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Entry
Database: PDB / ID: 7wff
TitleSubcomplexes B,M and L in the Cylic electron transfer supercomplex NDH-PSI from Arabidopsis
Components
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 6
  • (Photosynthetic NDH subunit of lumenal location ...) x 4
  • (Photosynthetic NDH subunit of subcomplex B ...) x 4
  • Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplastic
  • NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
  • NDH dependent flow 6
KeywordsELECTRON TRANSPORT / Subcomplex B / subcomplex M / subcomplex L / Arabidopisis / plant / cyclic electron transport supercomplex
Function / homology
Function and homology information


NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / chloroplast stromal thylakoid / thylakoid lumen / protein histidine kinase binding / chloroplast membrane / ubiquinone biosynthetic process / P450-containing electron transport chain ...NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / chloroplast stromal thylakoid / thylakoid lumen / protein histidine kinase binding / chloroplast membrane / ubiquinone biosynthetic process / P450-containing electron transport chain / chloroplast thylakoid / NADPH dehydrogenase activity / chloroplast thylakoid lumen / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosystem II oxygen evolving complex / photosynthetic electron transport in photosystem I / thylakoid / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plastid / extrinsic component of membrane / photosynthesis, light reaction / chloroplast thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / photosynthesis / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 2 iron, 2 sulfur cluster binding / protein folding / carbohydrate binding / response to oxidative stress / carbohydrate metabolic process / calcium ion binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Photosynthetic NDH subunit of subcomplex B 4, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of lumenal location 4-like / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / : / PsbP, C-terminal / PsbP / : / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus ...Photosynthetic NDH subunit of subcomplex B 4, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of lumenal location 4-like / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / : / PsbP, C-terminal / PsbP / : / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / NADH-quinone oxidoreductase chain 4 / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / Mog1/PsbP, alpha/beta/alpha sandwich / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Glycoside hydrolase-type carbohydrate-binding / 2Fe-2S iron-sulfur cluster binding domain / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / Galactose mutarotase-like domain superfamily / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / 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-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain 5-like / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / NADH:ubiquinone oxidoreductase / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Cyclophilin-like domain superfamily / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Beta-grasp domain superfamily / Peptidyl-prolyl cis-trans isomerase domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-SQD / NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NDH dependent flow 6 / Photosynthetic NDH subunit of lumenal location 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic ...FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-SQD / NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NDH dependent flow 6 / Photosynthetic NDH subunit of lumenal location 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / Photosynthetic NDH subunit of subcomplex B 2, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / Photosynthetic NDH subunit of lumenal location 5, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of subcomplex B 3, chloroplastic / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / Photosynthetic NDH subunit of lumenal location 4, chloroplastic / Photosynthetic NDH subunit of lumenal location 3, chloroplastic / Photosynthetic NDH subunit of lumenal location 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsPan, X.W. / Li, M.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China (NSFC)31770778 China
National Natural Science Foundation of China (NSFC)31930064 China
National Natural Science Foundation of China (NSFC)31970264 China
CitationJournal: Mol Plant / Year: 2022
Title: Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana.
Authors: Xiaodong Su / Duanfang Cao / Xiaowei Pan / Lifang Shi / Zhenfeng Liu / Luca Dall'Osto / Roberto Bassi / Xinzheng Zhang / Mei Li /
Abstract: Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane- ...Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like (NDH) complex that contains at least 29 protein subunits and associates with photosystem I (PSI) to form the NDH-PSI supercomplex. Here, we report the 3.9 Å resolution structure of the Arabidopsis thaliana NDH-PSI (AtNDH-PSI) supercomplex. We constructed structural models for 26 AtNDH subunits, among which 11 are unique to chloroplasts and stabilize the core part of the NDH complex. In the supercomplex, one NDH can bind up to two PSI-light-harvesting complex I (PSI-LHCI) complexes at both sides of its membrane arm. Two minor LHCIs, Lhca5 and Lhca6, each present in one PSI-LHCI, interact with NDH and contribute to supercomplex formation and stabilization. Collectively, our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants.
History
DepositionDec 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Assembly

Deposited unit
A: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
B: NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic
C: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
D: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
E: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
F: NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic
G: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
a: Photosynthetic NDH subunit of subcomplex B 1, chloroplastic
b: Photosynthetic NDH subunit of subcomplex B 2, chloroplastic
c: Photosynthetic NDH subunit of subcomplex B 3, chloroplastic
d: NDH dependent flow 6
e: Photosynthetic NDH subunit of subcomplex B 5, chloroplastic
f: Photosynthetic NDH subunit of lumenal location 1, chloroplastic
g: Photosynthetic NDH subunit of lumenal location 2, chloroplastic
h: Photosynthetic NDH subunit of lumenal location 3, chloroplastic
i: Photosynthetic NDH subunit of lumenal location 4, chloroplastic
j: Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)565,36821
Polymers562,95117
Non-polymers2,4174
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NAD(P)H-quinone oxidoreductase subunit ... , 6 types, 6 molecules ABCEFG

#1: Protein NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / NAD(P)H dehydrogenase subunit 1 / NDH subunit 1 / NADH-plastoquinone oxidoreductase subunit 1


Mass: 40041.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q37165, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NAD(P)H dehydrogenase / subunit 2 / NADH-plastoquinone oxidoreductase subunit 2


Mass: 57018.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: A0A1B1W4Z4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: Protein NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H dehydrogenase subunit 3 / NADH-plastoquinone oxidoreductase subunit 3


Mass: 13846.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56751, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: Protein NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H dehydrogenase subunit 4L / NADH-plastoquinone oxidoreductase subunit 4L


Mass: 11297.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P26289, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic / NAD(P)H dehydrogenase subunit 5 / NADH-plastoquinone oxidoreductase subunit 5


Mass: 85300.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56752, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#7: Protein NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / NAD(P)H dehydrogenase subunit 6 / NADH-plastoquinone oxidoreductase subunit 6


Mass: 19218.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q95695, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Protein , 3 types, 3 molecules Ddj

#4: Protein NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H dehydrogenase / chain 4 / NADH-plastoquinone oxidoreductase chain 4


Mass: 56992.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: A0A1B1W4Z0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#11: Protein NDH dependent flow 6


Mass: 18699.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: B3H6Z4
#17: Protein Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplastic / Cyclophilin of 20 kDa 2 / Peptidyl-prolyl cis-trans isomerase CYP20-2 / PPIase CYP20-2 / Rotamase ...Cyclophilin of 20 kDa 2 / Peptidyl-prolyl cis-trans isomerase CYP20-2 / PPIase CYP20-2 / Rotamase CYP20-2 / Thylakoid lumen PPIase of 20 kDa / TLP20


Mass: 27915.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ASS6, peptidylprolyl isomerase

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Photosynthetic NDH subunit of subcomplex B ... , 4 types, 4 molecules abce

#8: Protein Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / Protein PnsB1 / NAD(P)H DEHYDROGENASE SUBUNIT 48 / NDH-DEPENDENT CYCLIC ELECTRON FLOW 1


Mass: 51080.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S9N6
#9: Protein Photosynthetic NDH subunit of subcomplex B 2, chloroplastic / Protein PnsB2 / NAD(P)H DEHYDROGENASE SUBUNIT 45 / NDH-DEPENDENT CYCLIC ELECTRON FLOW 2


Mass: 38048.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94AQ8
#10: Protein Photosynthetic NDH subunit of subcomplex B 3, chloroplastic / Protein PnsB3 / NDH-DEPENDENT CYCLIC ELECTRON FLOW 4


Mass: 22448.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LU21
#12: Protein Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Protein PnsB5 / NAD(P)H dehydrogenase 18


Mass: 23767.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FG89

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Photosynthetic NDH subunit of lumenal location ... , 4 types, 4 molecules fghi

#13: Protein Photosynthetic NDH subunit of lumenal location 1, chloroplastic / PsbP-like protein 2


Mass: 26997.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O80634
#14: Protein Photosynthetic NDH subunit of lumenal location 2, chloroplastic / PsbQ-like protein 1


Mass: 22183.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9XI73
#15: Protein Photosynthetic NDH subunit of lumenal location 3, chloroplastic / PsbQ-like protein 2


Mass: 24811.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SGH4
#16: Protein Photosynthetic NDH subunit of lumenal location 4, chloroplastic / FK506-binding protein 16-2 / AtFKBP16-2 / Immunophilin FKBP16-2 / Peptidyl-prolyl cis-trans ...FK506-binding protein 16-2 / AtFKBP16-2 / Immunophilin FKBP16-2 / Peptidyl-prolyl cis-trans isomerase FKBP16-2 / PPIase FKBP16-2 / Rotamase


Mass: 23282.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SCY3, peptidylprolyl isomerase

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Non-polymers , 3 types, 4 molecules

#18: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#19: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#20: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: Cylic electron transfer supercomplex from Arabidopsis / Type: COMPLEX / Entity ID: #1-#17 / 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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136022 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00632900
ELECTRON MICROSCOPYf_angle_d0.89144616
ELECTRON MICROSCOPYf_dihedral_angle_d19.19611736
ELECTRON MICROSCOPYf_chiral_restr0.0485061
ELECTRON MICROSCOPYf_plane_restr0.0065530

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