[English] 日本語
Yorodumi
- PDB-5fl7: Structure of the F1c10 complex from Yarrowia lipolytica ATP synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fl7
TitleStructure of the F1c10 complex from Yarrowia lipolytica ATP synthase
Components(ATP SYNTHASE ...) x 6
KeywordsHYDROLASE / ATP SYNTHASE FAMILY / NUCLEOTIDE BINDING / PROTON TRANSPORTING / ROTATIONAL MECHANISM / ATP BIOSYNTHETIC PROCESS / ATP SYNTHESIS/HYDROLYSIS
Function / homology
Function and homology information


: / : / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism ...: / : / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / F1F0 ATP synthase subunit C / F1FO ATP Synthase ...ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / Pyruvate Kinase; Chain: A, domain 1 / 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, alpha subunit nucleotide-binding domain / 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 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. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit 9, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit beta, mitochondrial
Similarity search - Component
Biological speciesYARROWIA LIPOLYTICA (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsParey, K. / Bublitz, M. / Meier, T.
CitationJournal: Mol Cell / Year: 2016
Title: Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology.
Authors: Alexander Hahn / Kristian Parey / Maike Bublitz / Deryck J Mills / Volker Zickermann / Janet Vonck / Werner Kühlbrandt / Thomas Meier /
Abstract: We determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 ...We determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 of the 60 dimer subunits. Horizontal helices of subunit a in Fo wrap around the c-ring rotor, and a total of six vertical helices assigned to subunits a, b, f, i, and 8 span the membrane. Subunit 8 (A6L in human) is an evolutionary derivative of the bacterial b subunit. On the lumenal membrane surface, subunit f establishes direct contact between the two monomers. Comparison with a cryo-EM map of the F1Fo monomer identifies subunits e and g at the lateral dimer interface. They do not form dimer contacts but enable dimer formation by inducing a strong membrane curvature of ∼100°. Our structure explains the structural basis of cristae formation in mitochondria, a landmark signature of eukaryotic cell morphology.
History
DepositionOct 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT ALPHA
B: ATP SYNTHASE SUBUNIT ALPHA
C: ATP SYNTHASE SUBUNIT ALPHA
D: ATP SYNTHASE SUBUNIT BETA
E: ATP SYNTHASE SUBUNIT BETA
F: ATP SYNTHASE SUBUNIT BETA
G: ATP SYNTHASE SUBUNIT GAMMA CHAIN, MITOCHONDRIAL
H: ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL
I: ATP SYNTHASE EPSILON CHAIN, MITOCHONDRIAL
K: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
L: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
M: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
N: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
O: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
P: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
Q: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
R: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
T: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,47529
Polymers463,97719
Non-polymers2,49710
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.500, 182.200, 193.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
ATP SYNTHASE ... , 6 types, 19 molecules ABCDEFGHIKLMNOPQRST

#1: Protein ATP SYNTHASE SUBUNIT ALPHA / ATP SYNTHASE SUBUNIT ALPHA / MITOCHONDRIAL


Mass: 58147.430 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) / References: UniProt: Q6C326
#2: Protein ATP SYNTHASE SUBUNIT BETA / ATP SYNTHASE SUBUNIT BETA / MITOCHONDRIAL


Mass: 54590.828 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast)
References: UniProt: Q6CFT7, H+-transporting two-sector ATPase
#3: Protein ATP SYNTHASE SUBUNIT GAMMA CHAIN, MITOCHONDRIAL


Mass: 32378.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) / References: UniProt: Q6C338, EC: 3.6.1.34
#4: Protein ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL


Mass: 14811.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) / References: UniProt: Q6C877, EC: 3.6.1.34
#5: Protein/peptide ATP SYNTHASE EPSILON CHAIN, MITOCHONDRIAL


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) / References: EC: 3.6.1.34
#6: Protein
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL / LIPID-BINDING PROTEIN / OLIGOMYCIN RESISTANCE PROTEIN 1


Mass: 7719.265 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast)
References: UniProt: Q37695, H+-transporting two-sector ATPase

-
Non-polymers , 4 types, 27 molecules

#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsCHAIN I NOT ANNOTATED IN THE UNIPROT DATABANK

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS-HCL, POLYETHYLENE GLYCOL 400, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00774
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2015 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00774 Å / Relative weight: 1
ReflectionResolution: 3.5→49.19 Å / Num. obs: 75882 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19.47 % / Biso Wilson estimate: 157.51 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.84
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 0.61 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XOK

2xok


Resolution: 3.5→49.366 Å / SU ML: 0.64 / σ(F): 1.34 / Phase error: 38.06 / Stereochemistry target values: ML
Details: THE FOLLOWING RESIDUES ARE DISORDERED AND HAVE NOT BEEN MODELLED CHAIN A 1-48 534- -536 CHAIN B 1-48 429-434 534-536 CHAIN C 1-48 534-536 CHAIN D 1-36 507-510 CHAIN E 1-38 507-510 CHAIN F 1- ...Details: THE FOLLOWING RESIDUES ARE DISORDERED AND HAVE NOT BEEN MODELLED CHAIN A 1-48 534- -536 CHAIN B 1-48 429-434 534-536 CHAIN C 1-48 534-536 CHAIN D 1-36 507-510 CHAIN E 1-38 507-510 CHAIN F 1-36 507-510 CHAIN G 1-22 117-119 293 CHAIN H 1-14 95-100 134- -136 CHAIN I WAS MODELLED AND REFINED AS POLY-ALANINE CHAIN K 1 75-76 CHAIN L 1 74-76 CHAIN M 1 CHAIN N 76 CHAIN O 1 CHAIN P 76 CHAIN R 1 76 CHAIN S 1 76 CHAIN T 1 76
RfactorNum. reflection% reflection
Rfree0.3054 1897 2.5 %
Rwork0.2739 --
obs0.2747 75790 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.52 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29950 0 152 17 30119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00430573
X-RAY DIFFRACTIONf_angle_d0.44841382
X-RAY DIFFRACTIONf_dihedral_angle_d8.1218311
X-RAY DIFFRACTIONf_chiral_restr0.0394901
X-RAY DIFFRACTIONf_plane_restr0.0035326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.58750.38991470.39565181X-RAY DIFFRACTION100
3.5875-3.68450.39711150.37335233X-RAY DIFFRACTION100
3.6845-3.79290.40181470.35525227X-RAY DIFFRACTION100
3.7929-3.91520.38061240.32325191X-RAY DIFFRACTION100
3.9152-4.05510.37361450.3195223X-RAY DIFFRACTION100
4.0551-4.21740.31831300.29935256X-RAY DIFFRACTION100
4.2174-4.40920.30551270.27055225X-RAY DIFFRACTION100
4.4092-4.64150.33481390.25525263X-RAY DIFFRACTION100
4.6415-4.93210.27921300.25225279X-RAY DIFFRACTION100
4.9321-5.31250.31861390.27715259X-RAY DIFFRACTION100
5.3125-5.84630.35261350.28255310X-RAY DIFFRACTION100
5.8463-6.69050.32831420.28295300X-RAY DIFFRACTION100
6.6905-8.42250.31251350.25065378X-RAY DIFFRACTION100
8.4225-49.37110.24881420.25425568X-RAY DIFFRACTION100

+
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