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BMRB: 18049

2LLI

Low resolution structure of RNA-binding subunit of the TRAMP complex

Authors

Holub, P., Lalakova, J., Cerna, H., Sarazova, M., Pasulka, J., Hrazdilova, K., Arce, M.S., Stefl, R., Vanacova, S.

Assembly

RNA-binding subunit of the TRAMP complex

Entity

1. RNA-binding subunit of the TRAMP complex (polymer, Thiol state: free and other bound), 124 monomers, 14230.27 Da Detail

KEAAPKCNNC SQRGHLKKDC PHIICSYCGA TDDHYSRHCP KAIQCSKCDE VGHYRSQCPH KWKKVQCTLC KSKKHSKERC PSIWRAYILV DDNEKAKPKV LPFHTIYCYN CGGKGHFGDD CKEK

2. ZINC ION (non-polymer), 1 monomers, 65.409 × 5 Da

Total weight

14557.314 Da

Max. entity weight

14230.27 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 86.3 %, Completeness: 51.5 %, Completeness (bb): 65.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	51.5 % (752 of 1460)	52.3 % (405 of 775)	46.1 % (257 of 558)	70.9 % (90 of 127)
Backbone	65.6 % (479 of 730)	71.8 % (178 of 248)	58.1 % (212 of 365)	76.1 % (89 of 117)
Sidechain	43.6 % (369 of 847)	43.1 % (227 of 527)	45.5 % (141 of 310)	10.0 % (1 of 10)
Aromatic	13.3 % (17 of 128)	26.6 % (17 of 64)	0.0 % (0 of 62)	0.0 % (0 of 2)
Methyl	59.5 % (44 of 74)	59.5 % (22 of 37)	59.5 % (22 of 37)

1. RNA-binding subunit of the TRAMP complex

KEAAPKCNNC SQRGHLKKDC PHIICSYCGA TDDHYSRHCP KAIQCSKCDE VGHYRSQCPH KWKKVQCTLC KSKKHSKERC PSIWRAYILV DDNEKAKPKV LPFHTIYCYN CGGKGHFGDD CKEK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 8

#	Name	Isotope labeling	Concentration
1	RNA-binding_sub	[U-99% 13C; U-99% 15N]	100 uM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate buffer	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	beta-mercaptoethanol	natural abundance	10 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 2.43 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 2.43 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LLI, Strand ID: A Detail

Release date

2012-03-18

Citation

Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation
Holub, P., Lalakova, J., Cerna, H., Pasulka, J., Sarazova, M., Hrazdilova, K., Arce, M., Hobor, F., Stefl, R., Vanacova, S.
Nucleic Acids Res. (2012), 40, 5679-5693, PubMed 22402490 , DOI 10.1093/nar/gks223 , Abstract

Related entities 1. RNA-binding subunit of the TRAMP complex, : 1 : 2 : 106 entities Detail

Interaction partners 1. RNA-binding subunit of the TRAMP complex, : 23 interactors Detail

More details for 23 interactors identified by 11 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC