2HLD | pdb_00002hld

Crystal structure of yeast mitochondrial F1-ATPase

PDB DOI: https://doi.org/10.2210/pdb2HLD/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2006-07-06 Released: 2006-11-28
Deposition Author(s): Kabaleeswaran, V., Puri, N., Walker, J.E., Leslie, A.G., Mueller, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.244 (Depositor), 0.337 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Novel features of the rotary catalytic mechanism revealed in the structure of yeast F(1) ATPase.

Kabaleeswaran, V., Puri, N., Walker, J.E., Leslie, A.G., Mueller, D.M.

(2006) EMBO J 25: 5433-5442

PubMed: 17082766 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/sj.emboj.7601410
Primary Citation Related Structures:
2HLD

PubMed Abstract:
The crystal structure of yeast mitochondrial F(1) ATPase contains three independent copies of the complex, two of which have similar conformations while the third differs in the position of the central stalk relative to the alpha(3)beta(3) sub-assembly. All three copies display very similar asymmetric features to those observed for the bovine enzyme, but the yeast F(1) ATPase structures provide novel information. In particular, the active site that binds ADP in bovine F(1) ATPase has an ATP analog bound and therefore this structure does not represent the ADP-inhibited form. In addition, one of the complexes binds phosphate in the nucleotide-free catalytic site, and comparison with other structures provides a picture of the movement of the phosphate group during initial binding and subsequent catalysis. The shifts in position of the central stalk between two of the three copies of yeast F(1) ATPase and when these structures are compared to those of the bovine enzyme give new insight into the conformational changes that take place during rotational catalysis.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 1,119.27 kDa
Atom Count: 72,841
Modeled Residue Count: 9,599
Deposited Residue Count: 10,323
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase alpha chain, mitochondrial	A, B, C, J, K A, B, C, J, K, L, S, T, U	510	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.3.14 Membrane Entity: Yes
UniProt
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07251 Go to UniProtKB: P07251
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07251
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase beta chain, mitochondrial	D, E, F, M, N D, E, F, M, N, O, V, W, X	478	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP2 EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00830 Go to UniProtKB: P00830
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00830
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase gamma chain, mitochondrial	G, P, Y	278	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.3.14 Membrane Entity: Yes
UniProt
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38077 Go to UniProtKB: P38077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38077
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase delta chain, mitochondrial	H, Q, Z	138	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.3.14 Membrane Entity: Yes
UniProt
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12165 Go to UniProtKB: Q12165
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12165
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase epsilon chain, mitochondrial	AA [auth 1], I, R	61	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.3.14 Membrane Entity: Yes
UniProt
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21306 Go to UniProtKB: P21306
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21306
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain BB [auth U] SDF format, chain CA [auth A] SDF format, chain DB [auth V] SDF format, chain EA [auth B] SDF format, chain FB [auth X] SDF format, chain GA [auth C] SDF format, chain IA [auth D] SDF format, chain KA [auth F] SDF format, chain MA [auth J] SDF format, chain OA [auth K] SDF format, chain QA [auth L] SDF format, chain SA [auth M] SDF format, chain VA [auth O] SDF format, chain XA [auth S] SDF format, chain ZA [auth T] MOL2 format, chain BB [auth U] MOL2 format, chain CA [auth A] MOL2 format, chain DB [auth V] MOL2 format, chain EA [auth B] MOL2 format, chain FB [auth X] MOL2 format, chain GA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth F] MOL2 format, chain MA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain QA [auth L] MOL2 format, chain SA [auth M] MOL2 format, chain VA [auth O] MOL2 format, chain XA [auth S] MOL2 format, chain ZA [auth T] mmCIF format, chain BB [auth U] mmCIF format, chain CA [auth A] mmCIF format, chain DB [auth V] mmCIF format, chain EA [auth B] mmCIF format, chain FB [auth X] mmCIF format, chain GA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain KA [auth F] mmCIF format, chain MA [auth J] mmCIF format, chain OA [auth K] mmCIF format, chain QA [auth L] mmCIF format, chain SA [auth M] mmCIF format, chain VA [auth O] mmCIF format, chain XA [auth S] mmCIF format, chain ZA [auth T]	BB [auth U] CA [auth A] DB [auth V] EA [auth B] FB [auth X] BB [auth U], CA [auth A], DB [auth V], EA [auth B], FB [auth X], GA [auth C], IA [auth D], KA [auth F], MA [auth J], OA [auth K], QA [auth L], SA [auth M], VA [auth O], XA [auth S], ZA [auth T]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain BB [auth U] Focus chain CA [auth A] Focus chain DB [auth V] Focus chain EA [auth B] Focus chain FB [auth X] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain KA [auth F] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain QA [auth L] Focus chain SA [auth M] Focus chain VA [auth O] Focus chain XA [auth S] Focus chain ZA [auth T] Interactions & Density Focus chain BB [auth U] Focus chain CA [auth A] Focus chain DB [auth V] Focus chain EA [auth B] Focus chain FB [auth X] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain KA [auth F] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain QA [auth L] Focus chain SA [auth M] Focus chain VA [auth O] Focus chain XA [auth S] Focus chain ZA [auth T]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain TA [auth N] MOL2 format, chain TA [auth N] mmCIF format, chain TA [auth N]	TA [auth N]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain TA [auth N] Interactions & Density Focus chain TA [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AB [auth U] SDF format, chain BA [auth A] SDF format, chain CB [auth V] SDF format, chain DA [auth B] SDF format, chain EB [auth X] SDF format, chain FA [auth C] SDF format, chain HA [auth D] SDF format, chain JA [auth F] SDF format, chain LA [auth J] SDF format, chain NA [auth K] SDF format, chain PA [auth L] SDF format, chain RA [auth M] SDF format, chain UA [auth O] SDF format, chain WA [auth S] SDF format, chain YA [auth T] MOL2 format, chain AB [auth U] MOL2 format, chain BA [auth A] MOL2 format, chain CB [auth V] MOL2 format, chain DA [auth B] MOL2 format, chain EB [auth X] MOL2 format, chain FA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth F] MOL2 format, chain LA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain PA [auth L] MOL2 format, chain RA [auth M] MOL2 format, chain UA [auth O] MOL2 format, chain WA [auth S] MOL2 format, chain YA [auth T] mmCIF format, chain AB [auth U] mmCIF format, chain BA [auth A] mmCIF format, chain CB [auth V] mmCIF format, chain DA [auth B] mmCIF format, chain EB [auth X] mmCIF format, chain FA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth F] mmCIF format, chain LA [auth J] mmCIF format, chain NA [auth K] mmCIF format, chain PA [auth L] mmCIF format, chain RA [auth M] mmCIF format, chain UA [auth O] mmCIF format, chain WA [auth S] mmCIF format, chain YA [auth T]	AB [auth U] BA [auth A] CB [auth V] DA [auth B] EB [auth X] AB [auth U], BA [auth A], CB [auth V], DA [auth B], EB [auth X], FA [auth C], HA [auth D], JA [auth F], LA [auth J], NA [auth K], PA [auth L], RA [auth M], UA [auth O], WA [auth S], YA [auth T]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth U] Focus chain BA [auth A] Focus chain CB [auth V] Focus chain DA [auth B] Focus chain EB [auth X] Focus chain FA [auth C] Focus chain HA [auth D] Focus chain JA [auth F] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain PA [auth L] Focus chain RA [auth M] Focus chain UA [auth O] Focus chain WA [auth S] Focus chain YA [auth T] Interactions & Density Focus chain AB [auth U] Focus chain BA [auth A] Focus chain CB [auth V] Focus chain DA [auth B] Focus chain EB [auth X] Focus chain FA [auth C] Focus chain HA [auth D] Focus chain JA [auth F] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain PA [auth L] Focus chain RA [auth M] Focus chain UA [auth O] Focus chain WA [auth S] Focus chain YA [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.244 (Depositor), 0.337 (DCC)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.524	α = 90
b = 294.132	β = 101.67
c = 190.432	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-11-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-28
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

2HLD | pdb_00002hld

Crystal structure of yeast mitochondrial F1-ATPase

Literature

Novel features of the rotary catalytic mechanism revealed in the structure of yeast F(1) ATPase.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)