Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

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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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ATP-driven molecular chaperone machines.

(2013) Biopolymers 99

PubMed: 23877967 | PubMedCentral: PMC3814418 | DOI: 10.1002/bip.22361

Structures of Hsp70 in the open, domain docked (a) and closed (b) conformations (PDB ID: 4B9Q and 2KHO).

Publication Year: 2013

Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.

(2013) PLoS Comput Biol 9

PubMed: 24348227 | PubMedCentral: PMC3861046 | DOI: 10.1371/journal.pcbi.1003379

B: Cartoon diagram of the experimental X-ray structure of E. coli ATP-Hsp70 (PDB ID: 4B9Q) [69] .

Although the structure of the intermediate state found in MD and the crystallized open conformation of DnaK are quite different as discussed above, many contacts between ATP and the NBD found in ATP*-DnaK ( Fig. 4 B and C ) are also found in the experimental structure of ATP-bound DnaK (PDB ID: 4B9Q) [69] .

In ATP-bound Hsp70, the SBD is open with fast binding and release of the protein substrate, and the SBD and NBD are docked, as shown by SAXS data [82] , [83] and FRET data [84] , [85] and suggested by the X-ray structure of an ATP-Hsp110 homolog [86] , [87] and by a new open conformation of an ATP-bound DnaK mutant (PDB ID: 4B9Q) [69] stabilized by introducing disulphide bridges at specific positions deduced from the structure of the ATP-Hsp110 homolog ( Fig. 1 B ).

The intermediate structure of ATP*-DnaK is different from the very recent crystallized triple mutant ATP-bound DnaK (E47C, T199A, F529C) in an open conformational state with a SBD-α covalently bound to the NBD through a disulphide bridge 47C-529C (PDB ID: 4B9Q) [69] .

Comparison with the new published X-ray full-length ATP-bound open structure (PDB ID: 4B9Q) [69] , confirmed that the initial relaxed position of the ATP molecule (which mimic the ATP binding position in the full-length E. coli Hsp70 in a closed state) is realistic.

Publication Year: 2013

ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones.

(2014) PLoS Comput Biol 10

PubMed: 24831085 | PubMedCentral: PMC4022485 | DOI: 10.1371/journal.pcbi.1003624

Figure S2 Comparison of the collective dynamics obtained for the DnaK homology model (HM) proposed by Smock et al and the PDB structures 4B9Q and 4JNE, resolved by X-ray crystallography.

Diagrams B and D were generated using the PDB files 1DKX [7] and 4B9Q [25] , respectively.

We also repeated our calculations for the structures recently resolved for ATP-bound DnaK —PDB codes 4B9Q and 4JNE [25] , [26] — which showed that GNM and PRS results are insensitive to structural details and closely reproduced using these structures (see Text S1 for comparative results).

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4241170

6 − 10 To gain additional insight regarding how the interaction between PET-16 and DnaK may impact the DnaK SBD, we overlaid structurally corresponding Cα atoms of the SBD of DnaK-PET-... 6 with the following reported structures: a full-length ADP-bound DnaK NMR structure (PDB code 2KHO) 10 and two full-length ATP-bound DnaK X-ray structures (PDB codes 4JN4 and 4B9Q) 7 , 9 ( Supporting Information , Figure S3).

From this analysis, we noted that the crystal structure of DnaK-PET-16 is substantially different from the ATP-DnaK-SBD structures (an overall Cα rmsd = 26.243 and 26.039 Å for 4JN4 and 4B9Q, respectively).

Publication Year: 2014

C-terminal amino acids are essential for human heat shock protein 70 dimerization.

(2015) Cell Stress Chaperones 20

PubMed: 25030382 | PubMedCentral: PMC4255253 | DOI: 10.1007/s12192-014-0526-3

More recently, full-length E. coli DnaK structures in an ATP-bound state were solved using X-ray diffraction (PDB ID: 4B9Q, and 4JNE) (Kityk et al.

Publication Year: 2015

Human mitochondrial Hsp70 (mortalin): shedding light on ATPase activity, interaction with adenosine nucleotides, solution structure and domain organization.

(2015) PLoS One 10

PubMed: 25615450 | PubMedCentral: PMC4304843 | DOI: 10.1371/journal.pone.0117170

n. 4B9Q [ 46 ]) and the NMR structure for E. coli DnaK in the ADP state (in the closed conformation—PDB acc.

n. 4B9Q [ 46 ]) and in the closed (PDB acc.

n. 4B9Q), obtained bound to ATP and with the PDB in the open conformation [ 46 ], was used for its manual adjustment into mortalin ab initio model.

Publication Year: 2015

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4428496

(B) Model of Hsp70 ATP state structure [pdb 4B9Q (Kityk et al., 2012 )].

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4431665

The two high-resolution structures that best accommodate our XLs are the ADP- and ATP-bound states of DnaK (PDB IDs 2KHO and 4B9Q , respectively ( Bertelsen et al., 2009, Kityk et al.,... 2012 ).

We generated a homology model for the ATP state using the structure 4B9Q as a template.

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4457872

S8 Fig Alignment of the two ATP state PDB structures 4jne and 4b9q.

coli DnaK, for which high-resolution structures are available for both ATP- (PDB ID 4jne [ 22 ] and 4b9q [ 21 ]) and ADP-bound states (PDB ID 2kho [ 20 ]).

Regarding the former state, we use the higher resolution structure (PDB ID 4jne, see S1 Fig for analogous comparison with 4b9q and S1 Text for comments on the supplementary material).

Publication Year: 2015