Citations in PubMed

Primary Citation PubMed: 8943190 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 19

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Distinction between pore assembly by staphylococcal alpha-toxin versus leukotoxins.

(2007) J Biomed Biotechnol 2007

PubMed: 17497023 | PubMedCentral: PMC1847480 | DOI: 10.1155/2007/25935

(b) For comparison, view three protomers of the α -toxin heptamer (PDB code 7AHL) and polar interactions involving the N-terminal extremity of a given subunit (red) with residues of two adjace... t protomers (grey and dark grey) within the α -toxin pore lumen.

Publication Year: 2007

OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria.

(2011) Nucleic Acids Res 39

PubMed: 20952406 | PubMedCentral: PMC3013764 | DOI: 10.1093/nar/gkq863

We chose to exclude β-barrels that do not originate from Gram-negative bacteria, such as the mitochondrial voltage-dependent anion channel (PDB ID: 2JK4) ( 42 ), the MspA mycobacterial outer m... mbrane channel (PDB ID: 1UUN) ( 43 ) or the α-hemolysin (PDB ID: 7AHL) ( 44 ) and LukF (PDB ID:3LKF) ( 45 ) from Staphylococcus aureus .

Publication Year: 2011

Protein detection by nanopores equipped with aptamers.

(2012) J Am Chem Soc 134

PubMed: 22229655 | PubMedCentral: PMC3278221 | DOI: 10.1021/ja2105653

The models are based on pdb files 7AHL (αHL, gray), 3IAG (dsDNA, light blue and orange), and 148D (thrombin aptamer, red).

The models are based on pdb files 7AHL (αHL, gray), 3IAG (dsDNA, light blue and orange), and 148D (thrombin aptamer, red).

The models are based on pdb files 7AHL (αHL, gray), 3IAG (dsDNA, light blue and orange), 148D (thrombin aptamer, red), and 1HUT (thrombin and thrombin·aptamer complex, green and green plus red, respectively).

The model was made with PyMOL software ( ) based on the pdb files 7AHL (αHL, gray) and 3IAG (ssDNA, light blue).

Publication Year: 2012

Novel structurally designed vaccine for S. aureus ?-hemolysin: protection against bacteremia and pneumonia.

(2012) PLoS One 7

PubMed: 22701668 | PubMedCentral: PMC3368876 | DOI: 10.1371/journal.pone.0038567

The crystal structure of heptameric AT (PDB code 7AHL) [20] was selected for this study.

( A ) The relative topology of 1–62 and 1–62(GGG)–(223–236) AT constructs on the protein surface of a subunit from the 7AHL heptameric hemolysin crystal structure.

Publication Year: 2012

BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores.

(2012) J Chem Theory Comput 8

PubMed: 22798730 | PubMedCentral: PMC3396124 | DOI: 10.1021/ct3004244

38 2.3 Modeling of ss-DNA Dynamics in the α-Hemolysin Channel The structure for α-HL was taken from Protein Data Bank (Protein Data Bank entry: 7ahl ).

Publication Year: 2012

Electrostatic ratchet in the protective antigen channel promotes anthrax toxin translocation.

(2012) J Biol Chem 287

PubMed: 23115233 | PubMedCentral: PMC3527960 | DOI: 10.1074/jbc.M112.419598

A three-dimensional model of the 14-stranded β-barrel region of the PA channel (residues 275 to 352) was made by coaxially stacking multiple copies of the heptameric β-barrel from �... 3b1; hemolysin (PDB 7AHL ( 30 )).

Publication Year: 2012

Oroxylin A inhibits hemolysis via hindering the self-assembly of ?-hemolysin heptameric transmembrane pore.

(2013) PLoS Comput Biol 9

PubMed: 23349625 | PubMedCentral: PMC3547825 | DOI: 10.1371/journal.pcbi.1002869

However, the distance between the C α of Thr12 and the C α of Thr19 is 1.81 nm in the crystal structure of the α-HL heptamer, which is available in the Protein Data Bank under ... he accession number 7AHL.

Through comparing the structure of the loop in α-HL-ORO complex with the crystal structure of α-HL monomeric observed in the X-ray structure of the oligomer (PDB code: 7AHL), it is indicated that ORO blocks the required conformational transition of the loop by binding to the loop, which is the mechanism of decreasing the lytic activity of α-HL.

Publication Year: 2013

Molecular architecture and functional analysis of NetB, a pore-forming toxin from Clostridium perfringens.

(2013) J Biol Chem 288

PubMed: 23239883 | PubMedCentral: PMC3561570 | DOI: 10.1074/jbc.M112.430223

Molecular replacement was carried out using Phaser MR ( 20 ) and the αHL heptamer structure (PDB ID 7AHL ) as a search model.

Surface representation is shown of the rim domain of αHL (PDB ID 7AHL ) ( A ) and NetB ( B ) in the same orientation.

Molecular replacement using the αHL heptamer (PDB ID 7AHL ) resulted in a single solution with two heptamers in the asymmetric unit and a solvent content of 71%.

Publication Year: 2013

Structures of membrane proteins.

(2010) Q Rev Biophys 43

PubMed: 20667175 | PubMedCentral: PMC3604715 | DOI: 10.1017/S0033583510000041

The long helices B, C and F form the wall of the pore and the top is constricted by the N-terminus of helix A. Fig. 26 Pore forming toxins a) ClyA (2WCD) b) α-HL (7AHL).

Publication Year: 2010

A stimuli-responsive nanopore based on a photoresponsive host-guest system.

(2013) Sci Rep 3

PubMed: 23588705 | PubMedCentral: PMC3627192 | DOI: 10.1038/srep01662

Figure 1 Representation of an α -HL (PDB ID: 7AHL) and the interaction mechanism between SC 4 and V 2+ - trans -Az. (a) An α -HL nanopore is embedded in a lipid bilayer at the Tris-EDT... (pH 8.0).

Publication Year: 2013

An engineered dimeric protein pore that spans adjacent lipid bilayers.

(2013) Nat Commun 4

PubMed: 23591892 | PubMedCentral: PMC3644966 | DOI: 10.1038/ncomms2726

The space filling models of α7 (PDB 7AHL) and (α7) 2 were created in PyMOL.

Publication Year: 2013

Role of pore-forming toxins in neonatal sepsis.

(2013) Clin Dev Immunol 2013

PubMed: 23710203 | PubMedCentral: PMC3655490 | DOI: 10.1155/2013/608456

By far the largest class of membrane damaging toxins is that of the pore-forming toxins (structure: α -toxin from S. aureus , PDB ID 7AHL, [ 100 ]).

(c3) displays the heptameric pore structure of the AFT pore (PDB ID 7AHL, [ 100 ]), individual protomer, side and tops views.

Publication Year: 2013

Structural Insights into Clostridium perfringens Delta Toxin Pore Formation.

(2013) PLoS One 8

PubMed: 23805259 | PubMedCentral: PMC3689675 | DOI: 10.1371/journal.pone.0066673

g002 Figure 2 Superposition of C. perfringens Delta toxin structure with γHL-Hlg2 in grey (PDB ID: 3B07) (A), with γHL-LukF in pale green (PDB ID: 3B07) (B) and with a monomer of the &... x003b1;HL of S. aureus in yellow (PDB ID: 7AHL) (C).

Delta toxin was sequence aligned with a number of other known hemolysin-like atomic structures using ClustalW [36] and αHL (PDB ID 7AHL) [15] , and residues corresponding to the stem and latch domains in αHL were deleted from the final refined model of Delta toxin.

(Uniprot ID: B8QGZ7), C. perfringens Beta toxin (Uniprot ID: Q9L403), C. perfringens NetB (Uniprot ID: A8ULG6), S. aureus αHL (aHL; Uniprot ID: P09616; PDB ID: 7AHL), the F component of S. aureus leucocidin (LukF; Uniprot ID: P0A077; PDB ID: 1LKF), the F component of S. aureus Panton-Valentine leucocidin (LukF-PV; Uniprot ID: O50604; PDB ID: 1PVL), the S component of S. aureus Panton-Valentine leucocidin (LukS-PV; Uniprot ID: Q783R1; PDB ID: 1T5R), the F component of S. aureus γ-Hemolysin (LukF-gHL; Uniprot ID: Q931F3; PDB ID: 3B07) and the S component of S. aureus γ-Hemolysin (Hlg2-gHL; Uniprot ID: P0A071; PDB ID: 3B07).

The residues corresponding to the latch and stem domains from 7AHL where mutated to their corresponding residues in Delta toxin using Chainsaw [38] from CCP4 and these two domains added to the Delta toxin.

Publication Year: 2013

Staphylococcus aureus ?-toxin: nearly a century of intrigue.

(2013) Toxins (Basel) 5

PubMed: 23888516 | PubMedCentral: PMC3717774 | DOI: null

Crystal structure of α-toxin derived from the RCSB Protein Data Bank (PDB, 7AHL) and prepared using PYMOL, noting the regions of the toxin that demarcate the entry of the pore (Cap), the membr... ne-interfacing region (Rim), and the membrane perforating stem.

Publication Year: 2013

Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation.

(2014) Sci Rep 4

PubMed: 24463372 | PubMedCentral: PMC3902492 | DOI: 10.1038/srep03885

The peptide coordinates were merged with that of alpha-hemolysin (PDB ID: 7AHL) followed by subsequent rotation and translation to fit it at the trans-end of the pore.

Publication Year: 2014

Channel-forming bacterial toxins in biosensing and macromolecule delivery.

(2014) Toxins (Basel) 6

PubMed: 25153255 | PubMedCentral: PMC4147595 | DOI: 10.3390/toxins6082483

Channel current corresponds to ~100 pA in 1M KCl, pH 7.4; ( b ) Crystal structure of the αHL heptamer (top and side views are shown) (PDB 7AHL) [ 78 ].

Publication Year: 2014

Mechanisms of neutralization of a human anti-?-toxin antibody.

(2014) J Biol Chem 289

PubMed: 25210036 | PubMedCentral: PMC4207998 | DOI: 10.1074/jbc.M114.601328

A , superimposition of monomeric AT of this study ( green ) with pore-forming AT ( light blue , PDB code 7AHL ; Ref.

Stereographic representation of four out of seven AT protomers in a lytic pore ( orange , blue , gray , and light blue ; PDB code 7AHL ; Ref.

The structure of monomeric AT bound to MEDI4893 Fab was determined by molecular replacement using a modified model of an AT protomer in the heptameric conformation (PDB code 7AHL ) ( 12 ) and that of an unpublished Fab structure (MedImmune).

AT regions that undergo large conformational changes upon heptamerization (“latch” and stem; PDB code 7AHL ) are shown in red .

Excluding the stem and latch regions of AT and using the LSQKAB program ( 26 ), oligomeric AT (PDB code 7AHL ) superimposes well with the monomeric AT of this study with an r.m.s.d. of 0.7 Å over the C α atoms ( Fig. 3 A ).

Publication Year: 2014

Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force.

(2014) J Comput Chem 35

PubMed: 24403093 | PubMedCentral: PMC4274958 | DOI: 10.1002/jcc.23525

The αHL crystallographic structure coordinates were taken from Protein Data Bank (PDB) entry 7AHL.

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4387736

A structural region (in between strands 2 and 3; shown in red in Figure  4 ) that is present in analogous positions in these toxin structures and the Staphylococcus aureus α-hemolysin ... tructure (PDB codes: 1uyj, 1z52 and 7ahl respectively) has been implicated in membrane insertion ([ 31 , 32 ]).

Publication Year: 2015