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- PDB-5b0z: The crystal structure of the nucleosome containing H3.2, at 1.98 ... -

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Basic information

Entry
Database: PDB / ID: 5b0z
TitleThe crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.2
  • Histone H4
KeywordsDNA BINDING PROTEIN / histone-fold / nucleus
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / Packaging Of Telomere Ends / 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 ...negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / Packaging Of Telomere Ends / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / gene expression / killing of cells of another organism / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / chromatin binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
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 2A / Histone H2A / 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 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.987 Å
AuthorsSuzuki, Y. / Horikoshi, N. / Kato, D. / Kurumizaka, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
the Ministry of Education, Culture, Sports, Science and Technology (MEXT)25116002 Japan
the Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of the nucleosome containing histone H3 with crotonylated lysine 122
Authors: Suzuki, Y. / Horikoshi, N. / Kato, D. / Kurumizaka, H.
History
DepositionNov 14, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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

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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-B/E
D: Histone H2B type 1-J
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (146-MER)
J: DNA (146-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,50517
Polymers202,19910
Non-polymers3077
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56560 Å2
ΔGint-456 kcal/mol
Surface area72400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.685, 108.204, 168.286
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
11chain A
21chain E
12chain B
22chain F
13chain C
23chain G
14chain D
24chain H
15chain I
25chain J

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROCLCLchain AAA - K38 - 30142
21LYSLYSCLCLchain EEE - N37 - 30241
12ASNASNHOHHOHchain BBB - S25 - 21929
22LYSLYSHOHHOHchain FFF - W20 - 23924
13ARGARGHOHHOHchain CCC - T11 - 23515
23LYSLYSCLCLchain GGG - O15 - 30119
14ARGARGCLCLchain DDD - L31 - 30135
24LYSLYSHOHHOHchain HHH - Y34 - 21738
15DADAMNMNchain III - P1 - 3011
25DADAMNMNchain JJJ - Q147 - 3011

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2 / Histone H3/m / Histone H3/o


Mass: 15703.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D / Plasmid: pHCE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q71DI3
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Plasmid: pHCE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06899

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DNA chain , 1 types, 2 molecules IJ

#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 (E. coli) / Strain (production host): DH5alpha

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Non-polymers , 3 types, 332 molecules

#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.64 %
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-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 119479 / % possible obs: 96.3 % / Redundancy: 8 % / Biso Wilson estimate: 31.63 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.025 / Rrim(I) all: 0.077 / Χ2: 1.698 / Net I/av σ(I): 30.068 / Net I/σ(I): 13 / Num. measured all: 957221
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.055.30.481111270.370.2170.5310.78790.6
2.05-2.135.80.43113420.5540.1840.470.87792.3
2.13-2.236.20.357114620.7640.1470.3880.97993.5
2.23-2.356.70.298117160.8940.1170.3221.09995.2
2.35-2.497.20.244119320.9430.0920.2621.19897.1
2.49-2.697.90.183120950.9780.0660.1951.38798
2.69-2.968.90.134121950.9910.0450.1421.65398.7
2.96-3.39100.076123400.9980.0240.08299.2
3.39-4.2610.80.054124620.9990.0170.0562.36599.6
4.26-5010.70.048128080.9990.0150.052.6999

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.1phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-2000705bdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CV5

2cv5


Resolution: 1.987→38.942 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 5977 5 %Random selection
Rwork0.2112 113452 --
obs0.2133 119429 96.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.71 Å2 / Biso mean: 44.7713 Å2 / Biso min: 10.3 Å2
Refinement stepCycle: final / Resolution: 1.987→38.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5965 5980 7 325 12277
Biso mean--34.05 33.65 -
Num. residues----1044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412753
X-RAY DIFFRACTIONf_angle_d1.47918474
X-RAY DIFFRACTIONf_chiral_restr0.072100
X-RAY DIFFRACTIONf_plane_restr0.0091327
X-RAY DIFFRACTIONf_dihedral_angle_d28.8985261
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A924X-RAY DIFFRACTION8.111TORSIONAL
12E924X-RAY DIFFRACTION8.111TORSIONAL
21B748X-RAY DIFFRACTION8.111TORSIONAL
22F748X-RAY DIFFRACTION8.111TORSIONAL
31C958X-RAY DIFFRACTION8.111TORSIONAL
32G958X-RAY DIFFRACTION8.111TORSIONAL
41D838X-RAY DIFFRACTION8.111TORSIONAL
42H838X-RAY DIFFRACTION8.111TORSIONAL
51I2912X-RAY DIFFRACTION8.111TORSIONAL
52J2912X-RAY DIFFRACTION8.111TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9875-2.010.35311640.32273158332280
2.01-2.03370.34051780.31353516369491
2.0337-2.05850.33311680.30163589375792
2.0585-2.08450.32281850.29913601378692
2.0845-2.1120.31711720.28033620379293
2.112-2.14090.30031940.27393596379093
2.1409-2.17150.31962000.26353602380293
2.1715-2.20390.29382020.24983644384693
2.2039-2.23830.29642090.23843655386494
2.2383-2.2750.2522070.23053686389395
2.275-2.31420.30232010.2283681388295
2.3142-2.35630.252100.22263746395696
2.3563-2.40160.28061870.22223821400897
2.4016-2.45070.28582040.21973754395897
2.4507-2.50390.2691760.21673839401598
2.5039-2.56220.27461850.2163853403898
2.5622-2.62620.27921930.21753846403998
2.6262-2.69720.26282140.22233826404098
2.6972-2.77660.25552010.22753858405998
2.7766-2.86620.29642070.23783897410499
2.8662-2.96860.2942020.25333868407099
2.9686-3.08740.30992220.23783906412899
3.0874-3.22780.2811980.22963906410499
3.2278-3.39790.27222130.22093935414899
3.3979-3.61070.23732200.19153921414199
3.6107-3.88920.2252100.191339524162100
3.8892-4.28010.21182190.172139744193100
4.2801-4.89850.18912290.169939904219100
4.8985-6.16760.23431920.189140544246100
6.1676-38.9490.21622150.17394158437398

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