[English] 日本語
Yorodumi
- PDB-6l7o: cryo-EM structure of cyanobacteria Fd-NDH-1L complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l7o
Titlecryo-EM structure of cyanobacteria Fd-NDH-1L complex
Components
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 14
  • Ferredoxin-1
  • NAD(P)H-quinone oxidoreductase chain 4 1
  • NADH dehydrogenase subunit 5
  • NADH-quinone oxidoreductase subunit J
  • Tlr0472 protein
  • Tlr0636 protein
KeywordsPHOTOSYNTHESIS / photosystem I / cyclic electron transfer
Function / homology
Function and homology information


: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / photosynthesis, light reaction / plasma membrane-derived thylakoid membrane / NADH dehydrogenase activity / respiratory chain complex I ...: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / photosynthesis, light reaction / plasma membrane-derived thylakoid membrane / NADH dehydrogenase activity / respiratory chain complex I / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / aerobic respiration / electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein of unknown function DUF2996 / Protein of unknown function (DUF2996) / Helix Hairpins - #3510 / NADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NAD(P)H-quinone oxidoreductase subunit O / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / Cyanobacterial and plant NDH-1 subunit O / NAD(P)H-quinone oxidoreductase subunit M ...Protein of unknown function DUF2996 / Protein of unknown function (DUF2996) / Helix Hairpins - #3510 / NADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NAD(P)H-quinone oxidoreductase subunit O / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / Cyanobacterial and plant NDH-1 subunit O / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase, subunit N / NADH-quinone oxidoreductase chain 4 / Cyanobacterial and plastid NDH-1 subunit M / NADH dehydrogenase transmembrane subunit / NADH-quinone oxidoreductase cyanobacterial subunit N / NADH-plastoquinone oxidoreductase, subunit I / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / Ferredoxin [2Fe-2S], plant / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / SH3 type barrels. - #140 / 2Fe-2S iron-sulfur cluster binding domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / 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 / 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 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Beta-grasp domain superfamily / 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 / SH3 type barrels. / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Ferredoxin-1 / NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit 3 ...BETA-CAROTENE / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Ferredoxin-1 / NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H-quinone oxidoreductase subunit N / NADH dehydrogenase subunit 5 / NAD(P)H-quinone oxidoreductase chain 4 1 / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H-quinone oxidoreductase subunit 4L / NADH-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit I / NAD(P)H-quinone oxidoreductase subunit 1 / Tlr0636 protein / Tlr0472 protein / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit O / Proton-translocating NADH-quinone dehydrogenase subunit P NdhP / Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang, C. / Shuai, J. / Wu, J. / Lei, M.
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into NDH-1 mediated cyclic electron transfer.
Authors: Chunli Zhang / Jin Shuai / Zhaoxing Ran / Jiaohong Zhao / Zhenfang Wu / Rijing Liao / Jian Wu / Weimin Ma / Ming Lei /
Abstract: NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution ...NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution cryo-EM structure of the ferredoxin (Fd)-NDH-1L complex from the cyanobacterium Thermosynechococcus elongatus. The structure reveals three β-carotene and fifteen lipid molecules in the membrane arm of NDH-1L. Regulatory oxygenic photosynthesis-specific (OPS) subunits NdhV, NdhS and NdhO are close to the Fd-binding site whilst NdhL is adjacent to the plastoquinone (PQ) cavity, and they play different roles in PSI CET under high-light stress. NdhV assists in the binding of Fd to NDH-1L and accelerates PSI CET in response to short-term high-light exposure. In contrast, prolonged high-light irradiation switches on the expression and assembly of the NDH-1MS complex, which likely contains no NdhO to further accelerate PSI CET and reduce ROS production. We propose that this hierarchical mechanism is necessary for the survival of cyanobacteria in an aerobic environment.
History
DepositionNov 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Sep 22, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0849
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD(P)H-quinone oxidoreductase subunit 1
B: NAD(P)H-quinone oxidoreductase subunit 2
C: NAD(P)H-quinone oxidoreductase subunit 3
D: NAD(P)H-quinone oxidoreductase chain 4 1
E: NAD(P)H-quinone oxidoreductase subunit 4L
F: NADH dehydrogenase subunit 5
G: NADH-quinone oxidoreductase subunit J
H: NAD(P)H-quinone oxidoreductase subunit H
I: NAD(P)H-quinone oxidoreductase subunit I
J: NAD(P)H-quinone oxidoreductase subunit J
K: NAD(P)H-quinone oxidoreductase subunit K
L: NAD(P)H-quinone oxidoreductase subunit L
M: NAD(P)H-quinone oxidoreductase subunit M
N: NAD(P)H-quinone oxidoreductase subunit N
O: NAD(P)H-quinone oxidoreductase subunit O
P: NAD(P)H-quinone oxidoreductase subunit P
Q: NAD(P)H-quinone oxidoreductase subunit Q
R: Ferredoxin-1
S: Tlr0636 protein
V: Tlr0472 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)569,574103
Polymers480,93820
Non-polymers88,63783
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area134160 Å2
ΔGint-959 kcal/mol
Surface area145710 Å2

-
Components

-
NAD(P)H-quinone oxidoreductase subunit ... , 14 types, 14 molecules ABCEHIJKLMNOPQ

#1: Protein NAD(P)H-quinone oxidoreductase subunit 1 / NAD(P)H dehydrogenase I subunit 1 / NDH-1 subunit 1 / NDH-A


Mass: 40565.984 Da / Num. of mol.: 1 / Fragment: NdhA / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DL32, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H dehydrogenase subunit 2 / NADH-plastoquinone oxidoreductase subunit 2 / NDH-1 / subunit 2


Mass: 55168.543 Da / Num. of mol.: 1 / Fragment: NdhB / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DMR6, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: Protein NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H dehydrogenase subunit 3 / NADH-plastoquinone oxidoreductase subunit 3 / NDH-1 subunit 3 / NDH-C


Mass: 15013.919 Da / Num. of mol.: 1 / Fragment: NdhC / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DJ02, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: Protein NAD(P)H-quinone oxidoreductase subunit 4L / NAD(P)H dehydrogenase subunit 4L / NADH-plastoquinone oxidoreductase subunit 4L / NDH-1 / subunit 4L / NDH-E


Mass: 11140.265 Da / Num. of mol.: 1 / Fragment: NdhE / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DL29, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#8: Protein NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H dehydrogenase subunit H / NADH-plastoquinone oxidoreductase subunit H / NDH-1 subunit H / NDH-H


Mass: 45271.184 Da / Num. of mol.: 1 / Fragment: NdhH / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DJD9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#9: Protein NAD(P)H-quinone oxidoreductase subunit I / NAD(P)H dehydrogenase I subunit I / NDH-1 subunit I / NDH-I


Mass: 22444.801 Da / Num. of mol.: 1 / Fragment: NdhI / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DL31, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#10: Protein NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H dehydrogenase subunit J / NADH-plastoquinone oxidoreductase subunit J / NDH-1 subunit J / NDH-J


Mass: 19363.789 Da / Num. of mol.: 1 / Fragment: NdhJ / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DJ01, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#11: Protein NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H dehydrogenase I subunit K / NDH-1 subunit K / NDH-K


Mass: 25766.998 Da / Num. of mol.: 1 / Fragment: NdhK / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DKZ4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#12: Protein NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H dehydrogenase I subunit L / NDH-1 subunit L / NDH-L


Mass: 8575.137 Da / Num. of mol.: 1 / Fragment: NdhL / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DKZ3, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#13: Protein NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H dehydrogenase I subunit M / NDH-M


Mass: 12584.056 Da / Num. of mol.: 1 / Fragment: NdhM / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DLN5, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#14: Protein NAD(P)H-quinone oxidoreductase subunit N / NAD(P)H dehydrogenase I subunit N / NDH-N


Mass: 16656.182 Da / Num. of mol.: 1 / Fragment: NdhN / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DJU2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#15: Protein NAD(P)H-quinone oxidoreductase subunit O / NAD(P)H dehydrogenase I subunit O / NDH-1 subunit O / NDH-O


Mass: 7877.076 Da / Num. of mol.: 1 / Fragment: NdhO / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DMU4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#16: Protein/peptide NAD(P)H-quinone oxidoreductase subunit P


Mass: 4878.649 Da / Num. of mol.: 1 / Fragment: NdhP / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: V5V507*PLUS
#17: Protein/peptide NAD(P)H-quinone oxidoreductase subunit Q


Mass: 4844.698 Da / Num. of mol.: 1 / Fragment: NdhQ / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: V5V791*PLUS

-
Protein , 6 types, 6 molecules DFGRSV

#4: Protein NAD(P)H-quinone oxidoreductase chain 4 1 / NAD(P)H dehydrogenase I / chain 4 1 / NDH-1


Mass: 57847.504 Da / Num. of mol.: 1 / Fragment: NdhD1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DKY0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NADH dehydrogenase subunit 5


Mass: 72025.352 Da / Num. of mol.: 1 / Fragment: NdhF1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: Q8DKX9
#7: Protein NADH-quinone oxidoreductase subunit J


Mass: 21580.568 Da / Num. of mol.: 1 / Fragment: NdhG / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DL30, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#18: Protein Ferredoxin-1 / Ferredoxin I


Mass: 10853.959 Da / Num. of mol.: 1 / Fragment: Ferredoxin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / Gene: petF1, petF / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A3C9
#19: Protein Tlr0636 protein


Mass: 12462.559 Da / Num. of mol.: 1 / Fragment: NdhS / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: Q8DL61
#20: Protein Tlr0472 protein


Mass: 16016.489 Da / Num. of mol.: 1 / Fragment: NdhV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DLL4

-
Sugars , 1 types, 2 molecules

#23: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 7 types, 81 molecules

#21: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56
#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#24: Chemical...
ChemComp-AJP / Digitonin


Mass: 1229.312 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C56H92O29 / Comment: detergent*YM
#25: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H46O2
#26: 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.: 4 / Source method: obtained synthetically / Formula: C41H78O12S
#27: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#28: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Fd-NDH-1L complex / Type: COMPLEX / Entity ID: #1-#20 / Source: MULTIPLE SOURCES
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM softwareName: RELION / Version: 3 / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 338822 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more