5FL7 | pdb_00005fl7

Structure of the F1c10 complex from Yarrowia lipolytica ATP synthase

PDB DOI: https://doi.org/10.2210/pdb5FL7/pdb

Classification: HYDROLASE
Organism(s): Yarrowia lipolytica
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2015-10-22 Released: 2016-06-29
Deposition Author(s): Parey, K., Bublitz, M., Meier, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.305 (Depositor), 0.311 (DCC)
R-Value Work:
0.274 (Depositor), 0.278 (DCC)
R-Value Observed:
0.275 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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Literature

Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology.

Hahn, A., Parey, K., Bublitz, M., Mills, D.J., Zickermann, V., Vonck, J., Kuhlbrandt, W., Meier, T.

(2016) Mol Cell 63: 445

PubMed: 27373333 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.molcel.2016.05.037
Primary Citation Related Structures:
5FL7

PubMed 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 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.

Organizational Affiliation

Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 466.47 kDa
Atom Count: 30,119
Modeled Residue Count: 3,996
Deposited Residue Count: 4,341
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE SUBUNIT ALPHA	A, B, C	536	Yarrowia lipolytica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q6C326 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q6C326 Go to UniProtKB: Q6C326
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6C326
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE SUBUNIT BETA	D, E, F	509	Yarrowia lipolytica	Mutation(s): 0 EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q6CFT7 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q6CFT7 Go to UniProtKB: Q6CFT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6CFT7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE SUBUNIT GAMMA CHAIN, MITOCHONDRIAL	G	293	Yarrowia lipolytica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q6C338 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q6C338 Go to UniProtKB: Q6C338
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6C338
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL	H	137	Yarrowia lipolytica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q6C877 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q6C877 Go to UniProtKB: Q6C877
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6C877
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE EPSILON CHAIN, MITOCHONDRIAL	I	16	Yarrowia lipolytica	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL	J [auth K] K [auth L] L [auth M] M [auth N] N [auth O] J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T]	76	Yarrowia lipolytica	Mutation(s): 0 EC: 3.6.3.14 Membrane Entity: Yes
UniProt
Find proteins for Q37695 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q37695 Go to UniProtKB: Q37695
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q37695
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain V [auth B] SDF format, chain X [auth C] MOL2 format, chain T [auth A] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C] mmCIF format, chain T [auth A] mmCIF format, chain V [auth B] mmCIF format, chain X [auth C]	T [auth A], V [auth B], X [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain T [auth A] Focus chain V [auth B] Focus chain X [auth C] Interactions & Density Focus chain T [auth A] Focus chain V [auth B] Focus chain X [auth C]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain BA [auth F] MOL2 format, chain Z [auth D] MOL2 format, chain BA [auth F] mmCIF format, chain Z [auth D] mmCIF format, chain BA [auth F]	BA [auth F], Z [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth F] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth F] Focus chain Z [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain U [auth A] SDF format, chain Y [auth C] SDF format, chain W [auth B] SDF format, chain AA [auth D] MOL2 format, chain CA [auth F] MOL2 format, chain U [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain W [auth B] MOL2 format, chain AA [auth D] mmCIF format, chain CA [auth F] mmCIF format, chain U [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain W [auth B] mmCIF format, chain AA [auth D]	AA [auth D], CA [auth F], U [auth A], W [auth B], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth F] Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth F] Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.305 (Depositor), 0.311 (DCC)
R-Value Work: 0.274 (Depositor), 0.278 (DCC)
R-Value Observed: 0.275 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.5	α = 90
b = 182.2	β = 90
c = 193	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Parey, K.

Bublitz, M.

Meier, T.

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2016-07-20
Changes: Database references
Version 1.2: 2016-08-24
Changes: Database references
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description