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- PDB-6ltj: Structure of nucleosome-bound human BAF complex -

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Entry
Database: PDB / ID: 6ltj
TitleStructure of nucleosome-bound human BAF complex
Components
  • (DNA (119-MER)) x 2
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • AT-rich interactive domain-containing protein 1A
  • Actin, cytoplasmic 1
  • Actin-like protein 6A
  • Histone H2A type 1
  • Histone H2B
  • Histone H3.3H3F3A
  • Histone H4
  • SWI/SNF complex subunit SMARCC2
  • Transcription activator BRG1
  • Zinc finger protein ubi-d4
KeywordsGENE REGULATION / Chromatin remodeler / Complex
Function / homology
Function and homology information


negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / positive regulation of norepinephrine uptake / H3K9me3 modified histone binding / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / glucocorticoid receptor signaling pathway / cellular response to cytochalasin B ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / positive regulation of norepinephrine uptake / H3K9me3 modified histone binding / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / glucocorticoid receptor signaling pathway / cellular response to cytochalasin B / blastocyst hatching / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / negative regulation of androgen receptor signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Formation of annular gap junctions / neural retina development / GBAF complex / Gap junction degradation / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / dense body / Cell-extracellular matrix interactions / Tat protein binding / Folding of actin by CCT/TriC / regulation of double-strand break repair / XY body / nucleosome disassembly / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Ino80 complex / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / hepatocyte differentiation / blastocyst formation / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / positive regulation by host of viral transcription / tight junction / Sensory processing of sound by inner hair cells of the cochlea / Sensory processing of sound by outer hair cells of the cochlea / ATP-dependent chromatin remodeler activity / SWI/SNF complex / Interaction between L1 and Ankyrins / regulation of norepinephrine uptake / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / germ cell nucleus / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / cellular response to fatty acid / apical junction complex / nuclear androgen receptor binding / maintenance of blood-brain barrier / regulation of chromosome organization / establishment or maintenance of cell polarity / cortical cytoskeleton / nuclear chromosome / spinal cord development / positive regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Recycling pathway of L1 / androgen receptor signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / regulation of DNA replication / brush border / kinesin binding / regulation of embryonic development / calyx of Held / positive regulation of Wnt signaling pathway / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / intracellular estrogen receptor signaling pathway / regulation of DNA repair / ATP-dependent activity, acting on DNA / regulation of protein localization to plasma membrane / Chromatin modifying enzymes / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / positive regulation of DNA repair / EPHB-mediated forward signaling / substantia nigra development
Similarity search - Function
SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / DPF1-3, N-terminal domain / SMARCC, SWIRM-associated domain / SMARCC, N-terminal ...SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / DPF1-3, N-terminal domain / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / DPF1-3, N-terminal / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / : / SWI/SNF Subunit INI1, DNA binding domain / SWI/SNF complex subunit BRG1 / Chromatin-remodeling complex component Sfh1/SNF5 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / ARID/BRIGHT DNA binding domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SANT domain profile. / SANT domain / SWIB/MDM2 domain superfamily / Chromo/chromo shadow domain / Chromatin organization modifier domain / HMG (high mobility group) box / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone, subunit A / Myb-like DNA-binding domain / HMG boxes A and B DNA-binding domains profile. / Histone, subunit A / high mobility group / High mobility group box domain / High mobility group box domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Zinc finger C2H2 type domain profile. / Actin / Actin family / Actin / Zinc finger C2H2 superfamily / BRCT domain superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Histone H2B signature. / Zinc finger C2H2-type / 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 / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / AT-rich interactive domain-containing protein 1A / Actin-like protein 6A / Histone H2B 1.1 / Histone H2A type 1 / Transcription activator BRG1 / Actin, cytoplasmic 1 / Histone H4 ...DNA / DNA (> 10) / DNA (> 100) / AT-rich interactive domain-containing protein 1A / Actin-like protein 6A / Histone H2B 1.1 / Histone H2A type 1 / Transcription activator BRG1 / Actin, cytoplasmic 1 / Histone H4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / Histone H3.3 / SWI/SNF complex subunit SMARCC2 / Histone H2B / Zinc finger protein ubi-d4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHe, S. / Wu, Z. / Tian, Y. / Yu, Z. / Yu, J. / Wang, X. / Li, J. / Liu, B. / Xu, Y.
CitationJournal: Science / Year: 2020
Title: Structure of nucleosome-bound human BAF complex.
Authors: Shuang He / Zihan Wu / Yuan Tian / Zishuo Yu / Jiali Yu / Xinxin Wang / Jie Li / Bijun Liu / Yanhui Xu /
Abstract: Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to ...Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo-electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (ATPase) modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal α helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit SMARCC serve as a structural core and scaffold in the base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex.
History
DepositionJan 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 13, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Histone H3.3
B: Histone H4
C: Histone H2A type 1
D: Histone H2B
E: Histone H3.3
F: Histone H4
G: Histone H2A type 1
H: Histone H2B
I: Transcription activator BRG1
J: Actin-like protein 6A
K: Actin, cytoplasmic 1
L: AT-rich interactive domain-containing protein 1A
M: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
N: SWI/SNF complex subunit SMARCC2
O: SWI/SNF complex subunit SMARCC2
P: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Q: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
R: Zinc finger protein ubi-d4
X: DNA (119-MER)
Y: DNA (119-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,038,93321
Polymers1,038,86820
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 10 types, 15 molecules AEBFCGDHIJKLNOR

#1: Protein Histone H3.3 / H3F3A


Mass: 15360.983 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6PI79
#2: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 13993.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06897
#4: Protein Histone H2B /


Mass: 13873.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: H2B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92131, UniProt: P02281*PLUS
#5: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A


Mass: 184923.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#6: Protein Actin-like protein 6A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A


Mass: 45236.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTL6A, BAF53, BAF53A / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O96019
#7: Protein Actin, cytoplasmic 1 / / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P60709
#8: Protein AT-rich interactive domain-containing protein 1A / ARID domain-containing protein 1A / B120 / BRG1-associated factor 250 / BAF250 / BRG1-associated ...ARID domain-containing protein 1A / B120 / BRG1-associated factor 250 / BAF250 / BRG1-associated factor 250a / BAF250A


Mass: 142316.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID1A, BAF250, BAF250A / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O14497
#10: Protein SWI/SNF complex subunit SMARCC2 / / BRG1-associated factor 170 / BAF170


Mass: 133048.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8TAQ2
#13: Protein Zinc finger protein ubi-d4 / / Apoptosis response zinc finger protein / BRG1-associated factor 45D / BAF45D


Mass: 32781.926 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100, UNP residues 209-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2, BAF45D / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q92785

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SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules MPQ

#9: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / BRG1-associated factor 47 / BAF47


Mass: 38015.094 Da / Num. of mol.: 1 / Fragment: UNP residues 1-113, UNP residues 172-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCB1, BAF47 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q12824
#11: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1


Mass: 58311.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCD1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96GM5
#12: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1


Mass: 46710.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCE1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q969G3

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DNA chain , 2 types, 2 molecules XY

#14: DNA chain DNA (119-MER)


Mass: 36520.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#15: DNA chain DNA (119-MER)


Mass: 36929.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 1 molecules

#16: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of nucleosome-bound human BAF complexCOMPLEX#1-#150RECOMBINANT
2NucleosomeCOMPLEX#1-#4, #14-#151RECOMBINANT
3BAFCOMPLEX#5-#131RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Xenopus calcaratus (Biafran clawed frog)451444
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCell
22Escherichia coli BL21 (bacteria)511693BL21
33Homo sapiens (human)9606HEK293T
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.0.8 / Category: 3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 320658 / Symmetry type: POINT

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