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- PDB-5xtb: Cryo-EM structure of human respiratory complex I matrix arm -

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Entry
Database: PDB / ID: 5xtb
TitleCryo-EM structure of human respiratory complex I matrix arm
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 7
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 6
  • Acyl carrier protein, mitochondrial
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / Respiratory / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homologyThioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase flavoprotein 3 / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase subunit D/H ...Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase flavoprotein 3 / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase subunit D/H / [NiFe]-hydrogenase, large subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / 2Fe-2S ferredoxin-like superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Acyl carrier protein (ACP) / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Phosphopantetheine attachment site / Molybdopterin oxidoreductase / ETC complex I subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Ribosomal protein/NADH dehydrogenase domain / Complex 1 LYR protein / NADH-quinone oxidoreductase, chain G, C-terminal / Phosphopantetheine binding ACP domain / GRIM-19 / NADH:ubiquinone oxidoreductase subunit B14.5a / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase, chain I / NADH:ubiquinone oxidoreductase, subunit G / NADH ubiquinone oxidoreductase, F subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Carrier protein (CP) domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / 3-beta hydroxysteroid dehydrogenase/isomerase family / NmrA-like family / NAD(P)H-binding / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / Molybdopterin oxidoreductase / Complex 1 protein (LYR family) / Phosphopantetheine attachment site / NADH ubiquinone oxidoreductase, 20 Kd subunit / NAD dependent epimerase/dehydratase family / Respiratory-chain NADH dehydrogenase 51 Kd subunit / ETC complex I subunit conserved region / ETC complex I subunit conserved region / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NADH ubiquinone oxidoreductase subunit NDUFA12 / GRIM-19 protein / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Zinc-finger domain / SLBB domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / 4Fe-4S dicluster domain / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Phosphopantetheine attachment site. / NADH-quinone oxidoreductase subunit E-like / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NAD-dependent epimerase/dehydratase / NADH-quinone oxidoreductase, subunit D / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / positive regulation of peptidase activity / ubiquinone-6 biosynthetic process / reproductive system development / protein import into mitochondrial inner membrane / NADH dehydrogenase (ubiquinone)
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsGu, J. / Wu, M. / Yang, M.
CitationJournal: Cell / Year: 2017
Title: Architecture of Human Mitochondrial Respiratory Megacomplex IIIIIV.
Authors: Runyu Guo / Shuai Zong / Meng Wu / Jinke Gu / Maojun Yang
Abstract: The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, ...The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-IIIIIV (MCIIIIIV) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCIIIIIV forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 18, 2017 / Release: Aug 30, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 30, 2017Structure modelrepositoryInitial release
1.1Sep 6, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
1.2Dec 6, 2017Structure modelData processing / Database referencescitation / em_software_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
E: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
F: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
G: Acyl carrier protein, mitochondrial
H: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
I: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
J: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
K: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
L: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
M: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
N: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
O: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
P: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
T: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,62229
Polyers397,41818
Non-polymers4,20411
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)87770
ΔGint (kcal/M)-505
Surface area (Å2)125730

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Components

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules AKO

#1: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-51kD / CI-51kD / NADH dehydrogenase flavoprotein 1 / NADH-ubiquinone oxidoreductase 51 kDa subunit


Mass: 47323.938 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-457 / Source: (natural) Homo sapiens (human)
References: UniProt: P49821, NADH dehydrogenase (ubiquinone), NADH dehydrogenase
#10: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Complex I-9kD / CI-9kD / NADH-ubiquinone oxidoreductase 9 kDa subunit / Renal carcinoma antigen NY-REN-4


Mass: 3900.312 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 74-106 / Source: (natural) Homo sapiens (human) / References: UniProt: P56181
#14: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 24 kDa subunit


Mass: 23430.881 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 36-247 / Source: (natural) Homo sapiens (human)
References: UniProt: P19404, NADH dehydrogenase (ubiquinone), NADH dehydrogenase

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 6 types, 6 molecules BCLPQT

#2: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Complex I-23kD / CI-23kD / NADH-ubiquinone oxidoreductase 23 kDa subunit / TYKY subunit


Mass: 20314.037 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: O00217, NADH dehydrogenase (ubiquinone), NADH dehydrogenase
#3: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / CI-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit / PSST subunit


Mass: 17887.928 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 58-213 / Source: (natural) Homo sapiens (human)
References: UniProt: O75251, NADH dehydrogenase (ubiquinone), NADH dehydrogenase
#11: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / CI-18 kDa / Complex I-AQDQ / CI-AQDQ / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 13721.598 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 58-175 / Source: (natural) Homo sapiens (human) / References: UniProt: O43181
#15: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Complex I-30kD / CI-30kD / NADH-ubiquinone oxidoreductase 30 kDa subunit


Mass: 24432.656 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 43-250 / Source: (natural) Homo sapiens (human)
References: UniProt: O75489, NADH dehydrogenase (ubiquinone), NADH dehydrogenase
#16: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / CI-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 43987.625 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 79-463 / Source: (natural) Homo sapiens (human)
References: UniProt: O75306, NADH dehydrogenase (ubiquinone), NADH dehydrogenase
#17: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Complex I-13kD-A / CI-13kD-A / NADH-ubiquinone oxidoreductase 13 kDa-A subunit


Mass: 10578.848 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O75380

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 7 types, 7 molecules EFHIJNW

#4: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / CI-B14 / LYR motif-containing protein 6 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 13758.070 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-154 / Source: (natural) Homo sapiens (human) / References: UniProt: P56556
#5: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Complex I-B8 / CI-B8 / NADH-ubiquinone oxidoreductase B8 subunit


Mass: 9535.905 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 14-96 / Source: (natural) Homo sapiens (human) / References: UniProt: O43678
#7: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Complex I subunit B13 / Complex I-13kD-B / CI-13kD-B / NADH-ubiquinone oxidoreductase 13 kDa-B subunit


Mass: 13119.208 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q16718
#8: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Complex I-B14.5a / CI-B14.5a / NADH-ubiquinone oxidoreductase subunit B14.5a


Mass: 12282.051 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 4-113 / Source: (natural) Homo sapiens (human) / References: UniProt: O95182
#9: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / CI-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 38387.594 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 40-375 / Source: (natural) Homo sapiens (human) / References: UniProt: Q16795
#13: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / 13 kDa differentiation-associated protein / Complex I-B17.2 / CIB17.2 / NADH-ubiquinone oxidoreductase subunit B17.2


Mass: 16880.068 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UI09
#18: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic and interferon-induced mortality 19 protein / Gene associated with retinoic and IFN-induced mortality 19 protein / NADH-ubiquinone oxidoreductase B16.6 subunit


Mass: 2560.952 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 7-28 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J0

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Protein/peptide , 2 types, 2 molecules GM

#6: Protein/peptide Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 9845.247 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O14561
#12: Protein/peptide NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Complex I-75kD / CI-75kD


Mass: 75471.484 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-716 / Source: (natural) Homo sapiens (human)
References: UniProt: P28331, NADH dehydrogenase (ubiquinone), NADH dehydrogenase

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Non-polymers , 5 types, 11 molecules

#19: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Formula: Fe4S4
#20: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Formula: C17H21N4O9P / Flavin mononucleotide
#21: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Formula: C23H45N2O8PS
#22: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Formula: C21H30N7O17P3
#23: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human respiratory complex I matrix arm / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.2 mg/ml / Embedding 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2.1particle selection
2AutoEMation2.0image acquisition
4CTFFIND3.0CTF correction
7Coot0.8.2model fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIX1.11.1model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 167761 / Symmetry type: POINT

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