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- PDB-7aqq: Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core) -

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Entry
Database: PDB / ID: 7aqq
TitleCryo-EM structure of Arabidopsis thaliana Complex-I (membrane core)
Components
  • (Gamma carbonic anhydrase ...) x 2
  • (NADH dehydrogenase ...) x 5
  • (NADH-ubiquinone oxidoreductase chain ...) x 6
  • AT3G07480.1
  • At2g46540/F11C10.23
  • At4g16450
  • Excitatory amino acid transporter
  • Gamma carbonic anhydrase-like 2, mitochondrial
  • P1
  • Uncharacterized protein At2g27730, mitochondrial
  • unknown
KeywordsELECTRON TRANSPORT / Complex-I
Function / homology
Function and homology information


anther dehiscence / vegetative to reproductive phase transition of meristem / NADH dehydrogenase complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / respiratory chain complex I ...anther dehiscence / vegetative to reproductive phase transition of meristem / NADH dehydrogenase complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / respiratory chain complex I / regulation of reactive oxygen species metabolic process / plastid / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / protein homotrimerization / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / response to salt stress / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / peroxisome / mitochondrial inner membrane / copper ion binding / nucleolus / mitochondrion / extracellular region / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 ...At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / Hexapeptide repeat / GRIM-19 / GRIM-19 protein / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / Bacterial transferase hexapeptide (six repeats) / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Trimeric LpxA-like superfamily / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / CHCH domain / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
: / Chem-PC7 / Chem-PGT / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLETHANOLAMINE / Phosphatidylinositol / Ubiquinone-9 / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L ...: / Chem-PC7 / Chem-PGT / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLETHANOLAMINE / Phosphatidylinositol / Ubiquinone-9 / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / At4g16450 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Excitatory amino acid transporter / Gamma carbonic anhydrase 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / Gamma carbonic anhydrase-like 2, mitochondrial / At2g46540/F11C10.23 / Uncharacterized protein At2g27730, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsKlusch, N. / Kuehlbrandt, W. / Yildiz, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Plant Cell / Year: 2021
Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.
History
DepositionOct 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase chain 3
H: NADH-ubiquinone oxidoreductase chain 1
J: NADH-ubiquinone oxidoreductase chain 6
K: NADH dehydrogenase subunit 4L
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
N: NADH-ubiquinone oxidoreductase chain 2
O: AT3G07480.1
X: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
Z: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
b: At2g46540/F11C10.23
d: Excitatory amino acid transporter
e: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
f: At4g16450
i: P1
u: unknown
v: Uncharacterized protein At2g27730, mitochondrial
x: Gamma carbonic anhydrase-like 2, mitochondrial
y: Gamma carbonic anhydrase 2, mitochondrial
z: Gamma carbonic anhydrase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,95431
Polymers475,70821
Non-polymers6,24610
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules AHJLMN

#1: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 13941.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P92533, NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 36020.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: B5TM92, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 23690.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: A0A2P2CLG1, NADH:ubiquinone reductase (H+-translocating)
#5: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 74497.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: B5TM94, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 56055.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: B5TM93, NADH:ubiquinone reductase (H+-translocating)
#7: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 55486.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: O05000, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase ... , 5 types, 5 molecules KXZae

#4: Protein NADH dehydrogenase subunit 4L /


Mass: 11165.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A2P2CLH7
#9: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B


Mass: 11985.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LGE7
#10: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Protein MATERNAL EFFECT EMBRYO ARREST 4


Mass: 16145.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8RWA7
#11: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 7349.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C9Z5
#14: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B


Mass: 9914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LZI6

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Protein , 7 types, 7 molecules Obdfivx

#8: Protein AT3G07480.1


Mass: 17626.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A384LA38
#12: Protein At2g46540/F11C10.23 / Expressed protein / F11C10.23/F11C10.23 / Fiber


Mass: 6810.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZPY5
#13: Protein Excitatory amino acid transporter


Mass: 9220.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94AL6
#15: Protein At4g16450 / NADH-ubiquinone oxidoreductase


Mass: 11355.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q84W12
#16: Protein P1


Mass: 11808.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178W1I8
#18: Protein Uncharacterized protein At2g27730, mitochondrial


Mass: 11965.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZUX4
#19: Protein Gamma carbonic anhydrase-like 2, mitochondrial / GAMMA CAL2


Mass: 27985.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SMN1

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Protein/peptide , 1 types, 1 molecules u

#17: Protein/peptide unknown


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

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Gamma carbonic anhydrase ... , 2 types, 2 molecules yz

#20: Protein Gamma carbonic anhydrase 2, mitochondrial / GAMMA CA2 / Transcription factor APFI


Mass: 30102.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9C6B3, Lyases; Carbon-oxygen lyases; Hydro-lyases
#21: Protein Gamma carbonic anhydrase 1, mitochondrial / GAMMA CA1


Mass: 30010.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9FWR5, Lyases; Carbon-oxygen lyases; Hydro-lyases

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Non-polymers , 9 types, 10 molecules

#22: Chemical ChemComp-UQ9 / Ubiquinone-9 / 2,3-dimethoxy-5-methyl-6-[(2E,6E,10E,14Z,18E,22E,26E,30Z)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18 ,22,26,30,34-nonaen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 795.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H82O4
#23: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#24: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#25: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#26: Chemical ChemComp-PC7 / (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 1-PALMITOYL-2-STEAROYL-PC / Phosphatidylcholine


Mass: 763.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#27: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#28: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT) / Phosphatidylglycerol


Mass: 751.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#29: Chemical ChemComp-PSF / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLSERINE / Phosphatidylserine


Mass: 455.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34NO10P
#30: Chemical ChemComp-T7X / Phosphatidylinositol / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H83O13P

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Details

Has ligand of interestN

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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: Arabidopsis complex I - membrane core / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459177 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00323819
ELECTRON MICROSCOPYf_angle_d0.53632232
ELECTRON MICROSCOPYf_dihedral_angle_d7.8353347
ELECTRON MICROSCOPYf_chiral_restr0.0413674
ELECTRON MICROSCOPYf_plane_restr0.0043961

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