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- EMDB-12174: The catalytic core lobe of human telomerase in complex with a tel... -

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Basic information

Entry
Database: EMDB / ID: EMD-12174
TitleThe catalytic core lobe of human telomerase in complex with a telomeric DNA substrate
Map dataPost-processed map
Sample
  • Complex: Human telomerase catalytic core in complex with a telomeric DNA substrate
    • Complex: Telomerase reverse transcriptase
      • Protein or peptide: Telomerase reverse transcriptase,Telomerase reverse transcriptase
      • RNA: RNA (256-MER)
    • Complex: Histone
      • Protein or peptide: Histone H2B
      • Protein or peptide: Histone H2A
    • Complex: DNA
      • DNA: DNA (5'-D(P*TP*TP*AP*GP*GP*G)-3')
KeywordsReverse transcriptase / ribonucleoprotein / complex / DNA / RNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / telomerase activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / nuclear telomere cap complex / siRNA processing / telomere maintenance via recombination / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / DNA biosynthetic process / RNA-templated transcription / telomeric DNA binding / positive regulation of stem cell proliferation / mitochondrial nucleoid / negative regulation of cellular senescence / replicative senescence / Telomere Extension By Telomerase / positive regulation of Wnt signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of G1/S transition of mitotic cell cycle / response to cadmium ion / positive regulation of protein binding / telomere maintenance via telomerase / negative regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / positive regulation of D-glucose import / mitochondrion organization / Formation of the beta-catenin:TCF transactivating complex / PML body / regulation of protein stability / positive regulation of miRNA transcription / RNA-directed DNA polymerase / transcription coactivator binding / RNA-directed DNA polymerase activity / positive regulation of angiogenesis / protein import into nucleus / structural constituent of chromatin / nucleosome / protein-folding chaperone binding / heart development / cellular response to hypoxia / negative regulation of neuron apoptotic process / tRNA binding / chromosome, telomeric region / nuclear speck / protein heterodimerization activity / RNA-directed RNA polymerase activity / nucleolus / protein homodimerization activity / DNA binding / RNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. ...: / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Histone H2A / Histone H2B / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsNguyen THD / Ghanim GE
Funding support United Kingdom, United States, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/19 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM054198 United States
CitationJournal: Nature / Year: 2021
Title: Structure of human telomerase holoenzyme with bound telomeric DNA.
Authors: George E Ghanim / Adam J Fountain / Anne-Marie M van Roon / Ramya Rangan / Rhiju Das / Kathleen Collins / Thi Hoang Duong Nguyen /
Abstract: Telomerase adds telomeric repeats at chromosome ends to compensate for the telomere loss that is caused by incomplete genome end replication. In humans, telomerase is upregulated during embryogenesis ...Telomerase adds telomeric repeats at chromosome ends to compensate for the telomere loss that is caused by incomplete genome end replication. In humans, telomerase is upregulated during embryogenesis and in cancers, and mutations that compromise the function of telomerase result in disease. A previous structure of human telomerase at a resolution of 8 Å revealed a vertebrate-specific composition and architecture, comprising a catalytic core that is flexibly tethered to an H and ACA (hereafter, H/ACA) box ribonucleoprotein (RNP) lobe by telomerase RNA. High-resolution structural information is necessary to develop treatments that can effectively modulate telomerase activity as a therapeutic approach against cancers and disease. Here we used cryo-electron microscopy to determine the structure of human telomerase holoenzyme bound to telomeric DNA at sub-4 Å resolution, which reveals crucial DNA- and RNA-binding interfaces in the active site of telomerase as well as the locations of mutations that alter telomerase activity. We identified a histone H2A-H2B dimer within the holoenzyme that was bound to an essential telomerase RNA motif, which suggests a role for histones in the folding and function of telomerase RNA. Furthermore, this structure of a eukaryotic H/ACA RNP reveals the molecular recognition of conserved RNA and protein motifs, as well as interactions that are crucial for understanding the molecular pathology of many mutations that cause disease. Our findings provide the structural details of the assembly and active site of human telomerase, which paves the way for the development of therapeutic agents that target this enzyme.
History
DepositionJan 6, 2021-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bg9
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bg9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12174.png

Downloads & links

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Map

FileDownload / File: emd_12174.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 240 pix.
= 266.4 Å		1.11 Å/pix.
x 240 pix.
= 266.4 Å		1.11 Å/pix.
x 240 pix.
= 266.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.052251868 - 0.08463936
Average (Standard dev.)0.00036842295 (±0.0027956716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 266.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z266.400266.400266.400
α/β/γ90.00090.00090.000
start NX/NY/NZ278280246
NX/NY/NZ474891
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0520.0850.000

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Supplemental data

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Half map: #2

Fileemd_12174_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_12174_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human telomerase catalytic core in complex with a telomeric DNA s...

EntireName: Human telomerase catalytic core in complex with a telomeric DNA substrate
Components
  • Complex: Human telomerase catalytic core in complex with a telomeric DNA substrate
    • Complex: Telomerase reverse transcriptase
      • Protein or peptide: Telomerase reverse transcriptase,Telomerase reverse transcriptase
      • RNA: RNA (256-MER)
    • Complex: Histone
      • Protein or peptide: Histone H2B
      • Protein or peptide: Histone H2A
    • Complex: DNA
      • DNA: DNA (5'-D(P*TP*TP*AP*GP*GP*G)-3')

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Supramolecule #1: Human telomerase catalytic core in complex with a telomeric DNA s...

SupramoleculeName: Human telomerase catalytic core in complex with a telomeric DNA substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: Telomerase reverse transcriptase

SupramoleculeName: Telomerase reverse transcriptase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Histone

SupramoleculeName: Histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Telomerase reverse transcriptase,Telomerase reverse transcriptase

MacromoleculeName: Telomerase reverse transcriptase,Telomerase reverse transcriptase
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
Molecular weightTheoretical: 149.158578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTAALAQHD EAVDNKFNKE QQNAFYEILH LPNLNEEQRN AFIQSLKDDP SQSANLLAEA KKLNDAQAPK VDNKFNKEQQ NAFYEILHL PNLNEEQRNA FIQSLKDDPS QSANLLAEAK KLNGAQAPKV DANSAGKSTD YDIPTTASEN LYFQGHKLGT F QGPWSHPQ ...String:
MKTAALAQHD EAVDNKFNKE QQNAFYEILH LPNLNEEQRN AFIQSLKDDP SQSANLLAEA KKLNDAQAPK VDNKFNKEQQ NAFYEILHL PNLNEEQRNA FIQSLKDDPS QSANLLAEAK KLNGAQAPKV DANSAGKSTD YDIPTTASEN LYFQGHKLGT F QGPWSHPQ FEKGSAGSAA GSGAGWSHPQ FEKSRPTTAS GTMPRAPRCR AVRSLLRSHY REVLPLATFV RRLGPQGWRL VQ RGDPAAF RALVAQCLVC VPWDARPPPA APSFRQVSCL KELVARVLQR LCERGAKNVL AFGFALLDGA RGGPPEAFTT SVR SYLPNT VTDALRGSGA WGLLLRRVGD DVLVHLLARC ALFVLVAPSC AYQVCGPPLY QLGAATQARP PPHASGPRRR LGCE RAWNH SVREAGVPLG LPAPGARRRG GSASRSLPLP KRPRRGAAPE PERTPVGQGS WAHPGRTRGP SDRGFCVVSP ARPAE EATS LEGALSGTRH SHPSVGRQHH AGPPSTSRPP RPWDTPCPPV YAETKHFLYS SGDKEQLRPS FLLSSLRPSL TGARRL VET IFLGSRPWMP GTPRRLPRLP QRYWQMRPLF LELLGNHAQC PYGVLLKTHC PLRAAVTPAA GVCAREKPQG SVAAPEE ED TDPRRLVQLL RQHSSPWQVY GFVRACLRRL VPPGLWGSRH NERRFLRNTK KFISLGKHAK LSLQELTWKM SVRDCAWL R RSPGVGCVPA AEHRLREEIL AKFLHWLMSV YVVELLRSFF YVTETTFQKN RLFFYRKSVW SKLQSIGIRQ HLKRVQLRE LSEAEVRQHR EARPALLTSR LRFIPKPDGL RPIVNMDYVV GARTFRREKR AERLTSRVKA LFSVLNYERA RRPGLLGASV LGLDDIHRA WRTFVLRVRA QDPPPELYFV KVDVTGAYDT IPQDRLTEVI ASIIKPQNTY CVRRYAVVQK AAHGHVRKAF K SHVSTLTD LQPYMRQFVA HLQETSPLRD AVVIEQSSSL NEASSGLFDV FLRFMCHHAV RIRGKSYVQC QGIPQGSILS TL LCSLCYG DMENKLFAGI RRDGLLLRLV DDFLLVTPHL THAKTFLRTL VRGVPEYGCV VNLRKTVVNF PVEDEALGGT AFV QMPAHG LFPWCGLLLD TRTLEVQSDY SSYARTSIRA SLTFNRGFKA GRNMRRKLFG VLRLKCHSLF LDLQVNSLQT VCTN IYKIL LLQAYRFHAC VLQLPFHQQV WKNPTFFLRV ISDTASLCYS ILKAKNAGMS LGAKGAAGPL PSEAVQWLCH QAFLL KLTR HRVTYVPLLG SLRTAQTQLS RKLPGTTLTA LEAAANPALP SDFKTILD

UniProtKB: Telomerase reverse transcriptase

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Macromolecule #3: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
Molecular weightTheoretical: 18.074932 KDa
SequenceString:
MPDPAKSAPA PKKGSKKAVT KVQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSNPRN LSPTKPGGSE DRQPPPSQLS AIPPFCLVLR A GIAGQV

UniProtKB: Histone H2B

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Macromolecule #4: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
Molecular weightTheoretical: 14.140584 KDa
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VRRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A

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Macromolecule #2: DNA (5'-D(P*TP*TP*AP*GP*GP*G)-3')

MacromoleculeName: DNA (5'-D(P*TP*TP*AP*GP*GP*G)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.514567 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DA)(DG)(DG)(DG)

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Macromolecule #5: RNA (256-MER)

MacromoleculeName: RNA (256-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
Molecular weightTheoretical: 145.477797 KDa
SequenceString: GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU GCCGCCUUCC ACCGUUCAUU C UAGAGCAA ...String:
GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU GCCGCCUUCC ACCGUUCAUU C UAGAGCAA ACAAAAAAUG UCAGCUGCUG GCCCGUUCGC CCCUCCCGGG GACCUGCGGC GGGUCGCCUG CCCAGCCCCC GA ACCCCGC CUGGAGGCCG CGGUCGGCCC GGGGCUUCUC CGGAGGCACC CACUGCCACC GCGAAGAGUU GGGCUCUGUC AGC CGCGGG UCUCUCGGGG GCGAGGGCGA GGUUCAGGCC UUUCAGGCCG CAGGAAGAGG AACGGAGCGA GUCCCCGCGC GCGG CGCGA UUCCCUGAGC UGUGGGACGU GCACCCAGGA CUCGGCUCAC ACAUGC

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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: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
2.0 mMMgCl2magnesium chloride
0.05 %(C2H4O)nC14H22OIgepal CA630
1.0 %C12H22O11Trehalose
1.0 mMC4H10O2S2DTT
GridModel: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4-5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 43639 / Average exposure time: 1.0 sec. / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
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

DetailsAll images were processed using RELION 3.1.
Particle selectionNumber selected: 15760434
Startup modelType of model: EMDB MAP
EMDB ID:

7521

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 168538
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 80
Output model

PDB-7bg9:
The catalytic core lobe of human telomerase in complex with a telomeric DNA substrate

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