Citations in PubMed

Primary Citation PubMed: 11313498 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

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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InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

(2007) Genome Biol 8

PubMed: 17868464 | PubMedCentral: PMC2375030 | DOI: 10.1186/gb-2007-8-9-r192

Both Rpb9 and Rpb1 are part of the co-crystallized Pol II complex in PDB (ID: 1I50).

Publication Year: 2007


Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure.

(2009) PLoS Biol 7

PubMed: 19419240 | PubMedCentral: PMC2675907 | DOI: 10.1371/journal.pbio.1000102

Figure S3 Stereo View of Superimposed Ca Traces of Archaeal Rpo8 and Eukaryotic Rpb8 Stereo view of superimposed Cα traces of archaeal Rpo8 (red ribbon) and eukaryotic Rpb8 (yellow ribbon; PDB... entry 1I50); N and C label respectively the N terminus and C terminus of Rpo8.

Publication Year: 2009


Pushing structural information into the yeast interactome by high-throughput protein docking experiments.

(2009) PLoS Comput Biol 5

PubMed: 19714207 | PubMedCentral: PMC2722787 | DOI: 10.1371/journal.pcbi.1000490

For RET1 the model used is based on the homologous protein in RNA Polymerase II in yeast (PDB id 1i50) and covers the entire sequence of the protein.

Publication Year: 2009


Modeling of loops in proteins: a multi-method approach.

(2010) BMC Struct Biol 10

PubMed: 20149252 | PubMedCentral: PMC2837870 | DOI: 10.1186/1472-6807-10-5

loop length PDB codes and loop ranges 4 7rsa 47-50, 4gcr 116-119, 2tgi 72-75, 2exo 161-164, 1xif 82-85, 1tml 42-45, 1tib 46-49, 1thw 194-197, 1rcf 111-114, 1ppn 42-45, 1plc 74-77, 1pbe 117-120, 1nfp 3... -40, 1frd 59-62, 1cbs 21-24, 1ads 99-102, 1aaj 82-85 5 7rsa 75-79, 2hbg 37-41, 2cmd 188-192, 1vcc 63-67, 1tml 147-151, 1tca 157-161, 1sbp 181-185, 1prn 187-191, 1noa 88-92, 1nfp 95-99, 1nar 56-60, 1kuh 37-41, 1hbq 158-162, 1hbg 19-23, 1frd 83-87, 153l 131-135 6 5p21 104-109, 3pte 256-261, 3pte 131-136, 2ayh 81-86, 1tca 94-99, 1tca 38-43, 1rge 73-78, 1noa 25-30, 1mrp 233-238, 1gca 100-105, 1ede 180-185, 1cbs 66-71, 1brt 253-258, 1brt 174-179, 1ads 150-155, 1ads 149-154 7 5p21 83-89, 2pth 95-101, 1tml 20-26, 1tca 132-138, 1php 135-141, 1mbd 17-23, 1lif 64-70, 1iab 142-148, 1hbg 46-52, 1gca 196-202, 1edg 309-315, 1dad 116-122, 1brt 226-232, 1bkf 64-70, 1ads 186-192 8 2ayh 194-201, 1tml 187-194, 1thw 18-25, 1prn 150-157, 1nwp 84-91, 1nls 97-104, 1nar 192-199, 1hbq 31-38, 1arb 136-143, 1alc 34-41, 1ads 274-281 9 3pte 107-115, 2ayh 169-177, 1xnb 133-141, 1xnb 116-124, 1php 91-99, 1nls 131-139, 1ede 257-265, 1arb 168-176, 1aac 58-66 10 7rsa 87-96, 7rsa 33-42, 7rsa 110-119, 2cmd 57-66, 1whi 47-56, 1tca 23-32, 1scs 65-74, 1ppn 190-199, 1plc 42-51, 1mrj 173-182, 1ixh 84-93, 1gvp 49-58, 1fkf 63-72, 1arb 41-50, 1amp 181-190, 1ads 171-180, 1ads 170-179, 135l 18-27 11 3pte 91-101, 2pth 8-18, 1rcf 122-132, 1ixh 120-130, 1dad 42-52, 153l 154-164 12 2ayh 21-32, 1ixh 160-171, 1bkf 9-20, 1arb 74-85, 153l 98-109 16 1tml 73-88, 1tml 219-234, 1tca 184-199, 1rge 37-52, 1prn 106-121, 1nar 10-25, 1iab 136-151, 1frd 33-48, 1edg 233-248, 1edg 167-182, 1brt 57-72, 1amp 98-113, 1ads 210-225 18 1tml 73-90, 1tml 219-236, 1tca 184-201, 1prn 106-123, 1nar 10-27, 1iab 136-153, 1byt 807-824, 1byt 700-717, 1byt 359-376, 1byt 230-247, 1bst 57-74, 1bst 129-146, 1b57 209-226, 1awj 2-19, 1amp 98-115, 1ahj 101-118, 1ads 210-227, 1acc 36-53, 1acc 183-200 20 1br4 390-409, 1br4 349-368, 1br4 291-310, 1br2 246-265, 1azx 362-381 22 1tml 219-240, 1prn 106-127, 1nar 10-31, 1kk7 291-312, 1jez 117-138, 1itk 179-200, 1itk 157-178, 1e04 351-372, 1clq 380-401, 1br4 71-92, 1br4 256-277, 1b3k 322-343, 1aoa 182-203 23 1nfb 253-275, 1lzj 2-24, 1izl 21-43, 1i50 46-68, 1dzg 367-389 24 1uoz 224-247, 1mnd 277-300, 1miu 93-116, 1i19 415-438, 1hfb 86-109 25 2hs0 319-343, 2gah 437-461, 2fqf 293-317, 2e4y 311-335, 1zba 16-40, 1tml 219-243, 1qme 127-151, 1prn 106-130, 1kmh 117-141, 1eah 247-271, 1dms 596-620, 1dhx 376-400, 1dhx 11-35 Using MODELLER, we generated 500 examples of individual loop regions, which were subsequently ranked by the DOPE statistical potential [ 22 ].

Publication Year: 2010


Computational simulation strategies for analysis of multisubunit RNA polymerases.

(2013) Chem Rev 113

PubMed: 23987500 | PubMedCentral: PMC3829680 | DOI: 10.1021/cr400046x

Table 1 Structures of RNAPs Used in Computational Simulations PDB ID resolution (Å) organism a protein nucleic acid nucleotide state TL b simulations c refs 1I6H 3.30 Sc 10 subunits T/R �... 0; pretranslocation open NMA (ENM) ( 13a ) 1I50 2.80 Sc 10 subunits       open NMA (ENM) ( 13a ) 1HQM 3.30 Ta α 2 ββ′ω       open NMA (ENM) ( 13a ) 1ARO 2.80 T7   T/N       NMA (ENM) ( 13 ) 1CEZ 2.40 T7           NMA (ENM) ( 13 ) 1I6H 3.30 Sc 10 subunits T/N/R   preinsertion open restricted MD ( 19 ) 1IW7 2.6 Tt α 2 ββ′ωσ     initiation open BNM ( 15 ) 1R9T 3.5 Sc 10 subunits T/N/R ATP (E site) posttranslocation open BD ( 9 ) 1H38 2.9 T7   T/N/R   preinsertion   MD and umbrella sampling ( 22 ) 1S77 2.69 T7   T/N/R PP i pretranslocation   MD and umbrella sampling ( 22 ) 2E2H 3.95 Sc 10 subunits T/N/R GTP posttranslocation closed MD, MSM,QM ( 7a , 16 , 17 , 21 , 29 ) 2E2J 3.5 Sc 10 subunits T/N/R GMPCPP posttranslocation open MD, MSM,QM ( 7a , 16 ) 2O5J 3.0 Tt α 2 ββ′ω T/N/R ATP posttranslocation closed MD ( 18 ) 2PPB 3.0 Tt α 2 ββ′ω T/N/R AMPCPP preinsertion open MD ( 18a , 18b ) 2NVZ 4.3 Sc 10 subunits T/N/R UTP posttranslocation closed QM ( 62 , 73 ) a Sc, Saccharomyces cerevisiae ; Ta, Thermus aquaticus ; T7, Enterobacteria phage T7; Tt, Thermus thermophilus .

Publication Year: 2013


Ribosome synthesis and MAPK activity modulate ionizing radiation-induced germ cell apoptosis in Caenorhabditis elegans.

(2013) PLoS Genet 9

PubMed: 24278030 | PubMedCentral: PMC3836707 | DOI: 10.1371/journal.pgen.1003943

In the crystal structure of the RNA pol II core complex from yeast ( [40] , PDB entry 1I50), the proline corresponding to the residue mutated in RPOA-2 maps to a region that lies distant to the cataly... ic centre of the polymerase, towards an outer surface of the core complex (not shown), suggesting that the synthesis of RNA is preserved and possibly explaining why the op259 mutants, unlike the ok1970 null animals, are viable.

Publication Year: 2013


Insights into how Spt5 functions in transcription elongation and repressing transcription coupled DNA repair.

(2014) Nucleic Acids Res 42

PubMed: 24813444 | PubMedCentral: PMC4066765 | DOI: 10.1093/nar/gku333

The dashed line indicates the open clamp position observed in the absence of Rpb4/7 [PDB 1I50 ( 44 )].

Publication Year: 2014


Solving the RNA polymerase I structural puzzle.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 25286842 | PubMedCentral: PMC4188003 | DOI: 10.1107/S1399004714015788

Crystal structures of Pol II were used for initial tests: ten subunits with open (PDB entry 1i3q ) and closed (PDB entry 1i50 ) clamps and 12 subunits (PDB entry 1wcm ) (Cramer et al. , 2001 ▶... ; Kettenberger et al. , 2004 ▶ ).

Publication Year: 2014