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Basic information

Entry
Database: PDB / ID: 3vr9
TitleMitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum with the specific inhibitor flutolanil
Components
  • Cytochrome b-large subunit
  • Flavoprotein subunit of complex II
  • Iron-sulfur subunit of succinate dehydrogenase
  • Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Ascaris suum / membrane protein / reductase / mitochondrial membrane / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / mitochondrial membrane / 2 iron, 2 sulfur cluster binding ...respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit ...Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 3 helical TM bundles of succinate and fumarate reductases / 4Fe-4S dicluster domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / Rhinovirus 14, subunit 4 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / Ubiquitin-like (UB roll) / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EPH / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-FTN / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b large subunit, mitochondrial ...Chem-EPH / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-FTN / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b large subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit 1, mitochondrial / Succinate dehydrogenase [rhodoquinone] flavoprotein subunit 1, mitochondrial
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsShimizu, H. / Shiba, T. / Inaoka, D.K. / Osanai, A. / Kita, K. / Sakamoto, K. / Harada, S.
CitationJournal: To be Published
Title: Crystal structure of mitochondrial quinol-fumarate reductase from parasitic nematode Ascaris suum
Authors: Shimizu, H. / Shiba, T. / Inaoka, D.K. / Osanai, A. / Kita, K. / Sakamoto, K. / Harada, S.
History
DepositionApr 7, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Non-polymer description
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavoprotein subunit of complex II
B: Iron-sulfur subunit of succinate dehydrogenase
C: Cytochrome b-large subunit
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
E: Flavoprotein subunit of complex II
F: Iron-sulfur subunit of succinate dehydrogenase
G: Cytochrome b-large subunit
H: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,04324
Polymers282,3228
Non-polymers6,72116
Water00
1
A: Flavoprotein subunit of complex II
B: Iron-sulfur subunit of succinate dehydrogenase
C: Cytochrome b-large subunit
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,52212
Polymers141,1614
Non-polymers3,3618
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21470 Å2
ΔGint-176 kcal/mol
Surface area42280 Å2
MethodPISA
2
E: Flavoprotein subunit of complex II
F: Iron-sulfur subunit of succinate dehydrogenase
G: Cytochrome b-large subunit
H: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,52212
Polymers141,1614
Non-polymers3,3618
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21950 Å2
ΔGint-177 kcal/mol
Surface area42170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.011, 135.333, 220.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Flavoprotein subunit of complex II / Rhodoquinol-fumarate reductase Fp subunit


Mass: 71304.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / Organelle: mitochondria / References: UniProt: Q33862
#2: Protein Iron-sulfur subunit of succinate dehydrogenase / Rhodoquinol-fumarate reductase Ip subunit


Mass: 31673.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / Organelle: mitochondria / References: UniProt: O44074
#3: Protein Cytochrome b-large subunit / Rhodoquinol-fumarate reductase CybL subunit


Mass: 21168.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / Organelle: mitochondria / References: UniProt: P92506
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Rhodoquinol-fumarate reductase CybS subunit / CybS / Cytochrome b558 small subunit / Succinate- ...Rhodoquinol-fumarate reductase CybS subunit / CybS / Cytochrome b558 small subunit / Succinate-ubiquinone reductase membrane anchor subunit


Mass: 17014.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / Organelle: mitochondria / References: UniProt: P92507

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Non-polymers , 8 types, 16 molecules

#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#9: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#10: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-FTN / N-[3-(1-methylethoxy)phenyl]-2-(trifluoromethyl)benzamide / flutolanil / N-(3-Isopropoxy-phenyl)-2-trifluoromethylbenzamide


Mass: 323.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16F3NO2
#12: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE


Mass: 709.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM

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Details

Has protein modificationY

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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: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 8.4
Details: 15% (w/v) PEG 3350, 100mM Tris-HCl pH 8.4, 200mM NaCl, 1mM sodium malonate, 0.06% (w/v) C12E8, 0.04% (w/v) C12M , MICRODIALYSIS, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 16, 2005 / Details: monochromator
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 68310 / Num. obs: 68310 / % possible obs: 92.6 % / Observed criterion σ(F): -0.5 / Redundancy: 4.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.23 / % possible all: 64.6

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZOY

1zoy


Resolution: 3.01→47.39 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / SU B: 23.298 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27743 3245 4.8 %RANDOM
Rwork0.21587 ---
obs0.21879 65024 100 %-
all-68310 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 3.01→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17884 0 378 0 18262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02218730
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.651.99225448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17552280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77823.24784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.456153114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.54615124
X-RAY DIFFRACTIONr_chiral_restr0.1090.22754
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.511360
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.036218270
X-RAY DIFFRACTIONr_scbond_it1.20237370
X-RAY DIFFRACTIONr_scangle_it2.0834.57096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.012→3.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 167 -
Rwork0.35 3145 -
obs--100 %

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