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- EMDB-28083: Helical reconstruction of the human cardiac actin-tropomyosin-myo... -

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Basic information

Entry
Database: EMDB / ID: EMD-28083
TitleHelical reconstruction of the human cardiac actin-tropomyosin-myosin complex in the rigor form
Map dataPrimary map for the human cardiac actin-tropomyosin-beta-myosin II complex in the rigor conformation
Sample
  • Complex: Human cardiac actin-tropomyosin-beta-myosin II complex in the rigor form.
    • Complex: Cardiac F-actin complex
      • Protein or peptide: Actin, alpha cardiac muscle 1
    • Complex: Human cardiac myosin II
      • Protein or peptide: Myosin-7
    • Complex: Human cardiac tropomyosin
      • Protein or peptide: Tropomyosin alpha-1 chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / regulation of slow-twitch skeletal muscle fiber contraction / RHOB GTPase cycle / Striated Muscle Contraction / regulation of the force of skeletal muscle contraction / RHOA GTPase cycle / actin-myosin filament sliding / muscle myosin complex / bleb ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / regulation of slow-twitch skeletal muscle fiber contraction / RHOB GTPase cycle / Striated Muscle Contraction / regulation of the force of skeletal muscle contraction / RHOA GTPase cycle / actin-myosin filament sliding / muscle myosin complex / bleb / negative regulation of vascular associated smooth muscle cell migration / regulation of muscle contraction / muscle filament sliding / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / ruffle organization / myosin II complex / adult heart development / cardiac muscle hypertrophy in response to stress / Striated Muscle Contraction / positive regulation of ATP-dependent activity / myosin complex / regulation of heart contraction / structural constituent of muscle / sarcomere organization / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myosin binding / myofibril / mesenchyme migration / heart contraction / negative regulation of vascular associated smooth muscle cell proliferation / skeletal muscle contraction / positive regulation of cell adhesion / striated muscle contraction / Smooth Muscle Contraction / stress fiber / ATP metabolic process / cytoskeleton organization / cardiac muscle contraction / positive regulation of stress fiber assembly / regulation of heart rate / cytoskeletal protein binding / sarcomere / negative regulation of cell migration / filopodium / muscle contraction / actin filament organization / actin filament / wound healing / structural constituent of cytoskeleton / ruffle membrane / Z disc / cellular response to reactive oxygen species / actin filament binding / actin cytoskeleton / lamellipodium / cell body / actin binding / regulation of cell shape / cytoskeleton / calmodulin binding / protein heterodimerization activity / positive regulation of gene expression / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. ...Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Actin, alpha cardiac muscle 1 / Tropomyosin alpha-1 chain / Myosin-7
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human) / pig (pig)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDoran MH / Lehman W / Rynkiewicz MJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL036153 United States
CitationJournal: J Gen Physiol / Year: 2023
Title: Myosin loop-4 is critical for optimal tropomyosin repositioning on actin during muscle activation and relaxation.
Authors: Matthew H Doran / Michael J Rynkiewicz / Elumalai Pavadai / Skylar M L Bodt / David Rasicci / Jeffrey R Moore / Christopher M Yengo / Esther Bullitt / William Lehman /
Abstract: During force-generating steps of the muscle crossbridge cycle, the tip of the myosin motor, specifically loop-4, contacts the tropomyosin cable of actin filaments. In the current study, we determined ...During force-generating steps of the muscle crossbridge cycle, the tip of the myosin motor, specifically loop-4, contacts the tropomyosin cable of actin filaments. In the current study, we determined the corresponding effect of myosin loop-4 on the regulatory positioning of tropomyosin on actin. To accomplish this, we compared high-resolution cryo-EM structures of myosin S1-decorated thin filaments containing either wild-type or a loop-4 mutant construct, where the seven-residue portion of myosin loop-4 that contacts tropomyosin was replaced by glycine residues, thus removing polar side chains from residues 366-372. Cryo-EM analysis of fully decorated actin-tropomyosin filaments with wild-type and mutant S1, yielded 3.4-3.6 Å resolution reconstructions, with even higher definition at the actin-myosin interface. Loop-4 densities both in wild-type and mutant S1 were clearly identified, and side chains were resolved in the wild-type structure. Aside from loop-4, actin and myosin structural domains were indistinguishable from each other when filaments were decorated with either mutant or wild-type S1. In marked contrast, the position of tropomyosin on actin in the two reconstructions differed by 3 to 4 Å. In maps of filaments containing the mutant, tropomyosin was located closer to the myosin-head and thus moved in the direction of the C-state conformation adopted by myosin-free thin filaments. Complementary interaction energy measurements showed that tropomyosin in the mutant thin filaments sits on actin in a local energy minimum, whereas tropomyosin is positioned by wild-type S1 in an energetically unfavorable location. We propose that the high potential energy associated with tropomyosin positioning in wild-type filaments favors an effective transition to B- and C-states following release of myosin from the thin filaments during relaxation.
History
DepositionSep 8, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28083.png

Downloads & links

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Map

FileDownload / File: emd_28083.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map for the human cardiac actin-tropomyosin-beta-myosin II complex in the rigor conformation
Voxel sizeX=Y=Z: 1.078 Å
Density
Contour LevelBy AUTHOR: 0.0196
Minimum - Maximum-0.04460608 - 0.12564005
Average (Standard dev.)0.0003072702 (±0.004214454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 474.31998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28083_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-locally-filtered version of the primary map.

Fileemd_28083_additional_1.map
AnnotationNon-locally-filtered version of the primary map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_28083_half_map_1.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_28083_half_map_2.map
AnnotationHalf map 2.
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 cardiac actin-tropomyosin-beta-myosin II complex in the rig...

EntireName: Human cardiac actin-tropomyosin-beta-myosin II complex in the rigor form.
Components
  • Complex: Human cardiac actin-tropomyosin-beta-myosin II complex in the rigor form.
    • Complex: Cardiac F-actin complex
      • Protein or peptide: Actin, alpha cardiac muscle 1
    • Complex: Human cardiac myosin II
      • Protein or peptide: Myosin-7
    • Complex: Human cardiac tropomyosin
      • Protein or peptide: Tropomyosin alpha-1 chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human cardiac actin-tropomyosin-beta-myosin II complex in the rig...

SupramoleculeName: Human cardiac actin-tropomyosin-beta-myosin II complex in the rigor form.
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Cardiac actomyosin-tropomyosin complex.

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Supramolecule #2: Cardiac F-actin complex

SupramoleculeName: Cardiac F-actin complex / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #2 / Details: F-actin forms the backbone of the complex
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: Human cardiac myosin II

SupramoleculeName: Human cardiac myosin II / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #1
Details: The motor domain of the myosin saturates the actin filament.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Human cardiac tropomyosin

SupramoleculeName: Human cardiac tropomyosin / type: complex / Chimera: Yes / ID: 4 / Parent: 1 / Macromolecule list: #3 / Details: Tropomyosin wraps around the F-actin core.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Myosin-7

MacromoleculeName: Myosin-7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 223.445984 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MGDSEMAVFG AAAPYLRKSE KERLEAQTRP FDLKKDVFVP DDKQEFVKAK IVSREGGKVT AETEYGKTVT VKEDQVMQQN PPKFDKIED MAMLTFLHEP AVLYNLKDRY GSWMIYTYSG LFCVTVNPYK WLPVYTPEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD ...String:
MGDSEMAVFG AAAPYLRKSE KERLEAQTRP FDLKKDVFVP DDKQEFVKAK IVSREGGKVT AETEYGKTVT VKEDQVMQQN PPKFDKIED MAMLTFLHEP AVLYNLKDRY GSWMIYTYSG LFCVTVNPYK WLPVYTPEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD RENQSILITG ESGAGKTVNT KRVIQYFAVI AAIGDRSKKD QSPGKGTLED QIIQANPALE AFGNAKTVRN DN SSRFGKF IRIHFGATGK LASADIETYL LEKSRVIFQL KAERDYHIFY QILSNKKPEL LDMLLITNNP YDYAFISQGE TTV ASIDDA EELMATDNAF DVLGFTSEEK NSMYKLTGAI MHFGNMKFKL KQREEQAEPD GTEEADKSAY LMGLNSADLL KGLC HPRVK VGNEYVTKGQ NVQQVIYATG ALAKAVYERM FNWMVTRINA TLETKQPRQY FIGVLDIAGF EIFDFNSFEQ LCINF TNEK LQQFFNHHMF VLEQEEYKKE GIEWTFIDFG MDLQACIDLI EKPMGIMSIL EEECMFPKAT DMTFKAKLFD NHLGKS ANF QKPRNIKGKP EAHFSLIHYA GIVDYNIIGW LQKNKDPLNE TVVGLYQKSS LKLLSTLFAN YAGADAPIEK GKGKAKK GS SFQTVSALHR ENLNKLMTNL RSTHPHFVRC IIPNETKSPG VMDNPLVMHQ LRCNGVLEGI RICRKGFPNR ILYGDFRQ R YRILNPAAIP EGQFIDSRKG AEKLLSSLDI DHNQYKFGHT KVFFKAGLLG LLEEMRDERL SRIITRIQAQ SRGVLARME YKKLLERRDS LLVIQWNIRA FMGVKNWPWM KLYFKIKPLL KSAEREKEMA SMKEEFTRLK EALEKSEARR KELEEKMVSL LQEKNDLQL QVQAEQDNLA DAEERCDQLI KNKIQLEAKV KEMNERLEDE EEMNAELTAK KRKLEDECSE LKRDIDDLEL T LAKVEKEK HATENKVKNL TEEMAGLDEI IAKLTKEKKA LQEAHQQALD DLQAEEDKVN TLTKAKVKLE QQVDDLEGSL EQ EKKVRMD LERAKRKLEG DLKLTQESIM DLENDKQQLD ERLKKKDFEL NALNARIEDE QALGSQLQKK LKELQARIEE LEE ELEAER TARAKVEKLR SDLSRELEEI SERLEEAGGA TSVQIEMNKK REAEFQKMRR DLEEATLQHE ATAAALRKKH ADSV AELGE QIDNLQRVKQ KLEKEKSEFK LELDDVTSNM EQIIKAKANL EKMCRTLEDQ MNEHRSKAEE TQRSVNDLTS QRAKL QTEN GELSRQLDEK EALISQLTRG KLTYTQQLED LKRQLEEEVK AKNALAHALQ SARHDCDLLR EQYEEETEAK AELQRV LSK ANSEVAQWRT KYETDAIQRT EELEEAKKKL AQRLQEAEEA VEAVNAKCSS LEKTKHRLQN EIEDLMVDVE RSNAAAA AL DKKQRNFDKI LAEWKQKYEE SQSELESSQK EARSLSTELF KLKNAYEESL EHLETFKREN KNLQEEISDL TEQLGSSG K TIHELEKVRK QLEAEKMELQ SALEEAEASL EHEEGKILRA QLEFNQIKAE IERKLAEKDE EMEQAKRNHL RVVDSLQTS LDAETRSRNE ALRVKKKMEG DLNEMEIQLS HANRMAAEAQ KQVKSLQSLL KDTQIQLDDA VRANDDLKEN IAIVERRNNL LQAELEELR AVVEQTERSR KLAEQELIET SERVQLLHSQ NTSLINQKKK MDADLSQLQT EVEEAVQECR NAEEKAKKAI T DAAMMAEE LKKEQDTSAH LERMKKNMEQ TIKDLQHRLD EAEQIALKGG KKQLQKLEAR VRELENELEA EQKRNAESVK GM RKSERRI KELTYQTEED RKNLLRLQDL VDKLQLKVKA YKRQAEEAEE QANTNLSKFR KVQHELDEAE ERADIAESQV NKL RAKSRD IGTKGLNEE

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Macromolecule #2: Actin, alpha cardiac muscle 1

MacromoleculeName: Actin, alpha cardiac muscle 1 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 42.064891 KDa
SequenceString: MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVLSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWISKQEYDE AGPSIVHRKC F

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Macromolecule #3: Tropomyosin alpha-1 chain

MacromoleculeName: Tropomyosin alpha-1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.763621 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDAIKKKMQM LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY SEALKDAQEK LELAEKKATD AEADVASLN RRIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD R KYEEVARK ...String:
MDAIKKKMQM LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY SEALKDAQEK LELAEKKATD AEADVASLN RRIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD R KYEEVARK LVIIESDLER AEERAELSEG KCAELEEELK TVTNNLKSLE AQAEKYSQKE DRYEEEIKVL SDKLKEAETR AE FAERSVT KLEKSIDDLE DELYAQKLKY KAISEELDHA LNDMTSI

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #5: MAGNESIUM ION

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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.13 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 539 pixel / Digitization - Dimensions - Height: 539 pixel / Number grids imaged: 4 / Number real images: 3961 / Average exposure time: 3.12 sec. / Average electron dose: 53.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 1045903 / Software - Name: RELION (ver. 3.1.1)
Startup modelType of model: OTHER / Details: Featureless Cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.9 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 176178
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6x5z

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8efi:
Helical reconstruction of the human cardiac actin-tropomyosin-myosin complex in the rigor form

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