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- PDB-8r7c: MutSbeta bound to compound CHDI-00915542 in the canonical DNA-mis... -

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Basic information

Entry
Database: PDB / ID: 8r7c
TitleMutSbeta bound to compound CHDI-00915542 in the canonical DNA-mismatch bound form
Components
  • (DNA mismatch repair protein ...) x 2
  • DNA (5'-D(*CP*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*G)-3')
  • DNA (5'-D(P*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')
  • DNA (5'-D(P*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
KeywordsDNA BINDING PROTEIN / PROTEROS BIOSTRUCTURES GMBH / DNA mismatch Repair
Function / homology
Function and homology information


somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 / MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / positive regulation of helicase activity / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / B cell mediated immunity ...somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 / MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / positive regulation of helicase activity / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / B cell mediated immunity / maintenance of DNA repeat elements / positive regulation of isotype switching to IgA isotypes / centromeric DNA binding / positive regulation of isotype switching to IgG isotypes / mitotic recombination / mismatched DNA binding / negative regulation of DNA recombination / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / oxidative phosphorylation / response to UV-B / postreplication repair / mitotic intra-S DNA damage checkpoint signaling / ATP-dependent DNA damage sensor activity / germ cell development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ATP-dependent activity, acting on DNA / response to X-ray / somatic hypermutation of immunoglobulin genes / mismatch repair / B cell differentiation / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / male gonad development / double-strand break repair / double-stranded DNA binding / negative regulation of neuron apoptotic process / in utero embryonic development / damaged DNA binding / chromosome, telomeric region / DNA repair / chromatin binding / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV ...DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / : / DNA / DNA (> 10) / DNA mismatch repair protein Msh3 / DNA mismatch repair protein Msh2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsThomsen, M. / Thieulin-Pardo, G. / Steinbacher, S. / Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. ...Thomsen, M. / Thieulin-Pardo, G. / Steinbacher, S. / Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. / Ballantyne, G. / Lee, J.-H. / Witte, D. / Finley, M. / Prasad, B. / Monteagudo, E. / Plotnikov, N. / Pacifici, R. / Maillard, M. / Wilkinson, H. / Iyer, R. / Dominguez, C. / Vogt, T. / Felsenfeld, D. / Haque, T.
Funding support United States, 1items
OrganizationGrant numberCountry
CHDI Foundation United States
CitationJournal: Chemrxiv / Year: 2024
Title: Identification of orthosteric inhibitors of MutSbeta ATPase function
Authors: Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. / Ballantyne, G. / Lee, J.-H. / Thieulin-Pardo, G. / Steinbacher, S. / Thomsen, M. / Witte, D. ...Authors: Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. / Ballantyne, G. / Lee, J.-H. / Thieulin-Pardo, G. / Steinbacher, S. / Thomsen, M. / Witte, D. / Finley, M. / Prasad, B. / Monteagudo, E. / Plotnikov, N. / Pacifici, R. / Maillard, M. / Wilkinson, H. / Iyer, R. / Dominguez, C. / Vogt, T. / Felsenfeld, D. / Haque, T.
History
DepositionNov 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA mismatch repair protein Msh2
B: DNA mismatch repair protein Msh3
C: DNA (5'-D(P*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
D: DNA (5'-D(*CP*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*G)-3')
E: DNA mismatch repair protein Msh2
F: DNA mismatch repair protein Msh3
G: DNA (5'-D(P*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
H: DNA (5'-D(P*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,09320
Polymers446,8588
Non-polymers2,23512
Water1,24369
1
A: DNA mismatch repair protein Msh2
B: DNA mismatch repair protein Msh3
C: DNA (5'-D(P*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
D: DNA (5'-D(*CP*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,59610
Polymers223,4224
Non-polymers1,1756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-158 kcal/mol
Surface area81940 Å2
MethodPISA
2
E: DNA mismatch repair protein Msh2
F: DNA mismatch repair protein Msh3
G: DNA (5'-D(P*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
H: DNA (5'-D(P*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,49710
Polymers223,4374
Non-polymers1,0606
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15970 Å2
ΔGint-161 kcal/mol
Surface area81470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.222, 104.789, 121.263
Angle α, β, γ (deg.)110.029, 91.198, 110.501
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
32B
42F
53C
63G
74D
84H

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
111GLUGLUILEILEAA12 - 93012 - 930
221GLUGLUILEILEEE12 - 93012 - 930
332SERSERPHEPHEBB227 - 112611 - 910
442SERSERPHEPHEFF227 - 112611 - 910
553DCDCDGDGCC4 - 244 - 24
663DCDCDGDGGG4 - 244 - 24
774DCDCDADADD27 - 472 - 22
884DCDCDADAHH27 - 472 - 22

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8

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Components

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DNA mismatch repair protein ... , 2 types, 4 molecules AEBF

#1: Protein DNA mismatch repair protein Msh2


Mass: 104431.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Alignment does not recognize that ADP is residue 1001.
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43246
#2: Protein DNA mismatch repair protein Msh3


Mass: 104289.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20585

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DNA chain , 3 types, 4 molecules CGDH

#3: DNA chain DNA (5'-D(P*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')


Mass: 7345.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*CP*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*G)-3')


Mass: 7354.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(P*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')


Mass: 7369.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 81 molecules

#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-YKW / ~{N}-(4-chlorophenyl)-2-(4-ethylpiperazin-1-yl)pteridin-4-amine


Mass: 369.851 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20ClN7 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 MES pH 7.25; 0.2 M NH4 Acetate; 20- 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.82→112.46 Å / Num. obs: 73299 / % possible obs: 92.7 % / Redundancy: 2.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.047 / Rrim(I) all: 0.075 / Net I/σ(I): 5.5
Reflection shellResolution: 2.82→3.12 Å / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3665 / CC1/2: 0.701 / Rpim(I) all: 0.406 / Rrim(I) all: 0.66 / % possible all: 59.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→112.46 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.909 / SU B: 20.389 / SU ML: 0.367 / Cross valid method: FREE R-VALUE / ESU R Free: 0.478
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2305 3646 4.974 %
Rwork0.2013 69653 -
all0.203 --
obs-73299 70.106 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 66.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.228 Å2-0.237 Å20.342 Å2
2---0.072 Å2-0.212 Å2
3---0.436 Å2
Refinement stepCycle: LAST / Resolution: 2.82→112.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27707 1802 139 69 29717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01329392
X-RAY DIFFRACTIONr_bond_other_d0.0020.01727032
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.59940231
X-RAY DIFFRACTIONr_angle_other_deg1.1151.62761951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53853468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61623.2331302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.252154583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.515129
X-RAY DIFFRACTIONr_chiral_restr0.0480.24014
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0232130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026579
X-RAY DIFFRACTIONr_nbd_refined0.1480.25425
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1430.224712
X-RAY DIFFRACTIONr_nbtor_refined0.1480.213710
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.212848
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2572
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1260.217
X-RAY DIFFRACTIONr_nbd_other0.1460.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.24
X-RAY DIFFRACTIONr_mcbond_it2.6427.3513932
X-RAY DIFFRACTIONr_mcbond_other2.6427.3513933
X-RAY DIFFRACTIONr_mcangle_it4.5411.01517381
X-RAY DIFFRACTIONr_mcangle_other4.5411.01517381
X-RAY DIFFRACTIONr_scbond_it2.3727.74115460
X-RAY DIFFRACTIONr_scbond_other2.3727.74115461
X-RAY DIFFRACTIONr_scangle_it4.18411.59322850
X-RAY DIFFRACTIONr_scangle_other4.18411.59322851
X-RAY DIFFRACTIONr_lrange_it7.29186.23631645
X-RAY DIFFRACTIONr_lrange_other7.29186.23531646
X-RAY DIFFRACTIONr_ncsr_local_group_10.0420.059983
X-RAY DIFFRACTIONr_ncsr_local_group_20.0480.0510007
X-RAY DIFFRACTIONr_ncsr_local_group_30.0470.05453
X-RAY DIFFRACTIONr_ncsr_local_group_40.0220.05493
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.042210.05
12EX-RAY DIFFRACTIONLocal ncs0.042210.05
23BX-RAY DIFFRACTIONLocal ncs0.047960.05
24FX-RAY DIFFRACTIONLocal ncs0.047960.05
35CX-RAY DIFFRACTIONLocal ncs0.047240.05
36GX-RAY DIFFRACTIONLocal ncs0.047240.05
47DX-RAY DIFFRACTIONLocal ncs0.021810.05
48HX-RAY DIFFRACTIONLocal ncs0.021810.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.8910.24260.353153X-RAY DIFFRACTION2.0506
2.891-2.970.236320.347556X-RAY DIFFRACTION7.8067
2.97-3.0560.361770.3161336X-RAY DIFFRACTION19.3721
3.056-3.150.3281110.3062465X-RAY DIFFRACTION36.1442
3.15-3.2540.3161940.2913681X-RAY DIFFRACTION55.8438
3.254-3.3680.2712710.2684637X-RAY DIFFRACTION73.7158
3.368-3.4950.2982580.2485399X-RAY DIFFRACTION87.7598
3.495-3.6370.2473150.2335647X-RAY DIFFRACTION96.3789
3.637-3.7990.2363140.2115505X-RAY DIFFRACTION98.4103
3.799-3.9840.2222700.1925350X-RAY DIFFRACTION98.9262
3.984-4.1990.2022740.1755141X-RAY DIFFRACTION99.0307
4.199-4.4540.2152580.1624763X-RAY DIFFRACTION99.1313
4.454-4.7610.22300.1634536X-RAY DIFFRACTION99.3124
4.761-5.1410.2352200.174209X-RAY DIFFRACTION99.3049
5.141-5.6310.2492090.2023887X-RAY DIFFRACTION99.3451
5.631-6.2930.251780.233528X-RAY DIFFRACTION99.4899
6.293-7.2630.2541470.2223097X-RAY DIFFRACTION99.0837
7.263-8.8860.1951370.1822610X-RAY DIFFRACTION98.991
8.886-12.5280.159890.1552032X-RAY DIFFRACTION99.2978
12.528-112.460.201560.2331121X-RAY DIFFRACTION98.1651

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