEHELSPGVF ENVPSLVDEE VKVAVIRDTL RLMDPLKKKR ENQSQQLEKP FAGKEDALDG ELTSAPDCN ANPEAHLPSI CLKQVFPKYA KQFNYLRLVD RMANLFIRFL GIKGTMKLGP TGFRTFIRSC KLSSSSLSMA AVDILYIDIT RRWNSMTLD QRDSGMCLQA FVEAFFFLAQ RKFKMLPLHE QVASLIDLCE YHLSLLDEKR LVCGRGVPSG GRPPHRGPPQ E PSPSAQPA GDNPPPRTSC ANKLSHPRHT LS

UniProtKB: Haloalkane dehalogenase, Tubulin polyglutamylase TTLL11

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Macromolecule #4: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 4 / Number of copies: 4 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 6 / Number of copies: 2 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration2 mg/mL
BufferpH: 7
Details: 40 mM Tris-HCl, pH 7.0, 1 mM TCEP, 1 mM MgCl2, 5 % glycerol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: 14-pf microtubule generated model (Cook AD, Manka SW, Wang S, Moores CA, Atherton J. A microtubule RELION-based pipeline for cryo-EM image processing. J Struct Biol. 2020 Jan 1;209(1) ...In silico model: 14-pf microtubule generated model (Cook AD, Manka SW, Wang S, Moores CA, Atherton J. A microtubule RELION-based pipeline for cryo-EM image processing. J Struct Biol. 2020 Jan 1;209(1):107402. doi: 10.1016/j.jsb.2019.10.004. Epub 2019 Oct 11. PMID: 31610239; PMCID: PMC6961209.)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 239587
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1-v4


Chain - Chain ID: A / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9hq4:
TTLL11 bound to microtubule

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