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- PDB-5xm1: The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7... -

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Basic information

Entry
Database: PDB / ID: 5xm1
TitleThe mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4
Components
  • DNA (146-MER)
  • Histone H2A type 1-B
  • Histone H2B type 3-A
  • Histone H3mm7
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / nucleosome / chromatin / DNA-Protein complex / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine ...Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / Nonhomologous End-Joining (NHEJ) / Metalloprotease DUBs / HDACs deacetylate histones / PRC2 methylates histones and DNA / UCH proteinases / Processing of DNA double-strand break ends / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / pericentric heterochromatin formation / Ub-specific processing proteases / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / oogenesis / nucleus organization / spermatid development / chromosome, centromeric region / single fertilization / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / RNA polymerase II core promoter sequence-specific DNA binding / CENP-A containing nucleosome / embryo implantation / multicellular organism growth / nucleosome assembly / male gonad development / osteoblast differentiation / structural constituent of chromatin / nucleosome / chromatin organization / chromosome / positive regulation of cell growth / spermatogenesis / chromosome, telomeric region / cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / 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, subunit A / Histone, subunit A / : / 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. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B / Histone H4 / Histone H3.3 / H2B.U histone 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsTaguchi, H. / Horikoshi, N. / Kurumizaka, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
Ministry of Education, Culture, Sports, Science and Technology25116002 Japan
the Japan Agency for Medical Research and Development Japan
CitationJournal: Nat Commun / Year: 2018
Title: Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration.
Authors: Harada, A. / Maehara, K. / Ono, Y. / Taguchi, H. / Yoshioka, K. / Kitajima, Y. / Xie, Y. / Sato, Y. / Iwasaki, T. / Nogami, J. / Okada, S. / Komatsu, T. / Semba, Y. / Takemoto, T. / Kimura, ...Authors: Harada, A. / Maehara, K. / Ono, Y. / Taguchi, H. / Yoshioka, K. / Kitajima, Y. / Xie, Y. / Sato, Y. / Iwasaki, T. / Nogami, J. / Okada, S. / Komatsu, T. / Semba, Y. / Takemoto, T. / Kimura, H. / Kurumizaka, H. / Ohkawa, Y.
History
DepositionMay 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3mm7
B: Histone H4
C: Histone H2A type 1-B
D: Histone H2B type 3-A
E: Histone H3mm7
F: Histone H4
G: Histone H2A type 1-B
H: Histone H2B type 3-A
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)202,25110
Polymers202,25110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55660 Å2
ΔGint-399 kcal/mol
Surface area72320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.550, 109.380, 176.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and resseq 25:101)
21(chain F and resseq 25:101)
12(chain H and (resseq 34:81 or resseq 83:85 or resseq 87:123))
22(chain D and (resseq 34:81 or resseq 83:85 or resseq 87:123))
13(chain A and (resseq 38:52 or resseq 54:77 or (resid...
23(chain E and (resseq 38:52 or resseq 54:77 or (resid...
14(chain G and (resseq 16:38 or (resid 39 and (name...
24(chain C and (resseq 16:38 or (resid 39 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNGLYGLY(chain B and resseq 25:101)BB25 - 10129 - 105
211ASNASNGLYGLY(chain F and resseq 25:101)FF25 - 10129 - 105
112LYSLYSALAALA(chain H and (resseq 34:81 or resseq 83:85 or resseq 87:123))HH34 - 8138 - 85
122TYRTYRLYSLYS(chain H and (resseq 34:81 or resseq 83:85 or resseq 87:123))HH83 - 8587 - 89
132SERSERSERSER(chain H and (resseq 34:81 or resseq 83:85 or resseq 87:123))HH87 - 12391 - 127
212LYSLYSALAALA(chain D and (resseq 34:81 or resseq 83:85 or resseq 87:123))DD34 - 8138 - 85
222TYRTYRLYSLYS(chain D and (resseq 34:81 or resseq 83:85 or resseq 87:123))DD83 - 8587 - 89
232SERSERSERSER(chain D and (resseq 34:81 or resseq 83:85 or resseq 87:123))DD87 - 12391 - 127
113PROPROARGARG(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA38 - 5242 - 56
123TYRTYRASPASP(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA54 - 7758 - 81
133PHEPHEPHEPHE(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA7882
143PROPROARGARG(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA38 - 13442 - 138
153PROPROARGARG(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA38 - 13442 - 138
163PROPROARGARG(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA38 - 13442 - 138
173PROPROARGARG(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA38 - 13442 - 138
183PROPROARGARG(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA38 - 13442 - 138
193PROPROARGARG(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA38 - 13442 - 138
1103PROPROARGARG(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA38 - 13442 - 138
1113PROPROARGARG(chain A and (resseq 38:52 or resseq 54:77 or (resid...AA38 - 13442 - 138
213PROPROARGARG(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE38 - 5242 - 56
223TYRTYRASPASP(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE54 - 7758 - 81
233PHEPHEPHEPHE(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE7882
243PROPROALAALA(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE38 - 13542 - 139
253PROPROALAALA(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE38 - 13542 - 139
263PROPROALAALA(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE38 - 13542 - 139
273PROPROALAALA(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE38 - 13542 - 139
283PROPROALAALA(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE38 - 13542 - 139
293PROPROALAALA(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE38 - 13542 - 139
2103PROPROALAALA(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE38 - 13542 - 139
2113PROPROALAALA(chain E and (resseq 38:52 or resseq 54:77 or (resid...EE38 - 13542 - 139
114THRTHRASNASN(chain G and (resseq 16:38 or (resid 39 and (name...GG16 - 3820 - 42
124TYRTYRTYRTYR(chain G and (resseq 16:38 or (resid 39 and (name...GG3943
134LYSLYSLYSLYS(chain G and (resseq 16:38 or (resid 39 and (name...GG15 - 11819 - 122
144LYSLYSLYSLYS(chain G and (resseq 16:38 or (resid 39 and (name...GG15 - 11819 - 122
154LYSLYSLYSLYS(chain G and (resseq 16:38 or (resid 39 and (name...GG15 - 11819 - 122
164LYSLYSLYSLYS(chain G and (resseq 16:38 or (resid 39 and (name...GG15 - 11819 - 122
174LYSLYSLYSLYS(chain G and (resseq 16:38 or (resid 39 and (name...GG15 - 11819 - 122
184LYSLYSLYSLYS(chain G and (resseq 16:38 or (resid 39 and (name...GG15 - 11819 - 122
194LYSLYSLYSLYS(chain G and (resseq 16:38 or (resid 39 and (name...GG15 - 11819 - 122
1104LYSLYSLYSLYS(chain G and (resseq 16:38 or (resid 39 and (name...GG15 - 11819 - 122
1114LYSLYSLYSLYS(chain G and (resseq 16:38 or (resid 39 and (name...GG15 - 11819 - 122
214THRTHRASNASN(chain C and (resseq 16:38 or (resid 39 and (name...CC16 - 3820 - 42
224TYRTYRTYRTYR(chain C and (resseq 16:38 or (resid 39 and (name...CC3943
234ALAALALYSLYS(chain C and (resseq 16:38 or (resid 39 and (name...CC14 - 11818 - 122
244ALAALALYSLYS(chain C and (resseq 16:38 or (resid 39 and (name...CC14 - 11818 - 122
254ALAALALYSLYS(chain C and (resseq 16:38 or (resid 39 and (name...CC14 - 11818 - 122
264ALAALALYSLYS(chain C and (resseq 16:38 or (resid 39 and (name...CC14 - 11818 - 122
274ALAALALYSLYS(chain C and (resseq 16:38 or (resid 39 and (name...CC14 - 11818 - 122
284ALAALALYSLYS(chain C and (resseq 16:38 or (resid 39 and (name...CC14 - 11818 - 122
294ALAALALYSLYS(chain C and (resseq 16:38 or (resid 39 and (name...CC14 - 11818 - 122
2104ALAALALYSLYS(chain C and (resseq 16:38 or (resid 39 and (name...CC14 - 11818 - 122
2114ALAALALYSLYS(chain C and (resseq 16:38 or (resid 39 and (name...CC14 - 11818 - 122

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Histone H3mm7


Mass: 15639.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pH3mm7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P84244*PLUS
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4
Plasmid: pH4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62806
#3: Protein Histone H2A type 1-B


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist1h2ab / Plasmid: pH2A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C0HKE1
#4: Protein Histone H2B type 3-A


Mass: 14307.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist3h2ba / Plasmid: pH2B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9D2U9
#5: DNA chain DNA (146-MER)


Mass: 45053.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEM-T(easy) / Production host: Escherichia coli DH5alpha (bacteria) / Strain (production host): DH5alpha

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 28747 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 91.24 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.197 / Net I/σ(I): 6.9 / Num. measured all: 169255
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.45-3.575.80.42628150.771198.9
3.57-3.725.90.31228210.754199.3
3.72-3.895.90.26928450.879199.5
3.89-4.095.70.2228321.007199.4
4.09-4.355.80.16328521.137199.5
4.35-4.685.80.12628461.252199.2
4.68-5.156.20.10728731.277199.6
5.15-5.96.20.128761.341199.5
5.9-7.435.80.07829461.343199.7
7.43-505.70.05130412.144198.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000704wdata scaling
PHASER2.5.1phasing
PDB_EXTRACT3.22data extraction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AV2

3av2


Resolution: 3.45→34.875 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 26.76 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2544 1902 7.16 %
Rwork0.1997 24651 -
obs0.2037 26553 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.88 Å2 / Biso mean: 112.2299 Å2 / Biso min: 43.87 Å2
Refinement stepCycle: final / Resolution: 3.45→34.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5940 5980 0 0 11920
Num. residues----1042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112728
X-RAY DIFFRACTIONf_angle_d1.24718444
X-RAY DIFFRACTIONf_chiral_restr0.0612097
X-RAY DIFFRACTIONf_plane_restr0.0081325
X-RAY DIFFRACTIONf_dihedral_angle_d26.9016639
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B738X-RAY DIFFRACTION8.972TORSIONAL
12F738X-RAY DIFFRACTION8.972TORSIONAL
21H752X-RAY DIFFRACTION8.972TORSIONAL
22D752X-RAY DIFFRACTION8.972TORSIONAL
31A902X-RAY DIFFRACTION8.972TORSIONAL
32E902X-RAY DIFFRACTION8.972TORSIONAL
41G950X-RAY DIFFRACTION8.972TORSIONAL
42C950X-RAY DIFFRACTION8.972TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4501-3.53630.31821220.25281623174590
3.5363-3.63190.2981230.22711651177492
3.6319-3.73860.31651380.23761656179493
3.7386-3.85910.29511300.23211699182995
3.8591-3.99690.30461360.22121727186395
3.9969-4.15670.26721350.21141721185696
4.1567-4.34550.26021300.19991765189597
4.3455-4.57410.25261420.19291781192398
4.5741-4.860.23771300.18671787191799
4.86-5.23410.24611390.19371805194499
5.2341-5.75870.25711450.20951804194999
5.7587-6.58710.28821420.222118461988100
6.5871-8.28070.22841400.18431850199099
8.2807-34.87650.2081500.17131936208699

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