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- EMDB-33626: Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33626
TitleCryo-EM structure of the dimeric human CAF1LC-H3-H4 complex
Map datamap
Sample
  • Complex: Dimeric CAF1LC-H3-H4 complex
    • Complex: CAF1LC/RBBP4
      • Protein or peptide: Chromatin assembly factor 1 subunit A
      • Protein or peptide: Histone-binding protein RBBP4
      • Protein or peptide: Chromatin assembly factor 1 subunit B
    • Complex: H3-H4
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4
KeywordsHistone chaperone / Chromatin assembly factor / REPLICATION
Function / homology
Function and homology information


CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / chromo shadow domain binding / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / chromo shadow domain binding / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Polo-like kinase mediated events / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / Cyclin E associated events during G1/S transition / Packaging Of Telomere Ends / Cyclin A:Cdk2-associated events at S phase entry / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Regulation of TP53 Activity through Acetylation / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / negative regulation of cell migration / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / negative regulation of transforming growth factor beta receptor signaling pathway / Formation of the beta-catenin:TCF transactivating complex / brain development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / histone deacetylase binding / nucleosome / unfolded protein binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / chromatin remodeling / cadherin binding / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / DNA repair
Similarity search - Function
Chromatin assembly factor 1 subunit B, C-terminal domain / Chromatin assembly factor 1 subunit Cac2/CHAF1B/FAS2 / Chromatin assembly factor 1 complex p150 subunit, N-terminal / Chromatin assembly factor complex 1 subunit p60, C-terminal / Chromatin assembly factor 1 subunit p150, N-terminal / Chromatin assembly factor 1 subunit p150, C-terminal / CAF1 complex subunit p150, region binding to CAF1-p60 at C-term / CAF1 complex subunit p150, region binding to PCNA / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit A ...Chromatin assembly factor 1 subunit B, C-terminal domain / Chromatin assembly factor 1 subunit Cac2/CHAF1B/FAS2 / Chromatin assembly factor 1 complex p150 subunit, N-terminal / Chromatin assembly factor complex 1 subunit p60, C-terminal / Chromatin assembly factor 1 subunit p150, N-terminal / Chromatin assembly factor 1 subunit p150, C-terminal / CAF1 complex subunit p150, region binding to CAF1-p60 at C-term / CAF1 complex subunit p150, region binding to PCNA / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit A / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / G-protein, beta subunit / Histone-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H4 / Histone H3.1 / Histone-binding protein RBBP4 / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsLiu CP / Yu C / Yu ZY / Xu RM
Funding support China, 10 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31991162 China
National Natural Science Foundation of China (NSFC)91853204 China
National Natural Science Foundation of China (NSFC)92153302 China
National Natural Science Foundation of China (NSFC)31300614 China
Ministry of Science and Technology (MoST, China)2019YFA0508900 China
Ministry of Science and Technology (MoST, China)2018YFE0203300 China
Ministry of Science and Technology (MoST, China)2017YFA0506600 China
Chinese Academy of SciencesXDB37010100 China
Chinese Academy of Sciences2018125 China
Chinese Academy of Sciences2017131 China
CitationJournal: Science / Year: 2023
Title: Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1.
Authors: Chao-Pei Liu / Zhenyu Yu / Jun Xiong / Jie Hu / Aoqun Song / Dongbo Ding / Cong Yu / Na Yang / Mingzhu Wang / Juan Yu / Peini Hou / Kangning Zeng / Zhenyu Li / Zhuqiang Zhang / Xinzheng ...Authors: Chao-Pei Liu / Zhenyu Yu / Jun Xiong / Jie Hu / Aoqun Song / Dongbo Ding / Cong Yu / Na Yang / Mingzhu Wang / Juan Yu / Peini Hou / Kangning Zeng / Zhenyu Li / Zhuqiang Zhang / Xinzheng Zhang / Wei Li / Zhiguo Zhang / Bing Zhu / Guohong Li / Rui-Ming Xu /
Abstract: Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly ...Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly process is lacking. In this work, we report the crystal structure of human CAF-1 in the absence of histones and the cryo-electron microscopy structure of CAF-1 in complex with histones H3 and H4. One histone H3-H4 heterodimer is bound by one CAF-1 complex mainly through the p60 subunit and the acidic domain of the p150 subunit. We also observed a dimeric CAF-1-H3-H4 supercomplex in which two H3-H4 heterodimers are poised for tetramer assembly and discovered that CAF-1 facilitates right-handed DNA wrapping of H3-H4 tetramers. These findings signify the involvement of DNA in H3-H4 tetramer formation and suggest a right-handed nucleosome precursor in chromatin replication.
History
DepositionJun 17, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33626.png

Downloads & links

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Map

FileDownload / File: emd_33626.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.049660843 - 0.22472705
Average (Standard dev.)0.0008692447 (±0.015991328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33626_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharped map

Fileemd_33626_additional_1.map
Annotationsharped map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A map

Fileemd_33626_half_map_1.map
Annotationhalf_A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map

Fileemd_33626_half_map_2.map
Annotationhalf_B map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric CAF1LC-H3-H4 complex

EntireName: Dimeric CAF1LC-H3-H4 complex
Components
  • Complex: Dimeric CAF1LC-H3-H4 complex
    • Complex: CAF1LC/RBBP4
      • Protein or peptide: Chromatin assembly factor 1 subunit A
      • Protein or peptide: Histone-binding protein RBBP4
      • Protein or peptide: Chromatin assembly factor 1 subunit B
    • Complex: H3-H4
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4

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Supramolecule #1: Dimeric CAF1LC-H3-H4 complex

SupramoleculeName: Dimeric CAF1LC-H3-H4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 336 KDa

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Supramolecule #2: CAF1LC/RBBP4

SupramoleculeName: CAF1LC/RBBP4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: H3-H4

SupramoleculeName: H3-H4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Macromolecule #1: Chromatin assembly factor 1 subunit A

MacromoleculeName: Chromatin assembly factor 1 subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.228848 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KAEITRFFQK PKTPQAPKTL AGSCGKFAPF EIKEHMVLAP RRRTAFHPDL CSQLDQLLQQ QSGEFSFLKD LKGRQPLRSG PTHVSTRNA DIFNSDVVIV ERGKGDGVPE RRKFGRMKLL QFCENHRPAY WGTWNKKTAL IRARDPWAQD TKLLDYEVDS D EEWEEEEP ...String:
KAEITRFFQK PKTPQAPKTL AGSCGKFAPF EIKEHMVLAP RRRTAFHPDL CSQLDQLLQQ QSGEFSFLKD LKGRQPLRSG PTHVSTRNA DIFNSDVVIV ERGKGDGVPE RRKFGRMKLL QFCENHRPAY WGTWNKKTAL IRARDPWAQD TKLLDYEVDS D EEWEEEEP GESLSHSEGD DDDDMGEDED EDDGFFVPHG YLSEDEGVTE ECADPENHKV RQKLKAKEWD EFLAKGKRFR VL QPVKIGC VWAADRDCAG DDLKVLQQFA ACFLETLPAQ EEQTPKASKR ERRDEQILAQ LLPLLHGNVN GSKVIIREFQ EHC RRGLLS NHTGSPRSPS TTYLHTPTPS EDAAIPSKSR LKRLISENSV YEKRPDFRMC WYVHPQVLQS FQQEHLPVPC QWSY VTSVP SAPKEDS

UniProtKB: Chromatin assembly factor 1 subunit A

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Macromolecule #2: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #4: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.709527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN ...String:
MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN PDLRLRGHQK EGYGLSWNPN LSGHLLSASD DHTICLWDIS AVPKEGKVVD AKTIFTGHTA VVEDVSWHLL HE SLFGSVA DDQKLMIWDT RSNNTSKPSH SVDAHTAEVN CLSFNPYSEF ILATGSADKT VALWDLRNLK LKLHSFESHK DEI FQVQWS PHNETILASS GTDRRLNVWD LSKIGEEQSP EDAEDGPPEL LFIHGGHTAK ISDFSWNPNE PWVICSVSED NIMQ VWQMA ENIYNDEDPE GSVDPEGQGS

UniProtKB: Histone-binding protein RBBP4

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Macromolecule #5: Chromatin assembly factor 1 subunit B

MacromoleculeName: Chromatin assembly factor 1 subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.714941 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKVITCEIAW HNKEPVYSLD FQHGTAGRIH RLASAGVDTN VRIWKVEKGP DGKAIVEFLS NLARHTKAVN VVRFSPTGEI LASGGDDAV ILLWKVNDNK EPEQIAFQDE DEAQLNKENW TVVKTLRGHL EDVYDICWAT DGNLMASASV DNTAIIWDVS K GQKISIFN ...String:
MKVITCEIAW HNKEPVYSLD FQHGTAGRIH RLASAGVDTN VRIWKVEKGP DGKAIVEFLS NLARHTKAVN VVRFSPTGEI LASGGDDAV ILLWKVNDNK EPEQIAFQDE DEAQLNKENW TVVKTLRGHL EDVYDICWAT DGNLMASASV DNTAIIWDVS K GQKISIFN EHKSYVQGVT WDPLGQYVAT LSCDRVLRVY SIQKKRVAFN VSKMLSGIGA EGEARSYRMF HDDSMKSFFR RL SFTPDGS LLLTPAGCVE SGENVMNTTY VFSRKNLKRP IAHLPCPGKA TLAVRCCPVY FELRPVVETG VELMSLPYRL VFA VASEDS VLLYDTQQSF PFGYVSNIHY HTLSDISWSS DGAFLAISST DGYCSFVTFE KDELGIPLKE KPVLNMRTPD TAKK TKSQT HRGSSPGPRP VEGT

UniProtKB: Chromatin assembly factor 1 subunit B

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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

Concentration0.4 mg/mL
BufferpH: 7.5 / Details: 20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24904
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7y5u


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 321 / Target criteria: Correlation coefficient
Output model

PDB-7y5v:
Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex

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