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- EMDB-47841: CHD1-nucleosome complex (closed state) -

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Basic information

Entry
Database: EMDB / ID: EMD-47841
TitleCHD1-nucleosome complex (closed state)
Map data
Sample
  • Complex: CHD1-nucleosome complex (closed state)
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (205-MER)
    • DNA: DNA (205-MER)
    • Protein or peptide: Chromodomain-helicase-DNA-binding protein 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
Keywordschromatin / remodeler / genome organization / nuclear protein / TRANSLOCASE
Function / homology
Function and homology information


nucleosome organization / ATP-dependent chromatin remodeler activity / positive regulation by host of viral transcription / nuclear chromosome / : / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / DNA helicase ...nucleosome organization / ATP-dependent chromatin remodeler activity / positive regulation by host of viral transcription / nuclear chromosome / : / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / DNA helicase / Estrogen-dependent gene expression / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromatin remodeling / protein heterodimerization activity / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain ...CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal 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 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2B / Histone H3 / Chromodomain-helicase-DNA-binding protein 1 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJames AM / Farnung L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)ES036404 United States
CitationJournal: Mol Cell / Year: 2025
Title: Structural basis of human CHD1 nucleosome recruitment and pausing.
Authors: Allison M James / Lucas Farnung /
Abstract: Chromatin remodelers regulate gene expression and genome maintenance by controlling nucleosome positioning, but the structural basis for their regulated and directional activity remains poorly ...Chromatin remodelers regulate gene expression and genome maintenance by controlling nucleosome positioning, but the structural basis for their regulated and directional activity remains poorly understood. Here, we present three cryoelectron microscopy (cryo-EM) structures of human chromodomain helicase DNA-binding protein 1 (CHD1) bound to nucleosomes that reveal previously unobserved recruitment and regulatory states. We identify a structural element, termed the "anchor element," that connects the CHD1 ATPase motor to the nucleosome entry-side acidic patch. The anchor element coordinates with other regulatory modules, including the gating element, which undergoes a conformational switch critical for remodeling. Our structures demonstrate how the DNA-binding region of CHD1 binds entry- and exit-side DNA during remodeling to achieve directional sliding. The observed structural elements are conserved across chromatin remodelers, suggesting a unified mechanism for nucleosome recognition and remodeling. Our findings show how chromatin remodelers couple nucleosome recruitment to regulated DNA translocation, providing a framework for understanding chromatin remodeler mechanisms beyond DNA translocation.
History
DepositionNov 11, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47841.png

Downloads & links

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Map

FileDownload / File: emd_47841.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0182
Minimum - Maximum-0.027532537 - 1.8281279
Average (Standard dev.)0.002319303 (±0.032787275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47841_msk_1.map
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Additional map: #1

Fileemd_47841_additional_1.map
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Half map: #2

Fileemd_47841_half_map_1.map
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Half map: #1

Fileemd_47841_half_map_2.map
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Sample components

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Entire : CHD1-nucleosome complex (closed state)

EntireName: CHD1-nucleosome complex (closed state)
Components
  • Complex: CHD1-nucleosome complex (closed state)
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (205-MER)
    • DNA: DNA (205-MER)
    • Protein or peptide: Chromodomain-helicase-DNA-binding protein 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: CHD1-nucleosome complex (closed state)

SupramoleculeName: CHD1-nucleosome complex (closed state) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 387 KDa

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.463181 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MART(ML3)QTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIA QDF KTDLRFQSSA VMALQEASEA YLVALFEDTN LAAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 9.86159 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMDV VYALKRQGRT LYGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.494393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKTRSSRAGL QFPVGRVHRL LRKGNYAERV GAGAPVYLAA VLEYLTAEIL ELAGNAARDN KKTRIIPRHL QLAVRNDEEL NKLLGRVTI AQGGVLPNIQ SVLLPK

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.607212 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSAK

UniProtKB: Histone H2B

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Macromolecule #7: Chromodomain-helicase-DNA-binding protein 1

MacromoleculeName: Chromodomain-helicase-DNA-binding protein 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 151.787688 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNANGHSDEE SVRNSSGESS QSDDDSGSAS GSGSGSSSGS SSDGSSSQSG SSDSDSGSES GSQSESESDT SRENKVQAKP PKVDGAEFW KSSPSILAVQ RSAILKKQQQ QQQQQQHQAS SNSGSEEDSS SSEDSDDSSS EVKRKKHKDE DWQMSGSGSP S QSGSDSES ...String:
SNANGHSDEE SVRNSSGESS QSDDDSGSAS GSGSGSSSGS SSDGSSSQSG SSDSDSGSES GSQSESESDT SRENKVQAKP PKVDGAEFW KSSPSILAVQ RSAILKKQQQ QQQQQQHQAS SNSGSEEDSS SSEDSDDSSS EVKRKKHKDE DWQMSGSGSP S QSGSDSES EEEREKSSCD ETESDYEPKN KVKSRKPQNR SKSKNGKKIL GQKKRQIDSS EEDDDEEDYD NDKRSSRRQA TV NVSYKED EEMKTDSDDL LEVCGEDVPQ PEEEEFETIE RFMDCRIGRK GATGATTTIY AVEADGDPNA GFEKNKEPGE IQY LIKWKG WSHIHNTWET EETLKQQNVR GMKKLDNYKK KDQETKRWLK NASPEDVEYY NCQQELTDDL HKQYQIVERI IAHS NQKSA AGYPDYYCKW QGLPYSECSW EDGALISKKF QACIDEYFSR NQSKTTPFKD CKVLKQRPRF VALKKQPSYI GGHEG LELR DYQLNGLNWL AHSWCKGNSC ILADEMGLGK TIQTISFLNY LFHEHQLYGP FLLVVPLSTL TSWQREIQTW ASQMNA VVY LGDINSRNMI RTHEWTHHQT KRLKFNILLT TYEILLKDKA FLGGLNWAFI GVDEAHRLKN DDSLLYKTLI DFKSNHR LL ITGTPLQNSL KELWSLLHFI MPEKFSSWED FEEEHGKGRE YGYASLHKEL EPFLLRRVKK DVEKSLPAKV EQILRMEM S ALQKQYYKWI LTRNYKALSK GSKGSTSGFL NIMMELKKCC NHCYLIKPPD NNEFYNKQEA LQHLIRSSGK LILLDKLLI RLRERGNRVL IFSQMVRMLD ILAEYLKYRQ FPFQRLDGSI KGELRKQALD HFNAEGSEDF CFLLSTRAGG LGINLASADT VVIFDSDWN PQNDLQAQAR AHRIGQKKQV NIYRLVTKGS VEEDILERAK KKMVLDHLVI QRMDTTGKTV LHTGSAPSSS T PFNKEELS AILKFGAEEL FKEPEGEEQE PQEMDIDEIL KRAETHENEP GPLTVGDELL SQFKVANFSN MDEDDIELEP ER NSKNWEE IIPEDQRRRL EEEERQKELE EIYMLPRMRN CAKQISFNGS EGRRSRSRRY SGSDSDSISE GKRPKKRGRP RTI PRENIK GFSDAEIRRF IKSYKKFGGP LERLDAIARD AELVDKSETD LRRLGELVHN GCIKALKDSS SGTERTGGRL GKVK GPTFR ISGVQVNAKL VISHEEELIP LHKSIPSDPE ERKQYTIPCH TKAAHFDIDW GKEDDSNLLI GIYEYGYGSW EMIKM DPDL SLTHKILPDD PDKKPQAKQL QTRADYLIKL LSRDLAKKEA LSGAG

UniProtKB: Chromodomain-helicase-DNA-binding protein 1

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Macromolecule #5: DNA (205-MER)

MacromoleculeName: DNA (205-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 48.501918 KDa
SequenceString: (DA)(DT)(DT)(DC)(DC)(DA)(DG)(DC)(DC)(DA) (DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT) (DG)(DG)(DT)(DC)(DG)(DT) ...String:
(DA)(DT)(DT)(DC)(DC)(DA)(DG)(DC)(DC)(DA) (DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT) (DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA) (DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA) (DC)(DG)(DC) (DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT) (DT)(DA)(DA)(DC) (DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC) (DT)(DC)(DC)(DC)(DT) (DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG) (DT)(DG)(DT)(DC)(DA)(DG) (DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC)(DG)(DA) (DT)(DA)(DG)(DG)(DC)

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Macromolecule #6: DNA (205-MER)

MacromoleculeName: DNA (205-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.044227 KDa
SequenceString: (DG)(DC)(DC)(DT)(DA)(DT)(DC)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA) ...String:
(DG)(DC)(DC)(DT)(DA)(DT)(DC)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG) (DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG) (DC)(DG)(DC) (DG)(DT)(DA)(DC)(DG)(DT) (DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG) (DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG) (DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA)(DT) (DT)(DC)(DT)(DG)(DA)(DT)(DG)(DG)(DC)(DT) (DG)(DG)(DA)(DA)(DT)

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #9: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77190
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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