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Basic information

Entry
Database: PDB / ID: 2fug
TitleCrystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
Components
  • (NADH-quinone oxidoreductase chain ...) x 7
  • conserved hypothetical protein
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / RESPIRATORY CHAIN
Function / homology
Function and homology information


: / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdopterin cofactor binding / respiratory chain complex I / iron-sulfur cluster assembly / NADH dehydrogenase activity / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding ...: / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdopterin cofactor binding / respiratory chain complex I / iron-sulfur cluster assembly / NADH dehydrogenase activity / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / ferric iron binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / metal ion binding / plasma membrane
Similarity search - Function
NADH-quinone oxidoreductase subunit E / Alpha-Beta Plaits - #3270 / NADH-quinone oxidoreductase, subunit 15 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1450 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Rossmann fold - #12280 / Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily ...NADH-quinone oxidoreductase subunit E / Alpha-Beta Plaits - #3270 / NADH-quinone oxidoreductase, subunit 15 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1450 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Rossmann fold - #12280 / Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Metal Transport, Frataxin; Chain A / Frataxin/CyaY superfamily / de novo design (two linked rop proteins) / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Cro/C1-type helix-turn-helix domain / Soluble ligand binding domain / 2Fe-2S iron-sulfur cluster binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Aspartate decarboxylase-like domain superfamily / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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 / Helix non-globular / Special / Glutaredoxin / Glutaredoxin / Ubiquitin-like (UB roll) / Arc Repressor Mutant, subunit A / Thioredoxin-like superfamily / Alpha-Beta Plaits / Roll / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / : / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / : / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 15
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.3 Å
AuthorsSazanov, L.A. / Hinchliffe, P.
Citation
Journal: Science / Year: 2006
Title: Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus.
Authors: Sazanov, L.A. / Hinchliffe, P.
#1: Journal: Science / Year: 2005
Title: Organization of iron-sulfur clusters in respiratory complex I
Authors: Hinchliffe, P. / Sazanov, L.A.
History
DepositionJan 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: NADH-quinone oxidoreductase chain 1
2: NADH-quinone oxidoreductase chain 2
3: NADH-quinone oxidoreductase chain 3
4: NADH-quinone oxidoreductase chain 4
5: NADH-quinone oxidoreductase chain 5
6: NADH-quinone oxidoreductase chain 6
9: NADH-quinone oxidoreductase chain 9
7: conserved hypothetical protein
A: NADH-quinone oxidoreductase chain 1
B: NADH-quinone oxidoreductase chain 2
C: NADH-quinone oxidoreductase chain 3
D: NADH-quinone oxidoreductase chain 4
E: NADH-quinone oxidoreductase chain 5
F: NADH-quinone oxidoreductase chain 6
G: NADH-quinone oxidoreductase chain 9
H: conserved hypothetical protein
J: NADH-quinone oxidoreductase chain 1
K: NADH-quinone oxidoreductase chain 2
L: NADH-quinone oxidoreductase chain 3
M: NADH-quinone oxidoreductase chain 4
N: NADH-quinone oxidoreductase chain 5
O: NADH-quinone oxidoreductase chain 6
P: NADH-quinone oxidoreductase chain 9
Q: conserved hypothetical protein
S: NADH-quinone oxidoreductase chain 1
T: NADH-quinone oxidoreductase chain 2
U: NADH-quinone oxidoreductase chain 3
V: NADH-quinone oxidoreductase chain 4
W: NADH-quinone oxidoreductase chain 5
X: NADH-quinone oxidoreductase chain 6
Y: NADH-quinone oxidoreductase chain 9
Z: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,137,72372
Polymers1,124,64532
Non-polymers13,07840
Water00
1
1: NADH-quinone oxidoreductase chain 1
2: NADH-quinone oxidoreductase chain 2
3: NADH-quinone oxidoreductase chain 3
4: NADH-quinone oxidoreductase chain 4
5: NADH-quinone oxidoreductase chain 5
6: NADH-quinone oxidoreductase chain 6
9: NADH-quinone oxidoreductase chain 9
7: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,43118
Polymers281,1618
Non-polymers3,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37440 Å2
ΔGint-333 kcal/mol
Surface area82540 Å2
MethodPISA
2
A: NADH-quinone oxidoreductase chain 1
B: NADH-quinone oxidoreductase chain 2
C: NADH-quinone oxidoreductase chain 3
D: NADH-quinone oxidoreductase chain 4
E: NADH-quinone oxidoreductase chain 5
F: NADH-quinone oxidoreductase chain 6
G: NADH-quinone oxidoreductase chain 9
H: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,43118
Polymers281,1618
Non-polymers3,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37440 Å2
ΔGint-334 kcal/mol
Surface area82550 Å2
MethodPISA
3
J: NADH-quinone oxidoreductase chain 1
K: NADH-quinone oxidoreductase chain 2
L: NADH-quinone oxidoreductase chain 3
M: NADH-quinone oxidoreductase chain 4
N: NADH-quinone oxidoreductase chain 5
O: NADH-quinone oxidoreductase chain 6
P: NADH-quinone oxidoreductase chain 9
Q: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,43118
Polymers281,1618
Non-polymers3,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37430 Å2
ΔGint-328 kcal/mol
Surface area82490 Å2
MethodPISA
4
S: NADH-quinone oxidoreductase chain 1
T: NADH-quinone oxidoreductase chain 2
U: NADH-quinone oxidoreductase chain 3
V: NADH-quinone oxidoreductase chain 4
W: NADH-quinone oxidoreductase chain 5
X: NADH-quinone oxidoreductase chain 6
Y: NADH-quinone oxidoreductase chain 9
Z: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,43118
Polymers281,1618
Non-polymers3,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37500 Å2
ΔGint-334 kcal/mol
Surface area82440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.080, 266.112, 201.731
Angle α, β, γ (deg.)90.00, 104.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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NADH-quinone oxidoreductase chain ... , 7 types, 28 molecules 1AJS2BKT3CLU4DMV5ENW6FOX9GPY

#1: Protein
NADH-quinone oxidoreductase chain 1 / NADH dehydrogenase I / chain 1 / NDH-1 / chain 1


Mass: 48693.715 Da / Num. of mol.: 4 / Fragment: Hydrophilic domain / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56222, NADH dehydrogenase (quinone)
#2: Protein
NADH-quinone oxidoreductase chain 2 / NADH dehydrogenase I / chain 2 / NDH-1 / chain 2


Mass: 20309.162 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56221, NADH dehydrogenase (quinone)
#3: Protein
NADH-quinone oxidoreductase chain 3 / NADH dehydrogenase I / chain 3 / NDH-1 / chain 3


Mass: 86656.203 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56223, NADH dehydrogenase (quinone)
#4: Protein
NADH-quinone oxidoreductase chain 4 / NADH dehydrogenase I / chain 4 / NDH-1 / chain 4


Mass: 46428.027 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56220, NADH dehydrogenase (quinone)
#5: Protein
NADH-quinone oxidoreductase chain 5 / NADH dehydrogenase I / chain 5 / NDH-1 / chain 5


Mass: 23893.254 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56219, NADH dehydrogenase (quinone)
#6: Protein
NADH-quinone oxidoreductase chain 6 / NADH dehydrogenase I / chain 6 / NDH-1 / chain 6


Mass: 20262.564 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56218, NADH dehydrogenase (quinone)
#7: Protein
NADH-quinone oxidoreductase chain 9 / NADH dehydrogenase I / chain 9 / NDH-1 / chain 9


Mass: 20106.309 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56224, NADH dehydrogenase (quinone)

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Protein , 1 types, 4 molecules 7HQZ

#8: Protein
conserved hypothetical protein


Mass: 14812.074 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771878, UniProt: Q5SKZ7*PLUS

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Non-polymers , 3 types, 40 molecules

#9: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2
#11: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P

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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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.4-0.5M NaCl, 0.1M CaCl2 and 8-10% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97564 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2004
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97564 Å / Relative weight: 1
ReflectionResolution: 3.3→29.988 Å / Num. all: 196320 / Num. obs: 195669 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.158 / Net I/σ(I): 6.1
Reflection shellResolution: 3.3→3.48 Å / % possible obs: 89.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.7 / Num. measured all: 84269 / Num. unique all: 26742 / Num. unique obs: 26742 / Rsym value: 0.552 / % possible all: 89.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.3→20 Å / Rfactor Rfree error: 0.005 / FOM work R set: 0.744 / Isotropic thermal model: isotropic restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The number of reflections used in refinement included two derivatives and Fe-edge, at lower resolution, were merged in SHARP during phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.298 3914 2 %random
Rwork0.265 ---
all0.265 195669 --
obs0.265 195669 95.3 %-
Displacement parametersBiso mean: 64.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.51 Å
Luzzati d res low-7 Å
Luzzati sigma a0.76 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms73536 0 380 0 73916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.63
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.1
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.396 342 1.9 %
Rwork0.399 17784 -
obs-17784 88.7 %

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