[English] 日本語
Yorodumi
- PDB-6tmk: Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tmk
TitleCryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, composite model
Components
  • (ATP synthase subunit ...) x 5
  • ATPTG1
  • ATPTG10
  • ATPTG11
  • ATPTG12
  • ATPTG13
  • ATPTG14
  • ATPTG15
  • ATPTG16
  • ATPTG17
  • ATPTG2
  • ATPTG3
  • ATPTG4
  • ATPTG5
  • ATPTG6
  • ATPTG7
  • ATPTG8
  • ATPTG9
  • Inhibitor of F1
  • Oligomycin sensitivity conferring protein (OSCP)
  • subunit 8
  • subunit a
  • subunit b
  • subunit c
  • subunit d
  • subunit f
  • subunit i/j
  • subunit k
KeywordsMEMBRANE PROTEIN / mitochondrial / ATP synthase / dimer / lipids
Function / homology
Function and homology information


mitochondrial electron transport, ubiquinol to cytochrome c / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / : / proton motive force-driven mitochondrial ATP synthesis / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / chloroplast ...mitochondrial electron transport, ubiquinol to cytochrome c / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / : / proton motive force-driven mitochondrial ATP synthesis / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / chloroplast / ADP binding / electron transfer activity / mitochondrial inner membrane / hydrolase activity / lipid binding / heme binding / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / metal ion binding
Similarity search - Function
: / ATPTG10-like / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c1 / Cytochrome C1 family / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily ...: / ATPTG10-like / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c1 / Cytochrome C1 family / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / Thioredoxin / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Thioredoxin domain / Thioredoxin-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Uncharacterized protein / Putative ATP synthase F0 subunit 9 / Uncharacterized protein / ATP synthase F1, delta subunit protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Uncharacterized protein / Putative ATP synthase F0 subunit 9 / Uncharacterized protein / ATP synthase F1, delta subunit protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Uncharacterized protein / Putative membrane protein / Transmembrane protein / ATPTG10-like domain-containing protein / Transmembrane protein / Uncharacterized protein / Putative ATP synthase / Transmembrane protein / Transmembrane protein / Uncharacterized protein / ATP synthase subunit gamma, mitochondrial / CHCH domain-containing protein / Uncharacterized protein / ATP synthase subunit beta / Transmembrane protein / Transmembrane protein / ATP synthase subunit alpha / Thioredoxin domain-containing protein / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / Putative atp synthase F1, epsilon subunit / Uncharacterized protein / Transmembrane protein / Putative myosin heavy chain / Cytochrome c1, heme protein / Uncharacterized protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
Toxoplasma gondii GT1 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMuhleip, A. / Kock Flygaard, R. / Amunts, A.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research CouncilERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Molecular Biology OrganizationALTF 260-2017 Sweden
CitationJournal: Nat Commun / Year: 2021
Title: ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria.
Authors: Alexander Mühleip / Rasmus Kock Flygaard / Jana Ovciarikova / Alice Lacombe / Paula Fernandes / Lilach Sheiner / Alexey Amunts /
Abstract: Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has ...Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has been observed, but its structural basis is unknown. Here, we report that the apicomplexan ATP synthase assembles into cyclic hexamers, essential to shape their distinct cristae. Cryo-EM was used to determine the structure of the hexamer, which is held together by interactions between parasite-specific subunits in the lumenal region. Overall, we identified 17 apicomplexan-specific subunits, and a minimal and nuclear-encoded subunit-a. The hexamer consists of three dimers with an extensive dimer interface that includes bound cardiolipins and the inhibitor IF. Cryo-ET and subtomogram averaging revealed that hexamers arrange into ~20-megadalton pentagonal pyramids in the curved apical membrane regions. Knockout of the linker protein ATPTG11 resulted in the loss of pentagonal pyramids with concomitant aberrantly shaped cristae. Together, this demonstrates that the unique macromolecular arrangement is critical for the maintenance of cristae morphology in Apicomplexa.
History
DepositionDec 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10524
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
q: ATPTG11
i: ATPTG7
t: ATPTG14
g: ATPTG5
o: subunit k
k: subunit a
j: subunit i/j
s: ATPTG13
u: ATPTG15
h: ATPTG6
e: ATPTG3
x: ATPTG17
b: subunit b
r: ATPTG12
p: ATPTG10
v: subunit f
l: ATPTG8
c: ATPTG1
d: ATPTG2
m: subunit 8
n: ATPTG9
f: ATPTG4
w: ATPTG16
a: subunit d
Q: ATPTG11
I: ATPTG7
T: ATPTG14
G: ATPTG5
O: subunit k
K: subunit a
J: subunit i/j
S: ATPTG13
U: ATPTG15
H: ATPTG6
E: ATPTG3
X: ATPTG17
B: subunit b
R: ATPTG12
P: ATPTG10
V: subunit f
L: ATPTG8
C: ATPTG1
D: ATPTG2
M: subunit 8
N: ATPTG9
F: ATPTG4
W: ATPTG16
A: subunit d
i2: Inhibitor of F1
A2: ATP synthase subunit alpha,subunit alpha
E2: ATP synthase subunit alpha,subunit alpha
C2: ATP synthase subunit alpha,subunit alpha
B2: ATP synthase subunit beta
F2: ATP synthase subunit beta
D2: ATP synthase subunit beta
g2: ATP synthase subunit gamma
d2: ATP synthase subunit delta
e2: ATP synthase subunit epsilon
G2: Oligomycin sensitivity conferring protein (OSCP)
H2: subunit c
I2: subunit c
J2: subunit c
K2: subunit c
L2: subunit c
M2: subunit c
N2: subunit c
O2: subunit c
P2: subunit c
Q2: subunit c
i1: Inhibitor of F1
A1: ATP synthase subunit alpha,subunit alpha
E1: ATP synthase subunit alpha,subunit alpha
C1: ATP synthase subunit alpha,subunit alpha
B1: ATP synthase subunit beta
F1: ATP synthase subunit beta
D1: ATP synthase subunit beta
g1: ATP synthase subunit gamma
d1: ATP synthase subunit delta
e1: ATP synthase subunit epsilon
G1: Oligomycin sensitivity conferring protein (OSCP)
H1: subunit c
I1: subunit c
J1: subunit c
K1: subunit c
L1: subunit c
M1: subunit c
N1: subunit c
O1: subunit c
P1: subunit c
Q1: subunit c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,562,832144
Polymers2,515,34490
Non-polymers47,48954
Water00
1


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

-
Components

+
Protein , 27 types, 72 molecules qQiItTgGoOkKjJsSuUhHeExXbBrRpP...

#1: Protein ATPTG11


Mass: 15425.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YPS4
#2: Protein ATPTG7


Mass: 26866.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7VXW3
#3: Protein ATPTG14


Mass: 14424.515 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YLH9
#4: Protein ATPTG5


Mass: 28162.615 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7WD71
#5: Protein subunit k


Mass: 17963.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YTD7
#6: Protein subunit a


Mass: 24562.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YSI9
#7: Protein subunit i/j


Mass: 26600.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7UQ82
#8: Protein ATPTG13


Mass: 14923.235 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YLN4
#9: Protein ATPTG15


Mass: 13871.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YRP0
#10: Protein ATPTG6


Mass: 27477.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YL08
#11: Protein ATPTG3


Mass: 35159.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YLR0
#12: Protein ATPTG17


Mass: 9486.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7W180
#13: Protein subunit b


Mass: 64811.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7V2T0
#14: Protein ATPTG12


Mass: 15400.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YKF7
#15: Protein ATPTG10


Mass: 15165.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YMA7
#16: Protein subunit f


Mass: 13029.997 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7UQT7
#17: Protein ATPTG8


Mass: 23365.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7W7F1
#18: Protein ATPTG1


Mass: 46025.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7W9J5
#19: Protein ATPTG2


Mass: 35238.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YV76
#20: Protein subunit 8


Mass: 22344.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YPQ4
#21: Protein ATPTG9


Mass: 18426.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YUZ2
#22: Protein ATPTG4


Mass: 28557.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7UVZ7
#23: Protein ATPTG16


Mass: 11587.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7VTI0
#24: Protein subunit d


Mass: 61362.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7V493
#25: Protein Inhibitor of F1


Mass: 16167.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YJP2
#31: Protein Oligomycin sensitivity conferring protein (OSCP)


Mass: 27669.994 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YKF8
#32: Protein
subunit c


Mass: 17753.504 Da / Num. of mol.: 20 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YJV2

-
ATP synthase subunit ... , 5 types, 18 molecules A2E2C2A1E1C1B2F2D2B1F1D1g2g1d2d1e2e1

#26: Protein
ATP synthase subunit alpha,subunit alpha


Mass: 61189.168 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote), (natural) Toxoplasma gondii GT1 (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7UU80
#27: Protein
ATP synthase subunit beta


Mass: 59983.316 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1
References: UniProt: A0A125YYY4, H+-transporting two-sector ATPase
#28: Protein ATP synthase subunit gamma


Mass: 34573.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YUH0
#29: Protein ATP synthase subunit delta


Mass: 19476.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YRE2
#30: Protein ATP synthase subunit epsilon


Mass: 8492.709 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7VV10

-
Sugars , 1 types, 14 molecules

#34: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 5 types, 40 molecules

#33: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#35: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#36: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 749.073 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H83NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#37: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#38: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mitochondrial ATP synthase dimer, composite model / Type: COMPLEX / Entity ID: #1-#32 / Source: NATURAL
Molecular weightValue: 1.85 MDa / Experimental value: NO
Source (natural)Organism: Toxoplasma gondii GT1 (eukaryote)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: 3 seconds blot.

-
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 magnification: 165000 X / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 4860
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20

-
Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2EPUimage acquisition
4GctfCTF correction
9RELION3initial Euler assignment
10RELION3final Euler assignment
12RELION33D reconstruction
13PHENIX1.17rc2-3612model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101505 / Symmetry type: POINT
Atomic model buildingSpace: REAL

+
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