3OFN

Structure of four mutant forms of yeast F1 ATPase: alpha-N67I

PDB DOI: https://doi.org/10.2210/pdb3OFN/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2010-08-15 Released: 2010-09-15
Deposition Author(s): Arsenieva, D., Symersky, J., Wang, Y., Pagadala, V., Mueller, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.276
R-Value Work: 0.210
R-Value Observed: 0.212

Starting Model: experimental
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Literature

Crystal structures of mutant forms of the yeast f1 ATPase reveal two modes of uncoupling.

Arsenieva, D., Symersky, J., Wang, Y., Pagadala, V., Mueller, D.M.

(2010) J Biol Chem 285: 36561-36569

PubMed: 20843806 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M110.174383
Primary Citation of Related Structures:
3OE7, 3OEH, 3OFN

PubMed Abstract:
The mitochondrial ATP synthase couples the flow of protons with the phosphorylation of ADP. A class of mutations, the mitochondrial genome integrity (mgi) mutations, has been shown to uncouple this process in the yeast mitochondrial ATP synthase. Four mutant forms of the yeast F(1) ATPase with mgi mutations were crystallized; the structures were solved and analyzed. The analysis identifies two mechanisms of structural uncoupling: one in which the empty catalytic site is altered and in doing so, apparently disrupts substrate (phosphate) binding, and a second where the steric hindrance predicted between γLeu83 and β(DP) residues, Leu-391 and Glu-395, located in Catch 2 region, is reduced allowing rotation of the γ-subunit with less impedance. Overall, the structures provide key insights into the critical interactions in the yeast ATP synthase involved in the coupling process.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois 60064, USA.

Macromolecule Content

Total Structure Weight: 1,105.44 kDa
Atom Count: 70,481
Modelled Residue Count: 9,432
Deposited Residue Count: 10,178
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C, J, K A, B, C, J, K, L, S, T, U	510	Saccharomyces cerevisiae	Mutation(s): 1 Gene Names: ATP1, YBL0827, YBL099W EC: 3.6.3.14
UniProt
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07251 Go to UniProtKB: P07251
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07251
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D, E, F, M, N D, E, F, M, N, O, V, W, X	484	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP2, J2041, YJR121W EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00830 Go to UniProtKB: P00830
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00830
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit gamma	G, P, Y	278	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP3, ATP3a, ATP3b, YBR039W, YBR0408 EC: 3.6.3.14
UniProt
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38077 Go to UniProtKB: P38077
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UniProt Group	P38077
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit delta	H, Q	138	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP16, D2935, YD8119.03, YDL004W EC: 3.6.3.14
UniProt
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12165 Go to UniProtKB: Q12165
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UniProt Group	Q12165
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit epsilon	I, R	61	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP15, P0345, YPL271W EC: 3.6.3.14
UniProt
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21306 Go to UniProtKB: P21306
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UniProt Group	P21306
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain BB [auth X] SDF format, chain DA [auth C] SDF format, chain FA [auth D] SDF format, chain HA [auth F] SDF format, chain JA [auth J] SDF format, chain LA [auth K] SDF format, chain NA [auth L] SDF format, chain PA [auth M] SDF format, chain RA [auth O] SDF format, chain TA [auth S] SDF format, chain VA [auth T] SDF format, chain XA [auth U] SDF format, chain Z [auth A] SDF format, chain ZA [auth V] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth X] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain HA [auth F] MOL2 format, chain JA [auth J] MOL2 format, chain LA [auth K] MOL2 format, chain NA [auth L] MOL2 format, chain PA [auth M] MOL2 format, chain RA [auth O] MOL2 format, chain TA [auth S] MOL2 format, chain VA [auth T] MOL2 format, chain XA [auth U] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth V] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth X] mmCIF format, chain DA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain HA [auth F] mmCIF format, chain JA [auth J] mmCIF format, chain LA [auth K] mmCIF format, chain NA [auth L] mmCIF format, chain PA [auth M] mmCIF format, chain RA [auth O] mmCIF format, chain TA [auth S] mmCIF format, chain VA [auth T] mmCIF format, chain XA [auth U] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth V]	BA [auth B] BB [auth X] DA [auth C] FA [auth D] HA [auth F] BA [auth B], BB [auth X], DA [auth C], FA [auth D], HA [auth F], JA [auth J], LA [auth K], NA [auth L], PA [auth M], RA [auth O], TA [auth S], VA [auth T], XA [auth U], Z [auth A], ZA [auth V]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain BA [auth B] Focus chain BB [auth X] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain HA [auth F] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain RA [auth O] Focus chain TA [auth S] Focus chain VA [auth T] Focus chain XA [auth U] Focus chain Z [auth A] Focus chain ZA [auth V] Interactions & Density Focus chain BA [auth B] Focus chain BB [auth X] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain HA [auth F] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain RA [auth O] Focus chain TA [auth S] Focus chain VA [auth T] Focus chain XA [auth U] Focus chain Z [auth A] Focus chain ZA [auth V]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth V] SDF format, chain CA [auth B] SDF format, chain CB [auth X] SDF format, chain EA [auth C] SDF format, chain GA [auth D] SDF format, chain IA [auth F] SDF format, chain KA [auth J] SDF format, chain MA [auth K] SDF format, chain OA [auth L] SDF format, chain QA [auth M] SDF format, chain SA [auth O] SDF format, chain UA [auth S] SDF format, chain WA [auth T] SDF format, chain YA [auth U] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth V] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth X] MOL2 format, chain EA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain IA [auth F] MOL2 format, chain KA [auth J] MOL2 format, chain MA [auth K] MOL2 format, chain OA [auth L] MOL2 format, chain QA [auth M] MOL2 format, chain SA [auth O] MOL2 format, chain UA [auth S] MOL2 format, chain WA [auth T] MOL2 format, chain YA [auth U] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth V] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth X] mmCIF format, chain EA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain IA [auth F] mmCIF format, chain KA [auth J] mmCIF format, chain MA [auth K] mmCIF format, chain OA [auth L] mmCIF format, chain QA [auth M] mmCIF format, chain SA [auth O] mmCIF format, chain UA [auth S] mmCIF format, chain WA [auth T] mmCIF format, chain YA [auth U]	AA [auth A] AB [auth V] CA [auth B] CB [auth X] EA [auth C] AA [auth A], AB [auth V], CA [auth B], CB [auth X], EA [auth C], GA [auth D], IA [auth F], KA [auth J], MA [auth K], OA [auth L], QA [auth M], SA [auth O], UA [auth S], WA [auth T], YA [auth U]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth V] Focus chain CA [auth B] Focus chain CB [auth X] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain IA [auth F] Focus chain KA [auth J] Focus chain MA [auth K] Focus chain OA [auth L] Focus chain QA [auth M] Focus chain SA [auth O] Focus chain UA [auth S] Focus chain WA [auth T] Focus chain YA [auth U] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth V] Focus chain CA [auth B] Focus chain CB [auth X] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain IA [auth F] Focus chain KA [auth J] Focus chain MA [auth K] Focus chain OA [auth L] Focus chain QA [auth M] Focus chain SA [auth O] Focus chain UA [auth S] Focus chain WA [auth T] Focus chain YA [auth U]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.276
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.019	α = 90
b = 290.619	β = 102.34
c = 188.465	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3OFN

Structure of four mutant forms of yeast F1 ATPase: alpha-N67I

Crystal structures of mutant forms of the yeast f1 ATPase reveal two modes of uncoupling.

Entity ID: 1

UniProt

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Experimental Data

Structure Validation

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Deposition Data

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