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- PDB-8onk: Human insulin in complex with the analytical antibody S1 Fab and ... -

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Basic information

Entry
Database: PDB / ID: 8onk
TitleHuman insulin in complex with the analytical antibody S1 Fab and the analytical antibody HUI-001 Fab
Components
  • (Heavy chain of analytical antibody ...) x 2
  • (Light chain of analytical antibody ...) x 2
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin / analytical antibody / HUI-001
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.403 Å
AuthorsJohansson, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Not funded Denmark
CitationJournal: To Be Published
Title: Macromolecular structure of insulin and IgE clonality impacts IgE-mediated activation of sensitized basophils
Authors: Christoffersen, S. / Baumann, K. / Millner, A.H. / Toft-Hansen, H. / Johansson, E. / Thorlaksen, C. / Skov, P.S.
History
DepositionApr 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of analytical antibody S1 Fab
L: Light chain of analytical antibody S1 Fab
I: Insulin A chain
B: Insulin B chain
C: Heavy chain of analytical antibody S1 Fab
E: Light chain of analytical antibody S1 Fab
D: Insulin A chain
A: Insulin B chain
F: Light chain of analytical antibody HUI-001 Fab
G: Heavy chain of analytical antibody HUI-001 Fab
J: Light chain of analytical antibody HUI-001 Fab
K: Heavy chain of analytical antibody HUI-001 Fab


Theoretical massNumber of molelcules
Total (without water)200,88012
Polymers200,88012
Non-polymers00
Water0
1
H: Heavy chain of analytical antibody S1 Fab
L: Light chain of analytical antibody S1 Fab
I: Insulin A chain
B: Insulin B chain
F: Light chain of analytical antibody HUI-001 Fab
G: Heavy chain of analytical antibody HUI-001 Fab


Theoretical massNumber of molelcules
Total (without water)100,4406
Polymers100,4406
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heavy chain of analytical antibody S1 Fab
E: Light chain of analytical antibody S1 Fab
D: Insulin A chain
A: Insulin B chain
J: Light chain of analytical antibody HUI-001 Fab
K: Heavy chain of analytical antibody HUI-001 Fab


Theoretical massNumber of molelcules
Total (without water)100,4406
Polymers100,4406
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)278.900, 52.326, 179.504
Angle α, β, γ (deg.)90.000, 101.140, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2(chain "C" and (resid 1 through 133 or resid 141 through 221))
d_2ens_2chain "H"
d_1ens_3chain "D"
d_2ens_3chain "I"
d_1ens_4(chain "E" and (resid 1 through 14 or resid 16...
d_2ens_4(chain "F" and (resid 1 through 14 or resid 16...
d_3ens_4(chain "J" and (resid 1 through 14 or resid 16...
d_4ens_4(chain "L" and (resid 1 through 14 or resid 16...
d_1ens_5chain "G"
d_2ens_5chain "K"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PHEPHEPROPROAH1 - 281 - 28
d_21ens_1PHEPHEPROPROBD1 - 281 - 28
d_11ens_2GLUGLUPROPROCE1 - 1331 - 133
d_12ens_2SERSERASPASPCE141 - 221141 - 221
d_21ens_2GLUGLUASPASPHA1 - 2141 - 214
d_11ens_3GLYGLYASNASNDG1 - 211 - 21
d_21ens_3GLYGLYASNASNIC1 - 211 - 21
d_11ens_4GLNGLNSERSEREF1 - 141 - 14
d_12ens_4GLYGLYGLUGLUEF16 - 1716 - 17
d_13ens_4VALVALCYSCYSEF19 - 2319 - 23
d_14ens_4ALAALAALAALAEF2525
d_15ens_4SERSERVALVALEF27 - 2927 - 29
d_16ens_4TYRTYRTRPTRPEF33 - 3433 - 34
d_17ens_4GLNGLNPROPROEF36 - 4336 - 43
d_18ens_4LEULEULEULEUEF4545
d_19ens_4ILEILETYRTYREF47 - 4847 - 48
d_110ens_4THRTHRPROPROEF50 - 5850 - 58
d_111ens_4ARGARGSERSEREF60 - 6960 - 69
d_112ens_4SERSERSERSEREF71 - 7571 - 75
d_113ens_4METMETTYRTYREF77 - 8577 - 85
d_114ens_4CYSCYSCYSCYSEF8787
d_115ens_4GLNGLNGLNGLNEF8989
d_116ens_4PROPROPROPROEF9494
d_117ens_4THRTHRTHRTHREF96 - 10196 - 101
d_118ens_4LEULEUASNASNEF103 - 211103 - 211
d_21ens_4GLNGLNSERSERFI1 - 141 - 14
d_22ens_4GLYGLYGLUGLUFI16 - 1716 - 17
d_23ens_4VALVALCYSCYSFI19 - 2319 - 23
d_24ens_4ALAALAALAALAFI2525
d_25ens_4SERSERVALVALFI27 - 2927 - 29
d_26ens_4TYRTYRTYRTYRFI3333
d_27ens_4TRPTRPTRPTRPFI3636
d_28ens_4GLNGLNPROPROFI38 - 4538 - 45
d_29ens_4LEULEULEULEUFI4747
d_210ens_4ILEILETYRTYRFI49 - 5049 - 50
d_211ens_4THRTHRPROPROFI52 - 6052 - 60
d_212ens_4ARGARGSERSERFI62 - 7162 - 71
d_213ens_4SERSERSERSERFI73 - 7773 - 77
d_214ens_4METMETTYRTYRFI79 - 8779 - 87
d_215ens_4CYSCYSCYSCYSFI8989
d_216ens_4GLNGLNGLNGLNFI9191
d_217ens_4PROPROPROPROFI9696
d_218ens_4THRTHRTHRTHRFI98 - 10398 - 103
d_219ens_4LEULEUASNASNFI105 - 213105 - 213
d_31ens_4GLNGLNSERSERJK1 - 141 - 14
d_32ens_4GLYGLYGLUGLUJK16 - 1716 - 17
d_33ens_4VALVALCYSCYSJK19 - 2319 - 23
d_34ens_4ALAALAALAALAJK2525
d_35ens_4SERSERVALVALJK27 - 2927 - 29
d_36ens_4TYRTYRTYRTYRJK3333
d_37ens_4TRPTRPTRPTRPJK3636
d_38ens_4GLNGLNPROPROJK38 - 4538 - 45
d_39ens_4LEULEULEULEUJK4747
d_310ens_4ILEILETYRTYRJK49 - 5049 - 50
d_311ens_4THRTHRPROPROJK52 - 6052 - 60
d_312ens_4ARGARGSERSERJK62 - 7162 - 71
d_313ens_4SERSERSERSERJK73 - 7773 - 77
d_314ens_4METMETTYRTYRJK79 - 8779 - 87
d_315ens_4CYSCYSCYSCYSJK8989
d_316ens_4GLNGLNGLNGLNJK9191
d_317ens_4PROPROPROPROJK9696
d_318ens_4THRTHRTHRTHRJK98 - 10398 - 103
d_319ens_4LEULEUASNASNJK105 - 213105 - 213
d_41ens_4GLNGLNSERSERLB1 - 141 - 14
d_42ens_4GLYGLYGLUGLULB16 - 1716 - 17
d_43ens_4VALVALCYSCYSLB19 - 2319 - 23
d_44ens_4ALAALAALAALALB2525
d_45ens_4SERSERVALVALLB27 - 2927 - 29
d_46ens_4TYRTYRTRPTRPLB33 - 3433 - 34
d_47ens_4GLNGLNPROPROLB36 - 4336 - 43
d_48ens_4LEULEULEULEULB4545
d_49ens_4ILEILETYRTYRLB47 - 4847 - 48
d_410ens_4THRTHRPROPROLB50 - 5850 - 58
d_411ens_4ARGARGSERSERLB60 - 6960 - 69
d_412ens_4SERSERSERSERLB71 - 7571 - 75
d_413ens_4METMETTYRTYRLB77 - 8577 - 85
d_414ens_4CYSCYSCYSCYSLB8787
d_415ens_4GLNGLNGLNGLNLB8989
d_416ens_4PROPROPROPROLB9494
d_417ens_4THRTHRTHRTHRLB96 - 10196 - 101
d_418ens_4LEULEUASNASNLB103 - 211103 - 211
d_11ens_5GLNGLNARGARGGJ1 - 2131 - 217
d_21ens_5GLNGLNARGARGKL1 - 2131 - 217

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(-0.576094457863, 0.674259030791, -0.462049710547), (0.576032370545, -0.0661525531921, -0.814745695165), (-0.579915410818, -0.735526069628, -0.3502849086)-4.17390816772, 76.4080325836, 84.3082441338
2given(-0.534197169748, 0.663488457121, -0.523847736561), (0.651997410575, -0.0710622635129, -0.754883786624), (-0.538082484789, -0.744804150077, -0.394631495945)1.08849447493, 70.1747859585, 87.8937479766
3given(-0.67094972524, 0.623037182527, -0.402058621831), (0.486357656692, -0.039518728509, -0.872865682608), (-0.559716621137, -0.781193279084, -0.276503824091)-6.5146299389, 82.9005264227, 78.1645002406
4given(0.338249274822, -0.394680772628, 0.854291821218), (0.853605316446, 0.51084264589, -0.101969382051), (-0.396163339821, 0.76371910992, 0.509693760335)-106.080108397, -9.38728428879, -61.8609780439
5given(0.379767421142, 0.0926345906896, -0.920432256305), (0.487706082823, -0.865517080154, 0.114118187595), (-0.786078547358, -0.492238780035, -0.373873642843)101.98339737, 51.7761375457, 159.522652568
6given(-0.536985472173, 0.661462439745, -0.523559016237), (0.661768447748, -0.0545975885639, -0.74771761039), (-0.523172174566, -0.747988331547, -0.408416860119)1.10216446794, 69.2710239405, 88.7592930313
7given(-0.669581916739, 0.493308357419, -0.555253925044), (0.621540971634, -0.037125666303, -0.782501441201), (-0.406628672572, -0.869061878926, -0.281752680982)-0.72114365887, 67.7019020396, 91.7788928201

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Components

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Protein/peptide , 2 types, 4 molecules IDBA

#3: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#4: Protein/peptide Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308

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Antibody , 4 types, 8 molecules HCLEFJGK

#1: Antibody Heavy chain of analytical antibody S1 Fab


Mass: 24219.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Light chain of analytical antibody S1 Fab


Mass: 23360.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Antibody Light chain of analytical antibody HUI-001 Fab


Mass: 23536.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#6: Antibody Heavy chain of analytical antibody HUI-001 Fab


Mass: 23505.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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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: 3.2 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M TRIS pH 7.5, 15%(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.403→45.61 Å / Num. obs: 35523 / % possible obs: 98.96 % / Redundancy: 3.3 % / Biso Wilson estimate: 92.02 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.2022 / Rpim(I) all: 0.1293 / Rrim(I) all: 0.2407 / Net I/σ(I): 5.9
Reflection shellResolution: 3.403→3.525 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.041 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 3330 / CC1/2: 0.594 / CC star: 0.863 / Rpim(I) all: 0.6749 / Rrim(I) all: 1.245 / % possible all: 93.41

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.403→45.61 Å / SU ML: 0.5596 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.9323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3109 1769 4.99 %
Rwork0.2575 33679 -
obs0.2602 35448 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113 Å2
Refinement stepCycle: LAST / Resolution: 3.403→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13896 0 0 0 13896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001614249
X-RAY DIFFRACTIONf_angle_d0.413919412
X-RAY DIFFRACTIONf_chiral_restr0.03912178
X-RAY DIFFRACTIONf_plane_restr0.00392466
X-RAY DIFFRACTIONf_dihedral_angle_d3.17051946
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2HX-RAY DIFFRACTIONTorsion NCS0.598482356166
ens_2d_2EX-RAY DIFFRACTIONTorsion NCS0.595201608107
ens_3d_2GX-RAY DIFFRACTIONTorsion NCS1.4141622078
ens_4d_2FX-RAY DIFFRACTIONTorsion NCS1.27601913327
ens_4d_3FX-RAY DIFFRACTIONTorsion NCS1.37341548612
ens_4d_4FX-RAY DIFFRACTIONTorsion NCS0.440447621237
ens_5d_2JX-RAY DIFFRACTIONTorsion NCS1.32812903386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.403-3.50.461260.46472394X-RAY DIFFRACTION91.7
3.5-3.60.40471320.37672515X-RAY DIFFRACTION99.44
3.6-3.710.371400.32712635X-RAY DIFFRACTION99.57
3.71-3.850.44341290.33212502X-RAY DIFFRACTION99.58
3.85-40.37071390.31822635X-RAY DIFFRACTION99.64
4-4.180.3691340.30132547X-RAY DIFFRACTION99.48
4.18-4.40.31941370.25632597X-RAY DIFFRACTION99.71
4.4-4.680.28421360.22872594X-RAY DIFFRACTION99.64
4.68-5.040.28021370.23212595X-RAY DIFFRACTION99.71
5.04-5.550.26621370.21712599X-RAY DIFFRACTION99.74
5.55-6.350.27641380.23572641X-RAY DIFFRACTION99.68
6.35-7.990.30761400.24842658X-RAY DIFFRACTION99.82
7.99-45.610.24821440.19422767X-RAY DIFFRACTION99.52

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