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- PDB-6tt7: Ovine ATP synthase 1a state -

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Basic information

Entry
Database: PDB / ID: 6tt7
TitleOvine ATP synthase 1a state
Components
  • (ATP synthase ...) x 14
  • ATP synthase-coupling factor 6, mitochondrial
  • Subunit DAPIT
  • Subunit e
KeywordsMEMBRANE PROTEIN / ATP synthase / mitochondrial / respiratory chain / mammalian
Function / homology
Function and homology information


negative regulation of cell adhesion involved in substrate-bound cell migration / ATP biosynthetic process / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / cellular response to interleukin-7 / proton-transporting ATP synthase complex / : / : ...negative regulation of cell adhesion involved in substrate-bound cell migration / ATP biosynthetic process / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / cellular response to interleukin-7 / proton-transporting ATP synthase complex / : / : / : / Mitochondrial protein degradation / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial nucleoid / MHC class I protein binding / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / positive regulation of blood vessel endothelial cell migration / proton-transporting ATP synthase complex, catalytic core F(1) / monoatomic ion transport / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / aerobic respiration / regulation of intracellular pH / mitochondrial membrane / lipid metabolic process / angiogenesis / mitochondrial inner membrane / lipid binding / cell surface / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / ATP synthase protein 8, metazoa ...ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / 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 / 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. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-P5S / Chem-S12 / ATP synthase peripheral stalk subunit OSCP / ATP synthase protein 8 / ATP synthase subunit a / ATP synthase subunit gamma, mitochondrial / ATP synthase F(0) complex subunit C1, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-P5S / Chem-S12 / ATP synthase peripheral stalk subunit OSCP / ATP synthase protein 8 / ATP synthase subunit a / ATP synthase subunit gamma, mitochondrial / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase subunit alpha / ATP synthase membrane subunit K, mitochondrial / Uncharacterized protein / ATP synthase subunit beta / ATP synthase subunit e, mitochondrial / ATP synthase F1 subunit delta / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit / ATP synthase subunit f, mitochondrial / ATP synthase subunit b
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPinke, G. / Zhou, L. / Sazanov, L.A.
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structure of the entire mammalian F-type ATP synthase.
Authors: Gergely Pinke / Long Zhou / Leonid A Sazanov /
Abstract: The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain ...The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the 'proton translocation cluster' attached to the c-ring and a more distant 'hook apparatus' holding subunit e. Unexpectedly, this subunit is anchored to a lipid 'plug' capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.
History
DepositionDec 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Dec 30, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / em_software / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_software.category / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _entity_src_nat.pdbx_end_seq_num / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
A: ATP synthase subunit alpha
E: ATP synthase subunit beta
D: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase subunit gamma
H: ATP synthase F1 subunit delta
I: ATP synthase F1 subunit epsilon
J: ATP synthase peripheral stalk subunit OSCP
K: ATP synthase subunit b
L: ATP synthase-coupling factor 6, mitochondrial
M: ATP synthase subunit d, mitochondrial
1: ATP synthase F(0) complex subunit C1, mitochondrial
2: ATP synthase F(0) complex subunit C1, mitochondrial
3: ATP synthase F(0) complex subunit C1, mitochondrial
4: ATP synthase F(0) complex subunit C1, mitochondrial
5: ATP synthase F(0) complex subunit C1, mitochondrial
6: ATP synthase F(0) complex subunit C1, mitochondrial
7: ATP synthase F(0) complex subunit C1, mitochondrial
8: ATP synthase F(0) complex subunit C1, mitochondrial
N: ATP synthase subunit a
O: Subunit DAPIT
P: ATP synthase membrane subunit 6.8PL
Q: ATP synthase protein 8
R: ATP synthase membrane subunit f
S: ATP synthase subunit
T: Subunit e
hetero molecules


Theoretical massNumber of molelcules
Total (without water)690,11347
Polymers677,85928
Non-polymers12,25519
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area135110 Å2
ΔGint-1030 kcal/mol
Surface area188210 Å2
MethodPISA

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Components

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ATP synthase ... , 14 types, 25 molecules BCAEDFGHIJKM12345678NPQRS

#1: Protein ATP synthase subunit alpha


Mass: 59779.492 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NY50
#2: Protein ATP synthase subunit beta


Mass: 56265.090 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: W5PEP7, H+-transporting two-sector ATPase
#3: Protein ATP synthase subunit gamma


Mass: 33133.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: XP_004014229.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: P05631*PLUS
#4: Protein ATP synthase F1 subunit delta


Mass: 17580.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PP03
#5: Protein ATP synthase F1 subunit epsilon


Mass: 5779.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: XP_027832792.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q3H8
#6: Protein ATP synthase peripheral stalk subunit OSCP / ATP synthase subunit O / mitochondrial / Oligomycin sensitivity conferral protein


Mass: 23435.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PTA0, UniProt: B9VH06*PLUS
#7: Protein ATP synthase subunit b


Mass: 28844.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: XP_004002367.2 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QEA9
#9: Protein ATP synthase subunit d, mitochondrial


Mass: 18747.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PP37
#10: Protein
ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase ...ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase proteolipid P1 / ATPase protein 9 / ATPase subunit c


Mass: 14201.577 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P17605
#11: Protein ATP synthase subunit a / F-ATPase protein 6


Mass: 24811.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78752
#13: Protein ATP synthase membrane subunit 6.8PL


Mass: 6846.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P913
#14: Protein ATP synthase protein 8 / A6L / F-ATPase subunit 8


Mass: 7918.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78751
#15: Protein ATP synthase membrane subunit f / ATP synthase subunit f / mitochondrial


Mass: 10315.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: XP_004016938.3 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QB48
#16: Protein ATP synthase subunit


Mass: 11428.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: XP_011950914.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q5U7

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Protein , 3 types, 3 molecules LOT

#8: Protein ATP synthase-coupling factor 6, mitochondrial / ATPase subunit F6


Mass: 12490.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q0Q5
#12: Protein Subunit DAPIT


Mass: 6443.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P5H1
#17: Protein Subunit e


Mass: 8336.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: XP_027827162.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PF18

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Non-polymers , 6 types, 19 molecules

#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#19: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#20: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#21: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO10P
#22: 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.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#23: Chemical ChemComp-S12 / O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine / 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine


Type: L-peptide linking / Mass: 523.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46NO9P

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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: Purified ATP synthase from sheep heart mitochondria / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ovis aries (sheep)
Buffer solutionpH: 7.4
Details: 20 mM HEPES pH7.4, 35 mM NaCl, 2 mM EDTA, 1% sucrose, 1 mM DTT, 0.1% LMNG, 0.2% CHAPS
SpecimenConc.: 2.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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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 / Calibrated magnification: 131951 X / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2400 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 106 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3053 / Details: 40 frames per movie
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategoryFitting-ID
2Gautomatch0.56particle selection
3EPUimage acquisition
5CTFFIND4.1.13CTF correction
8Coot0.8.9model fitting1
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
14PHENIX1.12_2829model refinement1
22Coot0.8.9model fitting2
28PHENIX1.12_2829model refinement2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 809000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35000 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceB value
1AB INITIO MODELREAL
2AB INITIO MODELREAL96
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15ARA

5ara

15ARA1PDBexperimental model
25ARA

5ara

25ARA1PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00840312
ELECTRON MICROSCOPYf_angle_d1.20954502
ELECTRON MICROSCOPYf_dihedral_angle_d11.05924397
ELECTRON MICROSCOPYf_chiral_restr0.0656344
ELECTRON MICROSCOPYf_plane_restr0.0086949

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