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- PDB-9dde: ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome -

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Basic information

Entry
Database: PDB / ID: 9dde
TitlencPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Components
  • (DNA (187-MER)) x 2
  • E3 ubiquitin-protein ligase RING2
  • Histone H1.4
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Polycomb complex protein BMI-1
  • RING1 and YY1-binding protein
  • Ubiquitin
KeywordsGene Regulation/DNA / DNA complex protein / Gene Regulation-DNA complex
Function / homology
Function and homology information


regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / PRC1 complex / regulation of kidney development / segment specification / sex chromatin / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division ...regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / PRC1 complex / regulation of kidney development / segment specification / sex chromatin / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / positive regulation of immature T cell proliferation in thymus / PcG protein complex / negative regulation of DNA recombination / SUMOylation of DNA methylation proteins / Apoptosis induced DNA fragmentation / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / hypothalamus gonadotrophin-releasing hormone neuron development / chromosome condensation / anterior/posterior axis specification / female meiosis I / positive regulation of protein monoubiquitination / positive regulation of ubiquitin-protein transferase activity / nucleosomal DNA binding / mitochondrion transport along microtubule / fat pad development / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA methylation-dependent constitutive heterochromatin formation / female gonad development / negative regulation of gene expression, epigenetic / seminiferous tubule development / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / male meiosis I / germ cell development / hemopoiesis / MLL1 complex / negative regulation of apoptotic signaling pathway / humoral immune response / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to interleukin-1 / ubiquitin ligase complex / heterochromatin / SUMOylation of DNA damage response and repair proteins / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / ER Quality Control Compartment (ERQC) / positive regulation of B cell proliferation / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / cellular response to dexamethasone stimulus / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Translesion synthesis by POLK / regulation of mitochondrial membrane potential
Similarity search - Function
Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Linker histone H1/H5 / linker histone H1 and H5 family / Zinc finger, C3HC4 type (RING finger) ...Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Linker histone H1/H5 / linker histone H1 and H5 family / Zinc finger, C3HC4 type (RING finger) / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / 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 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 / Histone H3 signature 1. / Zinc finger RING-type profile. / Histone H3 signature 2. / Zinc finger, RING-type / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Ubiquitin conserved site / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-B / Histone H1.4 / Polycomb complex protein BMI-1 / Histone H4 / Histone H3.2 ...DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-B / Histone H1.4 / Polycomb complex protein BMI-1 / Histone H4 / Histone H3.2 / RING1 and YY1-binding protein / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGodinez-Lopez, V. / Valencia-Sanchez, M.I. / Armache, J.P. / Armache, K.-J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115882 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA266978 United States
The Mark Foundation United States
CitationJournal: Nature / Year: 2024
Title: Read-write mechanisms of H2A ubiquitination by Polycomb repressive complex 1.
Authors: Victoria Godínez López / Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Jonathan F Thomas / Rachel Lee / Pablo De Ioannes / Brian A Sosa / Jean-Paul Armache / Karim-Jean Armache /
Abstract: Epigenetic inheritance of silent chromatin domains is fundamental to cellular memory during embryogenesis, but it must overcome the dilution of repressive histone modifications during DNA replication. ...Epigenetic inheritance of silent chromatin domains is fundamental to cellular memory during embryogenesis, but it must overcome the dilution of repressive histone modifications during DNA replication. One such modification, histone H2A lysine 119 monoubiquitination (H2AK119Ub), needs to be re-established by the Polycomb repressive complex 1 (PRC1) E3 ligase to restore the silent Polycomb domain. However, the exact mechanism behind this restoration remains unknown. Here, combining cryo-electron microscopy (cryo-EM) and functional approaches, we characterize the read-write mechanism of the non-canonical PRC1-containing RYBP (ncPRC1). This mechanism, which functions as a positive-feedback loop in epigenetic regulation, emphasizes the pivotal role of ncPRC1 in restoring H2AK119Ub. We observe an asymmetrical binding of ncPRC1 to H2AK119Ub nucleosomes, guided in part by the N-terminal zinc-finger domain of RYBP binding to residual H2AK119Ub on nascent chromatin. This recognition positions the RING domains of RING1B and BMI1 on the unmodified nucleosome side, enabling recruitment of the E2 enzyme to ubiquitinate H2AK119 within the same nucleosome (intra-nucleosome read-write) or across nucleosomes (inter-nucleosome read-write). Collectively, our findings provide key structural and mechanistic insights into the dynamic interplay of epigenetic regulation, highlighting the significance of ncPRC1 in H2AK119Ub restoration to sustain repressive chromatin domains.
History
DepositionAug 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (187-MER)
J: DNA (187-MER)
K: Polycomb complex protein BMI-1
L: E3 ubiquitin-protein ligase RING2
M: RING1 and YY1-binding protein
N: Ubiquitin
O: Histone H1.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,68120
Polymers355,35415
Non-polymers3275
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 9 types, 13 molecules AEBFCGDHKLMNO

#1: Protein Histone H3.2 / Histone H3


Mass: 15435.126 Da / Num. of mol.: 2 / Mutation: G103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#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 (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 14067.398 Da / Num. of mol.: 2 / Mutation: G100R, K119C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13979.291 Da / Num. of mol.: 2 / Mutation: S33T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein Polycomb complex protein BMI-1 / Polycomb group RING finger protein 4 / RING finger protein 51


Mass: 37006.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMI1, PCGF4, RNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P35226
#8: Protein E3 ubiquitin-protein ligase RING2 / Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG ...Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG / RING finger protein 1B / RING1b / RING finger protein 2 / RING finger protein BAP-1 / RING-type E3 ubiquitin transferase RING2


Mass: 37706.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF2, BAP1, DING, HIPI3, RING1B / Production host: Escherichia coli (E. coli)
References: UniProt: Q99496, RING-type E3 ubiquitin transferase
#9: Protein RING1 and YY1-binding protein / Apoptin-associating protein 1 / APAP-1 / Death effector domain-associated factor / DED-associated ...Apoptin-associating protein 1 / APAP-1 / Death effector domain-associated factor / DED-associated factor / YY1 and E4TF1-associated factor 1


Mass: 24863.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RYBP, DEDAF, YEAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N488
#10: Protein Ubiquitin


Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#11: Protein Histone H1.4 / Histone H1b / Histone H1s-4


Mass: 21931.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H1-4, H1F4, HIST1H1E / Production host: Escherichia coli (E. coli) / References: UniProt: P10412

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (187-MER)


Mass: 57982.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (187-MER)


Mass: 57488.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 5 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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
1ncPRC1RYBP bound to H2AK119Ub/H1.4 ChromatosomeCOMPLEX#1-#110RECOMBINANT
2HistonesCOMPLEX#1-#41RECOMBINANT
3DNACOMPLEX#5-#61RECOMBINANT
4ncPRC1-RYBPCOMPLEX#7-#91RECOMBINANT
5UbiquitinCOMPLEX#101RECOMBINANT
6Histone H3.2COMPLEX#12RECOMBINANT
7Histone H4COMPLEX#22RECOMBINANT
8Histone H2ACOMPLEX#32RECOMBINANT
9Histone H2B 1.1COMPLEX#42RECOMBINANT
10DNA (187-MER)COMPLEX#53RECOMBINANT
11DNA (187-MER)COMPLEX#63RECOMBINANT
12Polycomb complex protein BMI-1COMPLEX#74RECOMBINANT
13E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3COMPLEX#84RECOMBINANT
14RING1 and YY1-binding proteinCOMPLEX#94RECOMBINANT
15Histone H1.4COMPLEX#111RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
41NO
55
61NO
71NO
81NO
91NO
101NO
111NO
121NO
131NO
141NO
151NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Xenopus laevis (African clawed frog)8355
43synthetic construct (others)32630
54Homo sapiens (human)9606
65Homo sapiens (human)9606
76Xenopus laevis (African clawed frog)8355
87Xenopus laevis (African clawed frog)8355
98Xenopus laevis (African clawed frog)8355
109Xenopus laevis (African clawed frog)8355
1110synthetic construct (others)32630
1211synthetic construct (others)32630
1312Homo sapiens (human)9606
1413Homo sapiens (human)9606
1514Homo sapiens (human)9606
1615Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
54Escherichia coli (E. coli)562
65Escherichia coli (E. coli)562
76Escherichia coli (E. coli)562
87Escherichia coli (E. coli)562
98Escherichia coli (E. coli)562
109Escherichia coli (E. coli)562
1110Escherichia coli (E. coli)562
1211Escherichia coli (E. coli)562
1312Escherichia coli (E. coli)562
1413Escherichia coli (E. coli)562
1514Escherichia coli (E. coli)562
1615Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 61.06 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7820

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Processing

EM software
IDNameVersionCategory
2Leginonv 3.6image acquisition
7UCSF ChimeraX1.7.1model fitting
8Coot0.9.8.94model fitting
13cryoSPARC4.43D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1394967
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205635 / Symmetry type: POINT
Atomic model building
IDSpace
1REAL
2
Atomic model building
IDPDB-ID 3D fitting-IDDetailsSource nameTypeAccession codeInitial refinement model-ID
11Multimer predictionAlphaFoldin silico model
23tu4

3tu4

1PDBexperimental model3tu42
38H1T

8h1t

1PDBexperimental model8H1T3
48SVF

8svf

1PDBexperimental model8SVF4
54R8P

4r8p

1PDBexperimental model4R8P5
62D9G

2d9g

1PDBexperimental model2D9G6
71SwissModelTemplateSwissModelin silico model
81UBQ

1ubq

1PDBexperimental model1UBQ8
97PFV

7pfv

1PDBexperimental model7PFV9
102WWZ

2wwz

2PDBexperimental model2WWZ

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