1MIS

STRUCTURE OF RNA (5'-R(GP*CP*GP*GP*AP*CP*GP*C)-3') ANTI-PARALLEL RNA DUPLEX WITH TANDEM G:A MISMATCHES, NMR, MINIMIZED AVERAGE STRUCTURE


Citations in PubMed

Primary Citation PubMed: 8703939 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.

(2009) J Chem Theory Comput 5

PubMed: 20090924 | PubMedCentral: PMC2807739 | DOI: 10.1021/ct800540c

PDB IDs of (5′GCG GA CGC3′) 2 and (5′GCiG GA iCGC3′) 2 are 1MIS and 2O81 , respectively.

Colored nucleotides in a−d are the loop regions of NMR structures of 2O81 , 1MIS , 2O83 , and 1YFV , respectively, from the PDB.

Figure 7 5′G G 3′/3′CA̲5′, imino GA stacked on GC in 5′GCG GA CGC3′/3′CGC AG GCG5′ ( 1MIS ) after minimization with (a) amber99 force field and (b) modified amber99 force field.

Publication Year: 2009


Structure determination of noncanonical RNA motifs guided by H NMR chemical shifts.

(2014) Nat Methods 11

PubMed: 24584194 | PubMedCentral: PMC3985481 | DOI: 10.1038/nmeth.2876

Motif name PDB a N nt b rmsd-top1 c , d (Å) rmsd-top5 c , e (Å) Known structures Single G:G mismatch 1F5G 6 0.71 0.71 UUCG tetraloop 2KOC 6 0.84 0.84 Tandem GA:AG mismatch 1MIS 8 1.10 ... .10 Tandem UG:UA mismatch 2JSE 8 3.02 2.52 16S rRNA UUAAGU loop 1FJG 8 0.52 0.52 HIV-1 TAR apical loop 1ANR 8 5.86 5.86 tRNA i Met ASL 1SZY 9 3.89 1.35 Conserved SRP internal loop 1LNT 12 0.81 0.81 R2 retrotransposon 4×4 loop 2L8F 12 1.17 1.17 Hepatitis C virus IRES IIa 2PN4 13 3.21 1.48 GAAA tetraloop-receptor 2R8S 15 0.68 0.68 Sc.ai5γ 3-way junction 2LU0 16 3.66 1.74 Blind targets UAAC tetraloop f 4A4R 6 0.94 0.94 UCAC tetraloop f 4A4S 6 1.00 1.00 UGAC tetraloop f 4A4U 6 3.60 1.67 UUAC tetraloop f 4A4T 6 1.72 1.72 Chimp HAR1 GAA loop 2LHP 7 2.88 2.88 Human HAR1 GAA loop 2LUB 7 2.26 2.03 GU:UAU internal loop – g 9 1.37 1.37 tRNA Gly ASL (cuUCCaa) h 2LBL 9 3.28 1.41 tRNA Gly ASL (cuUCCcg) h 2LBK 9 3.42 1.94 tRNA Gly ASL (uuGCCaa) h 2LBJ 9 3.08 2.93 5′-GAGU/3′-UGAG loop 2LX1 12 1.10 1.10 rmsd < 1.50 Å – – 11/23 14/23 rmsd < 2.00 Å – – 12/23 18/23 Additional information and full motif names provided in Supplementary Tables 1 and 3 .

Publication Year: 2014


Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.

(2014) J Chem Theory Comput 10

PubMed: 24803859 | PubMedCentral: PMC3985902 | DOI: 10.1021/ct400861g

38 They used four solution structures (PDB numbers 1MIS, 2O83, 2O81, and 1YFV), 22 , 44 , 45 and they used thermodynamic integration to calculate free energy differences.

Publication Year: 2014