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- PDB-6hwh: Structure of a functional obligate respiratory supercomplex from ... -

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Entry
Database: PDB / ID: 6hwh
TitleStructure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis
Components
  • (Co-purified unknown peptide built as ...) x 2
  • (Co-purified unknown transmembrane helices built as ...) x 2
  • (Cytochrome c oxidase subunit ...) x 3
  • (Ubiquinol-cytochrome ...) x 2
  • Cytochrome bc1 complex cytochrome c subunit
  • Cytochrome c oxidase polypeptide 4
  • MSMEG_4693
  • Uncharacterized protein MSMEG_4692/MSMEI_4575
KeywordsELECTRON TRANSPORT / Membrane Protein / Cryo-EM / Respiratory supercomplex / Mycobacterium
Function / homology
Function and homology information


aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / : / respiratory electron transport chain / electron transport chain ...aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / : / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV / QcrA subunit N-terminal region / Cytochrome b(N-terminal)/b6/petB / Cytochrome c oxidase, subunit I bacterial type / : ...Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV / QcrA subunit N-terminal region / Cytochrome b(N-terminal)/b6/petB / Cytochrome c oxidase, subunit I bacterial type / : / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Cytochrome c / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-AS / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 / Probable cytochrome c oxidase subunit 3 / Cytochrome bc1 complex cytochrome c subunit / Cytochrome bc1 complex Rieske iron-sulfur subunit ...CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-AS / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 / Probable cytochrome c oxidase subunit 3 / Cytochrome bc1 complex cytochrome c subunit / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome b subunit / Cytochrome c oxidase polypeptide 4 / cytochrome-c oxidase / Cytochrome c oxidase subunit 1 / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Uncharacterized protein / Cytochrome bc1 complex cytochrome b subunit
Similarity search - Component
Biological speciesMycobacterium smegmatis MC2 155 (bacteria)
Mycobacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWiseman, B. / Nitharwal, R.G. / Fedotovskaya, O. / Schafer, J. / Guo, H. / Kuang, Q. / Benlekbir, S. / Sjostrand, D. / Adelroth, P. / Rubinstein, J.L. ...Wiseman, B. / Nitharwal, R.G. / Fedotovskaya, O. / Schafer, J. / Guo, H. / Kuang, Q. / Benlekbir, S. / Sjostrand, D. / Adelroth, P. / Rubinstein, J.L. / Brzezinski, P. / Hogbom, M.
Funding support Canada, Sweden, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health ResearchMOP 81294 Canada
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structure of a functional obligate complex IIIIV respiratory supercomplex from Mycobacterium smegmatis.
Authors: Benjamin Wiseman / Ram Gopal Nitharwal / Olga Fedotovskaya / Jacob Schäfer / Hui Guo / Qie Kuang / Samir Benlekbir / Dan Sjöstrand / Pia Ädelroth / John L Rubinstein / Peter Brzezinski / Martin Högbom /
Abstract: In the mycobacterial electron-transport chain, respiratory complex III passes electrons from menaquinol to complex IV, which in turn reduces oxygen, the terminal acceptor. Electron transfer is ...In the mycobacterial electron-transport chain, respiratory complex III passes electrons from menaquinol to complex IV, which in turn reduces oxygen, the terminal acceptor. Electron transfer is coupled to transmembrane proton translocation, thus establishing the electrochemical proton gradient that drives ATP synthesis. We isolated, biochemically characterized, and determined the structure of the obligate IIIIV supercomplex from Mycobacterium smegmatis, a model for Mycobacterium tuberculosis. The supercomplex has quinol:O oxidoreductase activity without exogenous cytochrome c and includes a superoxide dismutase subunit that may detoxify reactive oxygen species produced during respiration. We found menaquinone bound in both the Q and Q sites of complex III. The complex III-intrinsic diheme cytochrome cc subunit, which functionally replaces both cytochrome c and soluble cytochrome c in canonical electron-transport chains, displays two conformations: one in which it provides a direct electronic link to complex IV and another in which it serves as an electrical switch interrupting the connection.
History
DepositionOct 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 6, 2019Group: Data collection / Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria

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Assembly

Deposited unit
A: Ubiquinol-cytochrome c reductase iron-sulfur subunit
G: Co-purified unknown transmembrane helices built as polyALA
H: Co-purified unknown transmembrane helices built as polyALA
I: Co-purified unknown peptide built as polyALA
J: Co-purified unknown peptide built as polyALA
M: Cytochrome bc1 complex cytochrome c subunit
P: Cytochrome c oxidase subunit 2
R: MSMEG_4693
T: Uncharacterized protein MSMEG_4692/MSMEI_4575
V: Cytochrome c oxidase subunit 1
X: Cytochrome c oxidase polypeptide 4
Z: Cytochrome c oxidase subunit 3
b: Ubiquinol-cytochrome C reductase QcrB
B: Ubiquinol-cytochrome c reductase iron-sulfur subunit
C: Co-purified unknown transmembrane helices built as polyALA
D: Co-purified unknown transmembrane helices built as polyALA
E: Co-purified unknown peptide built as polyALA
F: Co-purified unknown peptide built as polyALA
K: Cytochrome bc1 complex cytochrome c subunit
L: Cytochrome c oxidase subunit 2
N: MSMEG_4693
O: Uncharacterized protein MSMEG_4692/MSMEI_4575
Q: Cytochrome c oxidase subunit 1
S: Cytochrome c oxidase polypeptide 4
W: Cytochrome c oxidase subunit 3
Y: Ubiquinol-cytochrome C reductase QcrB
i: Cytochrome bc1 complex cytochrome c subunit
j: Cytochrome bc1 complex cytochrome c subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)710,29660
Polymers686,08628
Non-polymers24,21032
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, native gel electrophoresis, microscopy, negative staining and cryo
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
2
A: Ubiquinol-cytochrome c reductase iron-sulfur subunit
G: Co-purified unknown transmembrane helices built as polyALA
H: Co-purified unknown transmembrane helices built as polyALA
I: Co-purified unknown peptide built as polyALA
J: Co-purified unknown peptide built as polyALA
M: Cytochrome bc1 complex cytochrome c subunit
P: Cytochrome c oxidase subunit 2
R: MSMEG_4693
T: Uncharacterized protein MSMEG_4692/MSMEI_4575
V: Cytochrome c oxidase subunit 1
X: Cytochrome c oxidase polypeptide 4
Z: Cytochrome c oxidase subunit 3
b: Ubiquinol-cytochrome C reductase QcrB
B: Ubiquinol-cytochrome c reductase iron-sulfur subunit
C: Co-purified unknown transmembrane helices built as polyALA
D: Co-purified unknown transmembrane helices built as polyALA
E: Co-purified unknown peptide built as polyALA
F: Co-purified unknown peptide built as polyALA
K: Cytochrome bc1 complex cytochrome c subunit
L: Cytochrome c oxidase subunit 2
N: MSMEG_4693
O: Uncharacterized protein MSMEG_4692/MSMEI_4575
Q: Cytochrome c oxidase subunit 1
S: Cytochrome c oxidase polypeptide 4
W: Cytochrome c oxidase subunit 3
Y: Ubiquinol-cytochrome C reductase QcrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)652,69155
Polymers630,33626
Non-polymers22,35429
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area157740 Å2
ΔGint-1432 kcal/mol
Surface area170610 Å2
MethodPISA

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Components

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Ubiquinol-cytochrome ... , 2 types, 4 molecules ABbY

#1: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 44869.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R051
#13: Protein Ubiquinol-cytochrome C reductase QcrB


Mass: 61271.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis MC2 155 (bacteria)
Gene: qcrB, MSMEI_4163 / Production host: Mycobacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7FGS8, UniProt: A0R052*PLUS, quinol-cytochrome-c reductase

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Co-purified unknown transmembrane helices built as ... , 2 types, 4 molecules GCHD

#2: Protein Co-purified unknown transmembrane helices built as polyALA


Mass: 6315.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis MC2 155 (bacteria)
#3: Protein Co-purified unknown transmembrane helices built as polyALA


Mass: 5549.833 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis MC2 155 (bacteria)

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Co-purified unknown peptide built as ... , 2 types, 4 molecules IEJF

#4: Protein/peptide Co-purified unknown peptide built as polyALA


Mass: 1720.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: chains M,K: transmembrane helix built and refined to density. chains i, j: homology model of soluble domain built as polyALA only rigid-body docked to density.
Source: (natural) Mycobacterium smegmatis MC2 155 (bacteria)
#5: Protein/peptide Co-purified unknown peptide built as polyALA


Mass: 2996.685 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis MC2 155 (bacteria)

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Protein , 4 types, 10 molecules MKijRNTOXS

#6: Protein
Cytochrome bc1 complex cytochrome c subunit


Mass: 27874.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: chains M,K: transmembrane helix built and refined into density chains i,j: homology model of the periplasmic soluble domain built as polyALA and rigid-body docked into low resolution density
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R050, quinol-cytochrome-c reductase
#8: Protein MSMEG_4693


Mass: 8365.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R1B6
#9: Protein Uncharacterized protein MSMEG_4692/MSMEI_4575


Mass: 15910.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R1B5
#11: Protein Cytochrome c oxidase polypeptide 4 / Cytochrome aa3 subunit 4 / Cytochrome c oxidase polypeptide IV


Mass: 15177.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R056, cytochrome-c oxidase

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Cytochrome c oxidase subunit ... , 3 types, 6 molecules PLVQZW

#7: Protein Cytochrome c oxidase subunit 2


Mass: 38077.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R057, cytochrome-c oxidase
#10: Protein Cytochrome c oxidase subunit 1


Mass: 64841.637 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R0M4, cytochrome-c oxidase
#12: Protein Cytochrome c oxidase subunit 3


Mass: 22196.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R049, cytochrome-c oxidase

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Non-polymers , 7 types, 32 molecules

#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#15: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#16: Chemical
ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C56H80O2
#17: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#18: Chemical
ChemComp-HAS / HEME-AS


Mass: 920.954 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C54H64FeN4O6
#19: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#20: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Respiratory Supercomplex from Mycobacterium smegmatis / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Molecular weightValue: 0.770 MDa / Experimental value: YES
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: deletion of the complex III operon qcrCAB (qcrCAB::hyg)
Cellular location: membrane
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 40 seconds at 20 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5316

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Processing

EM software
IDNameVersionCategory
4CTFFIND4CTF correction
7Coot0.8.9.1model fitting
8UCSF Chimera1.11.2model fitting
10Coot0.8.9.1model refinement
11PHENIX1.14-3228-000model refinement
13cryoSPARC2final Euler assignment
14cryoSPARC2classification
15cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 751329
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104198 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Model was built de novo; except for chains i,j which are polyALA homology models rigid-body docked into low resolution density.

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