1H8E

(ADP.AlF4)2(ADP.SO4) bovine F1-ATPase (all three catalytic sites occupied)

PDB DOI: https://doi.org/10.2210/pdb1H8E/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): Yes

Deposited: 2001-02-02 Released: 2001-08-10
Deposition Author(s): Menz, R.I., Walker, J.E., Leslie, A.G.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of Bovine Mitochondrial F1-ATPase with Nucleotide Bound to All Three Catalytic Sites: Implications for the Mechanism of Rotary Catalysis

Menz, R.I., Walker, J.E., Leslie, A.G.W.

(2001) Cell 106: 331

PubMed: 11509182 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(01)00452-4
Primary Citation of Related Structures:
1H8E

PubMed Abstract:
The crystal structure of a novel aluminium fluoride inhibited form of bovine mitochondrial F(1)-ATPase has been determined at 2 A resolution. In contrast to all previously determined structures of the bovine enzyme, all three catalytic sites are occupied by nucleotide. The subunit that did not bind nucleotide in previous structures binds ADP and sulfate (mimicking phosphate), and adopts a "half-closed" conformation. This structure probably represents the posthydrolysis, pre-product release step on the catalytic pathway. A catalytic scheme for hydrolysis (and synthesis) at physiological rates and a mechanism for the ATP-driven rotation of the gamma subunit are proposed based on the crystal structures of the bovine enzyme.

Organizational Affiliation

Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.

Macromolecule Content

Total Structure Weight: 375.48 kDa
Atom Count: 26,329
Modelled Residue Count: 3,209
Deposited Residue Count: 3,444
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BOVINE MITOCHONDRIAL F1-ATPASE	A, B, C	510	Bos taurus	Mutation(s): 1
UniProt
Find proteins for P19483 (Bos taurus) Explore P19483 Go to UniProtKB: P19483
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19483
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BOVINE MITOCHONDRIAL F1-ATPASE	D, E, F	482	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P00829 (Bos taurus) Explore P00829 Go to UniProtKB: P00829
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00829
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BOVINE MITOCHONDRIAL F1-ATPASE	G	272	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P05631 (Bos taurus) Explore P05631 Go to UniProtKB: P05631
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05631
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BOVINE MITOCHONDRIAL F1-ATPASE	H	146	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P05630 (Bos taurus) Explore P05630 Go to UniProtKB: P05630
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05630
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
BOVINE MITOCHONDRIAL F1-ATPASE	I	50	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P05632 (Bos taurus) Explore P05632 Go to UniProtKB: P05632
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05632
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain Z [auth F] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain T [auth D] SDF format, chain W [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain Z [auth F] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E]	J [auth A] M [auth B] Q [auth C] T [auth D] W [auth E] J [auth A], M [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
ALF Query on ALF Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain V [auth D] MOL2 format, chain BA [auth F] MOL2 format, chain V [auth D]	BA [auth F], V [auth D]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain BA [auth F] Focus chain V [auth D] Interactions & Density Focus chain BA [auth F] Focus chain V [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Y [auth E] MOL2 format, chain Y [auth E]	Y [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain Y [auth E] Interactions & Density Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain L [auth A]	L [auth A], O [auth B], P [auth B], S [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain K [auth A] SDF format, chain U [auth D] SDF format, chain X [auth E] SDF format, chain N [auth B] SDF format, chain R [auth C] MOL2 format, chain AA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C]	AA [auth F] K [auth A] N [auth B] R [auth C] U [auth D] AA [auth F], K [auth A], N [auth B], R [auth C], U [auth D], X [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.201
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 267.7	α = 90
b = 106.2	β = 90
c = 138.3	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

Entry History

Deposition Data

Released Date: 2001-08-10

Deposition Author(s):

Menz, R.I.

Walker, J.E.

Leslie, A.G.W.

Revision History (Full details and data files)

Version 1.0: 2001-08-10
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description