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- PDB-9o0v: Crystal structure of CRAF/MEK1 complex with PLX4720, CH5126766, a... -

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Basic information

Entry
Database: PDB / ID: 9o0v
TitleCrystal structure of CRAF/MEK1 complex with PLX4720, CH5126766, and AMPPNP
Components
  • Dual specificity mitogen-activated protein kinase kinase 1
  • RAF proto-oncogene serine/threonine-protein kinase
KeywordsTRANSFERASE / CRAF-MEK1 complex / MAPK pathway
Function / homology
Function and homology information


death-inducing signaling complex assembly / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / intermediate filament cytoskeleton organization / mitogen-activated protein kinase kinase / Golgi inheritance / placenta blood vessel development ...death-inducing signaling complex assembly / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / intermediate filament cytoskeleton organization / mitogen-activated protein kinase kinase / Golgi inheritance / placenta blood vessel development / MAP-kinase scaffold activity / positive regulation of muscle contraction / labyrinthine layer development / regulation of axon regeneration / cerebellar cortex formation / regulation of Rho protein signal transduction / melanosome transport / type B pancreatic cell proliferation / Signaling by MAP2K mutants / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / vesicle transport along microtubule / positive regulation of axonogenesis / positive regulation of Ras protein signal transduction / insulin secretion involved in cellular response to glucose stimulus / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / central nervous system neuron differentiation / triglyceride homeostasis / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / IFNG signaling activates MAPKs / regulation of stress-activated MAPK cascade / Frs2-mediated activation / GP1b-IX-V activation signalling / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / neurotrophin TRK receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / pseudopodium / endodermal cell differentiation / face development / MAP kinase kinase activity / Bergmann glial cell differentiation / positive regulation of ATP biosynthetic process / regulation of cell differentiation / thyroid gland development / Uptake and function of anthrax toxins / positive regulation of protein serine/threonine kinase activity / extrinsic apoptotic signaling pathway via death domain receptors / somatic stem cell population maintenance / protein kinase activator activity / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / type II interferon-mediated signaling pathway / negative regulation of protein-containing complex assembly / response to axon injury / Schwann cell development / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / keratinocyte differentiation / neuron projection morphogenesis / response to muscle stretch / ERK1 and ERK2 cascade / myelination / positive regulation of autophagy / protein serine/threonine/tyrosine kinase activity / CD209 (DC-SIGN) signaling / dendrite cytoplasm / insulin-like growth factor receptor signaling pathway / response to glucocorticoid / MAP3K8 (TPL2)-dependent MAPK1/3 activation / thymus development / adenylate cyclase activator activity / protein serine/threonine kinase activator activity / Signal transduction by L1 / cell motility / wound healing / positive regulation of transcription elongation by RNA polymerase II / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / small GTPase binding / Stimuli-sensing channels / neuron differentiation / chemotaxis / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cellular senescence / insulin receptor signaling pathway / late endosome / MAPK cascade / heart development / response to oxidative stress / protein tyrosine kinase activity
Similarity search - Function
: / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...: / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-324 / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-CHU / RAF proto-oncogene serine/threonine-protein kinase / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJang, D.M. / Eck, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA242461-06 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Characterization and inhibitor sensitivity of ARAF, BRAF, and CRAF kinases
Authors: Tkacik, E. / Jang, D.M. / Boxer, K. / Ha, B.H. / Eck, M.J.
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAF proto-oncogene serine/threonine-protein kinase
B: Dual specificity mitogen-activated protein kinase kinase 1
C: RAF proto-oncogene serine/threonine-protein kinase
D: Dual specificity mitogen-activated protein kinase kinase 1
E: RAF proto-oncogene serine/threonine-protein kinase
F: Dual specificity mitogen-activated protein kinase kinase 1
G: RAF proto-oncogene serine/threonine-protein kinase
H: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,89320
Polymers302,3278
Non-polymers5,56612
Water1448
1
A: RAF proto-oncogene serine/threonine-protein kinase
B: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9735
Polymers75,5822
Non-polymers1,3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RAF proto-oncogene serine/threonine-protein kinase
D: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9735
Polymers75,5822
Non-polymers1,3913
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RAF proto-oncogene serine/threonine-protein kinase
F: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9735
Polymers75,5822
Non-polymers1,3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: RAF proto-oncogene serine/threonine-protein kinase
H: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9735
Polymers75,5822
Non-polymers1,3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.936, 180.936, 366.828
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 341 through 359 or (resid 360...
d_2ens_1(chain "C" and (resid 341 through 392 or (resid 393...
d_3ens_1(chain "E" and (resid 341 through 359 or (resid 360...
d_4ens_1(chain "G" and (resid 341 through 392 or (resid 393...
d_1ens_2(chain "B" and (resid 31 through 37 or (resid 38...
d_2ens_2(chain "D" and (resid 31 through 37 or (resid 38...
d_3ens_2(chain "F" and (resid 31 through 77 or resid 80...
d_4ens_2(chain "H" and (resid 31 through 37 or (resid 38...

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_1ASPASPPHEPHEAA341 - 4436 - 108
d_12ens_1LEULEULEULEUAA445 - 489110 - 154
d_13ens_1THRTHRILEILEAA506 - 517171 - 182
d_14ens_1METMETSERSERAA519 - 612184 - 277
d_15ens_1324324324324AI701
d_21ens_1ASPASPPHEPHECC341 - 4436 - 108
d_22ens_1LEULEULEULEUCC445 - 489110 - 154
d_23ens_1THRTHRILEILECC506 - 517171 - 182
d_24ens_1METMETSERSERCC519 - 612184 - 277
d_25ens_1324324324324CL701
d_31ens_1ASPASPPHEPHEEE341 - 4436 - 108
d_32ens_1LEULEULEULEUEE445 - 489110 - 154
d_33ens_1THRTHRILEILEEE506 - 517171 - 182
d_34ens_1METMETSERSEREE519 - 612184 - 277
d_35ens_1324324324324EO701
d_41ens_1ASPASPPHEPHEGG341 - 4436 - 108
d_42ens_1LEULEULEULEUGG445 - 489110 - 154
d_43ens_1THRTHRILEILEGG506 - 517171 - 182
d_44ens_1METMETSERSERGG519 - 612184 - 277
d_45ens_1324324324324GR701
d_11ens_2GLUGLUGLYGLYBB31 - 7733 - 79
d_12ens_2GLYGLYLEULEUBB80 - 27382 - 275
d_13ens_2PROPROGLYGLYBB307 - 380309 - 382
d_14ens_2CHUCHUCHUCHUBJ401
d_15ens_2ANPANPANPANPBK402
d_21ens_2GLUGLUGLYGLYDD31 - 38033 - 382
d_22ens_2CHUCHUCHUCHUDM401
d_23ens_2ANPANPANPANPDN402
d_31ens_2GLUGLUGLYGLYFF31 - 7733 - 79
d_32ens_2GLYGLYLEULEUFF80 - 27382 - 275
d_33ens_2PROPROGLYGLYFF307 - 380309 - 382
d_34ens_2CHUCHUCHUCHUFP401
d_35ens_2ANPANPANPANPFQ402
d_41ens_2GLUGLUGLYGLYHH31 - 7733 - 79
d_42ens_2GLYGLYGLYGLYHH80 - 38082 - 382
d_43ens_2CHUCHUCHUCHUHS401
d_44ens_2ANPANPANPANPHT402

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.980233726164, -0.133278971299, 0.14621408243), (0.0237933284418, -0.813092583504, -0.581647941776), (0.196407025366, -0.566672009596, 0.800191923183)-59.3930058738, 149.5016499, 53.7062008787
2given(0.977383422437, 0.0881486988385, -0.192227605817), (-0.186489643391, -0.0693426399137, -0.980006740384), (-0.0997158886694, 0.993690799587, -0.0513355273079)36.1901551301, 78.9723181345, -85.7248772254
3given(-0.99644664795, -0.082580503283, -0.0165691963024), (-0.0437413480369, 0.675487075491, -0.736073301592), (0.0719775816522, -0.732733015035, -0.676699014642)-19.394922266, 23.2304981884, 61.5624374385
4given(-0.989674348766, -0.1278481036, 0.0648039026583), (0.0668821430384, -0.811784998344, -0.580113691794), (0.126773271381, -0.569789416249, 0.811953544726)-60.2038381798, 151.393950076, 50.9920279169
5given(0.956650090111, 0.152838106929, -0.247913529604), (-0.239362938727, -0.0723097244986, -0.968233797854), (-0.165909579753, 0.985602260962, -0.0325913260336)32.2325852928, 76.8544239707, -86.9950858192
6given(-0.979495477154, -0.19925673576, -0.0297550582087), (-0.126623251015, 0.72374587108, -0.678349811231), (0.156700869611, -0.660672889825, -0.734136343)-12.7430613648, 18.4082218658, 60.3204673038

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
RAF proto-oncogene serine/threonine-protein kinase / Proto-oncogene c-RAF / cRaf / Raf-1


Mass: 32005.803 Da / Num. of mol.: 4 / Mutation: Y340D, Y341D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04049, non-specific serine/threonine protein kinase
#2: Protein
Dual specificity mitogen-activated protein kinase kinase 1 / MAP kinase kinase 1 / MAPKK 1 / MKK1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK 1


Mass: 43576.039 Da / Num. of mol.: 4 / Mutation: S218A, S222A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q02750, mitogen-activated protein kinase kinase

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Non-polymers , 4 types, 20 molecules

#3: Chemical
ChemComp-324 / N-{3-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)carbonyl]-2,4-difluorophenyl}propane-1-sulfonamide


Mass: 413.826 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H14ClF2N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CHU / N-(3-fluoro-4-{[4-methyl-2-oxo-7-(pyrimidin-2-yloxy)-2H-chromen-3-yl]methyl}pyridin-2-yl)-N'-methylsulfuric diamide / CH5126766


Mass: 471.462 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H18FN5O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 0.1 M Sodium citrate pH 5.6, 4% Tacsimate pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 3.5→48.2 Å / Num. obs: 45366 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 96.69 Å2 / CC1/2: 0.997 / Net I/σ(I): 15.57
Reflection shellResolution: 3.5→3.58 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.09 / Num. unique obs: 3155 / CC1/2: 0.726 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→48.03 Å / SU ML: 0.4265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2537 2269 5 %
Rwork0.2054 43094 -
obs0.2078 45363 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.27 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18490 0 364 8 18862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003619277
X-RAY DIFFRACTIONf_angle_d0.824626046
X-RAY DIFFRACTIONf_chiral_restr0.05292834
X-RAY DIFFRACTIONf_plane_restr0.00613289
X-RAY DIFFRACTIONf_dihedral_angle_d15.94697344
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.35045875891
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.02628572135
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.84573647392
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.05705329816
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.993251639647
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.917927692811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.570.34021320.28862502X-RAY DIFFRACTION94.54
3.57-3.660.34061390.26312657X-RAY DIFFRACTION99.86
3.66-3.750.30311400.24142644X-RAY DIFFRACTION100
3.75-3.850.3291390.22942655X-RAY DIFFRACTION99.93
3.85-3.960.26241400.22162660X-RAY DIFFRACTION99.89
3.96-4.090.26871400.22452660X-RAY DIFFRACTION99.82
4.09-4.240.27261410.2142667X-RAY DIFFRACTION99.75
4.24-4.40.2481400.18512672X-RAY DIFFRACTION99.79
4.41-4.610.24871410.18382677X-RAY DIFFRACTION99.68
4.61-4.850.27081410.18942665X-RAY DIFFRACTION99.68
4.85-5.150.22951420.19582705X-RAY DIFFRACTION99.65
5.15-5.550.23941420.19712700X-RAY DIFFRACTION99.89
5.55-6.110.27091440.21072730X-RAY DIFFRACTION99.9
6.11-6.990.27811440.21762752X-RAY DIFFRACTION99.93
6.99-8.790.20841470.1882789X-RAY DIFFRACTION99.76
8.8-48.030.21011570.18762959X-RAY DIFFRACTION99.3

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