1W0J | pdb_00001w0j

Beryllium fluoride inhibited bovine F1-ATPase

PDB DOI: https://doi.org/10.2210/pdb1W0J/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2004-06-08 Released: 2004-07-08
Deposition Author(s): Kagawa, R., Montgomery, M.G., Braig, K., Walker, J.E., Leslie, A.G.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.236 (Depositor)
R-Value Work:
0.184 (Depositor), 0.188 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The Structure of Bovine F1-ATPase Inhibited by Adp and Beryllium Fluoride

Kagawa, R., Montgomery, M.G., Braig, K., Leslie, A.G.W., Walker, J.E.

(2004) EMBO J 23: 2734

PubMed: 15229653 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/sj.emboj.7600293
Primary Citation Related Structures:
1W0J, 1W0K

PubMed Abstract:
The structure of bovine F1-ATPase inhibited with ADP and beryllium fluoride at 2.0 angstroms resolution contains two ADP.BeF3- complexes mimicking ATP, bound in the catalytic sites of the beta(TP) and beta(DP) subunits. Except for a 1 angstrom shift in the guanidinium of alphaArg373, the conformations of catalytic side chains are very similar in both sites. However, the ordered water molecule that carries out nucleophilic attack on the gamma-phosphate of ATP during hydrolysis is 2.6 angstroms from the beryllium in the beta(DP) subunit and 3.8 angstroms away in the beta(TP) subunit, strongly indicating that the beta(DP) subunit is the catalytically active conformation. In the structure of F1-ATPase with five bound ADP molecules (three in alpha-subunits, one each in the beta(TP) and beta(DP) subunits), which has also been determined, the conformation of alphaArg373 suggests that it senses the presence (or absence) of the gamma-phosphate of ATP. Two catalytic schemes are discussed concerning the various structures of bovine F1-ATPase.

Organizational Affiliation

The Medical Research Council Dunn Human Nutrition Unit, Cambridge, UK.

Macromolecule Content

Total Structure Weight: 354.22 kDa
Atom Count: 24,480
Modeled Residue Count: 3,056
Deposited Residue Count: 3,248
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE ALPHA CHAIN HEART ISOFORM, MITOCHONDRIAL PRECURSOR	A, B, C	510	Bos taurus	Mutation(s): 0 EC: 3.6.3.14
UniProt
Find proteins for P19483 (Bos taurus) Explore P19483 Go to UniProtKB: P19483
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19483
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 PRECURSOR	D, E, F	482	Bos taurus	Mutation(s): 0 EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for P00829 (Bos taurus) Explore P00829 Go to UniProtKB: P00829
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00829
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR	G	272	Bos taurus	Mutation(s): 0 EC: 3.6.3.14
UniProt
Find proteins for P05631 (Bos taurus) Explore P05631 Go to UniProtKB: P05631
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05631
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 H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain V [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth F] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D] mmCIF format, chain V [auth F]	H [auth A], K [auth B], N [auth C], R [auth D], V [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain V [auth F]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth E] MOL2 format, chain U [auth E] mmCIF format, chain U [auth E]	U [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain U [auth E] Interactions & Density Focus chain U [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D]	J [auth A], M [auth B], P [auth C], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth D] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth D]
BEF Query on BEF Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain X [auth F] MOL2 format, chain T [auth D] MOL2 format, chain X [auth F] mmCIF format, chain T [auth D] mmCIF format, chain X [auth F]	T [auth D], X [auth F]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain T [auth D] Focus chain X [auth F] Interactions & Density Focus chain T [auth D] Focus chain X [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain S [auth D] SDF format, chain W [auth F] SDF format, chain O [auth C] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth D] MOL2 format, chain W [auth F] MOL2 format, chain O [auth C] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth D] mmCIF format, chain W [auth F] mmCIF format, chain O [auth C]	I [auth A], L [auth B], O [auth C], S [auth D], W [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236 (Depositor)
R-Value Work: 0.184 (Depositor), 0.188 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 283.52	α = 90
b = 107.374	β = 90
c = 137.936	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: 2004-07-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-07-08
Type: Initial release
Version 1.1: 2014-01-22
Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description