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- PDB-2gtt: Crystal structure of the rabies virus nucleoprotein-RNA complex -

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Basic information

Entry
Database: PDB / ID: 2gtt
TitleCrystal structure of the rabies virus nucleoprotein-RNA complex
Components
  • (RNA (99-MER)) x 2
  • Nucleoprotein
KeywordsVIRAL PROTEIN / RNA BINDING PROTEIN / PROTEIN-RNA COMPLEX / RABIES VIRUS / NUCLEOPROTEIN
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / Rhabdovirus nucleoprotein-like / Nucleoprotein / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesLyssavirus rabies
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.49 Å
AuthorsAlbertini, A.A.V. / Wernimont, A.K. / Muziol, T. / Ravelli, R.B.G. / Weissenhorn, W. / Ruigrok, R.W.H.
CitationJournal: Science / Year: 2006
Title: Crystal Structure of the Rabies Virus Nucleoprotein-RNA Complex
Authors: Albertini, A.A.V. / Wernimont, A.K. / Muziol, T. / Ravelli, R.B.G. / Clapier, C.R. / Schoehn, G. / Weissenhorn, W. / Ruigrok, R.W.H.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Oct 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_database_status / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct / struct_asym / struct_biol / struct_conf / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation.wavelength_id / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly.type / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _entity_src_gen.entity_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_contact_author.phone / _pdbx_database_status.SG_entry / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_TLS_residual_ADP_flag / _refine.pdbx_diffrn_id / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _software.name / _software.version / _struct.pdbx_CASP_flag / _struct_ncs_dom.details / _struct_ncs_dom.id / _struct_ncs_dom.pdbx_ens_id / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_seq_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.dom_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ncs_dom_lim.pdbx_ens_id / _struct_ncs_dom_lim.pdbx_refine_code / _struct_ncs_ens.id / _struct_ref.db_code / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _symmetry.space_group_name_Hall
Description: Polymer backbone linkage
Details: Residues 35 to 103 and 189 to 200 were out of register
Provider: author / Type: Coordinate replacement
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 24CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).ADDITIONALLY THE BIOLOGICAL ASSEMBLY COULD ALSO BE CONSIDERED TO BE A SINGLE MONOMER IN COMPLEX WITH 9 NUCLEOTIDES (LIKE CHAIN G AND THE NUCLEIC ACIDS INTERACTING WITH IT).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein
I: Nucleoprotein
J: Nucleoprotein
K: Nucleoprotein
L: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
P: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein
S: Nucleoprotein
T: Nucleoprotein
U: Nucleoprotein
V: Nucleoprotein
W: RNA (99-MER)
X: RNA (99-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,176,43626
Polymers1,176,24624
Non-polymers1902
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)270.430, 281.000, 236.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 6 through 448)
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1(chain "K" and resid 6 through 448)
d_12ens_1(chain "L" and resid 6 through 448)
d_13ens_1(chain "M" and resid 6 through 448)
d_14ens_1chain "N"
d_15ens_1(chain "O" and resid 6 through 448)
d_16ens_1(chain "P" and resid 6 through 448)
d_17ens_1chain "Q"
d_18ens_1chain "R"
d_19ens_1chain "S"
d_20ens_1chain "T"
d_21ens_1chain "U"
d_22ens_1(chain "V" and resid 6 through 448)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILESERA1 - 418
d_21ens_1ILESERB2 - 419
d_31ens_1ILESERC1 - 418
d_41ens_1ILESERD1 - 418
d_51ens_1ILESERE1 - 418
d_61ens_1ILESERF1 - 418
d_71ens_1ILESERG1 - 418
d_81ens_1ILESERH1 - 418
d_91ens_1ILESERI1 - 418
d_101ens_1ILESERJ1 - 418
d_111ens_1ILESERK3 - 420
d_121ens_1ILESERL2 - 419
d_131ens_1ILESERM3 - 420
d_141ens_1ILESERN1 - 418
d_151ens_1ILESERO2 - 419
d_161ens_1ILESERP3 - 420
d_171ens_1ILESERQ1 - 418
d_181ens_1ILESERR1 - 418
d_191ens_1ILESERS1 - 418
d_201ens_1ILESERT1 - 418
d_211ens_1ILESERU1 - 418
d_221ens_1ILESERV2 - 419

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Components

#1: Protein ...
Nucleoprotein / Nucleocapsid protein


Mass: 50641.289 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus rabies / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HF / References: UniProt: A8VR20
#2: RNA chain RNA (99-MER)


Mass: 31153.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (99-MER)


Mass: 30984.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P0DOF3*PLUS
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% TACSIMATE, 10% L-CYSTEIN, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
160% TACSIMATE11
210% L-CYSTEIN11
3water11
460% TACSIMATE12

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9394
SYNCHROTRONESRF ID14-420.9794
SYNCHROTRONESRF ID14-431.0372
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDMar 25, 2005
ADSC QUANTUM 4r2CCDJul 10, 2005
ADSC QUANTUM 4r3CCDAug 29, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1silicon 111SINGLE WAVELENGTHMx-ray1
2silicon 111SINGLE WAVELENGTHMx-ray2
3silicon 111SINGLE WAVELENGTHMx-ray5
Radiation wavelength
IDWavelength (Å)Relative weight
10.93941
20.97941
31.03721
51
ReflectionResolution: 3.49→25 Å / Num. all: 222605 / Num. obs: 226155 / % possible obs: 99.9 % / Biso Wilson estimate: 103.61 Å2 / Rsym value: 0.096 / Net I/σ(I): 12.15
Reflection shellResolution: 3.49→3.63 Å / Mean I/σ(I) obs: 3.36 / Rsym value: 0.457 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
ProDCdata collection
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.49→49.75 Å / SU ML: 0.4048 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.7461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 11055 4.88 %RANDOM
Rwork0.2237 215443 --
obs0.2253 226498 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.1 Å2
Refinement stepCycle: LAST / Resolution: 3.49→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms73171 4103 10 0 77284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012879511
X-RAY DIFFRACTIONf_angle_d1.3464108344
X-RAY DIFFRACTIONf_chiral_restr0.075711997
X-RAY DIFFRACTIONf_plane_restr0.011613191
X-RAY DIFFRACTIONf_dihedral_angle_d13.545412454
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.03713343265
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.39191104661
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.39793975962
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.28656426339
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS1.21525619101
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS1.27465287969
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS1.49754258061
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS1.12927288833
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS1.15027308195
ens_1d_11AX-RAY DIFFRACTIONTorsion NCS1.4290615434
ens_1d_12AX-RAY DIFFRACTIONTorsion NCS1.12496771739
ens_1d_13AX-RAY DIFFRACTIONTorsion NCS1.57902576876
ens_1d_14AX-RAY DIFFRACTIONTorsion NCS0.950556727271
ens_1d_15AX-RAY DIFFRACTIONTorsion NCS1.1792334758
ens_1d_16AX-RAY DIFFRACTIONTorsion NCS1.08377693245
ens_1d_17AX-RAY DIFFRACTIONTorsion NCS1.41981700661
ens_1d_18AX-RAY DIFFRACTIONTorsion NCS1.1954308707
ens_1d_19AX-RAY DIFFRACTIONTorsion NCS1.43441438373
ens_1d_20AX-RAY DIFFRACTIONTorsion NCS1.26886127925
ens_1d_21AX-RAY DIFFRACTIONTorsion NCS1.53334912821
ens_1d_22AX-RAY DIFFRACTIONTorsion NCS1.18078348888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.5300.3296042X-RAY DIFFRACTION80.39
3.53-3.5700.30457557X-RAY DIFFRACTION99.97
3.57-3.6100.29217492X-RAY DIFFRACTION100
3.61-3.660.323712440.29266311X-RAY DIFFRACTION99.96
3.66-3.710.32182220.28527368X-RAY DIFFRACTION99.99
3.71-3.7600.27497536X-RAY DIFFRACTION100
3.76-3.8100.25977527X-RAY DIFFRACTION99.84
3.81-3.870.287413560.25556210X-RAY DIFFRACTION99.91
3.87-3.9300.24287498X-RAY DIFFRACTION99.99
3.93-3.9900.24427596X-RAY DIFFRACTION99.95
3.99-4.060.2812410.25396287X-RAY DIFFRACTION99.99
4.06-4.1400.24647578X-RAY DIFFRACTION100
4.14-4.2200.23957561X-RAY DIFFRACTION99.99
4.22-4.30.287811250.24856454X-RAY DIFFRACTION100
4.3-4.400.23717561X-RAY DIFFRACTION99.95
4.4-4.500.23157562X-RAY DIFFRACTION100
4.5-4.610.26069750.22286631X-RAY DIFFRACTION99.99
4.61-4.7400.22387578X-RAY DIFFRACTION99.99
4.74-4.880.27778440.22836746X-RAY DIFFRACTION99.93
4.88-5.0300.2197609X-RAY DIFFRACTION100
5.03-5.210.27237820.22526810X-RAY DIFFRACTION100
5.21-5.4200.21737627X-RAY DIFFRACTION99.97
5.42-5.670.2546400.21396955X-RAY DIFFRACTION99.99
5.67-5.9700.22327628X-RAY DIFFRACTION99.99
5.97-6.340.26325480.21467125X-RAY DIFFRACTION99.97
6.34-6.830.25124690.20917180X-RAY DIFFRACTION99.97
6.83-7.510.22423970.1897304X-RAY DIFFRACTION99.92
7.51-8.590.18233440.1617360X-RAY DIFFRACTION99.83
8.59-10.810.18134890.15797286X-RAY DIFFRACTION99.71
10.81-49.750.23743790.23117464X-RAY DIFFRACTION97.6
Refinement TLS params.Method: refined / Origin x: 202.620831295 Å / Origin y: 190.11480652 Å / Origin z: 59.4626671576 Å
111213212223313233
T0.846386352269 Å2-0.0187468718448 Å20.0213609611108 Å2-0.761484664636 Å2-0.00807108645615 Å2--0.667045037956 Å2
L0.0509553720839 °2-0.0068919853765 °20.0212251483112 °2-0.0748887927249 °2-0.0767334950694 °2--0.160741692111 °2
S-0.014181492141 Å °-0.0422436101718 Å °-0.0386472205158 Å °0.0607978135913 Å °0.00123730028194 Å °0.0139711461895 Å °0.071666529637 Å °-0.041834922266 Å °0.0114970655449 Å °
Refinement TLS groupSelection details: all

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