5LR4 - JenaLib

Title :   RNA DUPLEX HAS CENTRAL CONSECUTIVE GA PAIRS FLANKED BY G-U BASEPAIRS WITH A METHYL GROUP ON THE ADENINE N6

Authors :   L. Huang, D. M. J. Lilley

Date :   18 Aug 16 (Deposition) - 21 Jun 17 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   N6-Methyladenine, Rna Folding, Watson-Crick Basepairs, Hoogsteen- Sugar Edge A-G Basepair, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Huang, S. Ashraf, J. Wang, D. M. Lilley
Control Of Box C/D Snornp Assembly By N(6)-Methylation Of Adenine.
Embo Rep. 2017
PubMed-ID: 28623187 | Reference-DOI: 10.15252/EMBR.201743967

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	6MZ	4	Mod. Nucleotide	N6-METHYLADENOSINE-5'-MONOPHOSPHATE
2	CBV	4	Mod. Nucleotide	5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
3	NA	4	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	6MZ	2	Mod. Nucleotide	N6-METHYLADENOSINE-5'-MONOPHOSPHATE
2	CBV	2	Mod. Nucleotide	5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	6MZ	2	Mod. Nucleotide	N6-METHYLADENOSINE-5'-MONOPHOSPHATE
2	CBV	2	Mod. Nucleotide	5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
3	NA	-1	Ligand/Ion	SODIUM ION

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CBV A:2	binding site for residue NA A 101
02	AC2	SOFTWARE	CBV C:2 , C C:3 , HOH C:207	binding site for residue NA C 101
03	AC3	SOFTWARE	CBV C:2	binding site for residue NA C 102
04	AC4	SOFTWARE	G D:1	binding site for residue NA D 101
05	AC5	SOFTWARE	G A:1 , G A:9 , C A:10 , HOH A:207 , C B:3 , C B:10 , HOH B:103 , HOH B:104 , HOH B:109	binding site for Di-nucleotide G B 1 and CBV B 2
06	AC6	SOFTWARE	G A:8 , G A:9 , C A:10 , HOH A:207 , G B:1 , G B:4 , HOH B:109 , HOH B:111 , HOH B:115	binding site for Di-nucleotide CBV B 2 and C B 3
07	AC7	SOFTWARE	G A:5 , 6MZ A:6 , G B:4 , U B:7 , HOH B:113 , G C:9 , C C:10	binding site for Di-nucleotide G B 5 and 6MZ B 6
08	AC8	SOFTWARE	C C:3 , NA C:101 , NA C:102 , HOH C:206 , HOH C:207 , HOH C:210 , G D:9 , C D:10	binding site for Di-nucleotide G C 1 and CBV C 2
09	AC9	SOFTWARE	C B:10 , G C:1 , G C:4 , NA C:101 , NA C:102 , HOH C:202 , HOH C:205 , HOH C:207 , HOH C:211 , G D:8 , G D:9 , C D:10	binding site for Di-nucleotide CBV C 2 and C C 3
10	AD1	SOFTWARE	G C:4 , U C:7 , HOH C:208 , G D:5 , 6MZ D:6 , HOH D:205 , HOH D:208	binding site for Di-nucleotide G C 5 and 6MZ C 6
11	AD2	SOFTWARE	G C:9 , C C:10 , HOH C:204 , C D:3 , NA D:101 , HOH D:207 , HOH D:214	binding site for Di-nucleotide G D 1 and CBV D 2
12	AD3	SOFTWARE	U A:7 , G C:8 , G C:9 , C C:10 , G D:1 , G D:4 , HOH D:207 , HOH D:211	binding site for Di-nucleotide CBV D 2 and C D 3
13	AD4	SOFTWARE	G C:5 , 6MZ C:6 , U C:7 , G D:4 , U D:7 , HOH D:201 , HOH D:204 , HOH D:205 , HOH D:208 , HOH D:212	binding site for Di-nucleotide G D 5 and 6MZ D 6

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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Chain A from PDB  Type:RNA  Length:10
                                         
                  5lr4 A  1 GxCGGxUGGC 10
                             |   |  10
                             |   |    
                             2-CBV    
                                 6-6MZ

Chain B from PDB  Type:RNA  Length:10
                                         
                  5lr4 B  1 GxCGGxUGGC 10
                             |   |  10
                             2-CBV    
                                 6-6MZ

Chain C from PDB  Type:RNA  Length:10
                                         
                  5lr4 C  1 GxCGGxUGGC 10
                             |   |  10
                             2-CBV    
                                 6-6MZ

Chain D from PDB  Type:RNA  Length:10
                                         
                  5lr4 D  1 GxCGGxUGGC 10
                             |   |  10
                             2-CBV    
                                 6-6MZ

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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