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Structural Basis for Recognition of the mRNA Class II AU-Rich Element by the Tandem Zinc Finger Domain of TIS11d
Authors
Hudson, B.P., Martinez-Yamout, M.A., Dyson, H.JANE., Wright, P.E.
Assembly
TIS11d TZF/ 5'-UUAUUUAUU-3' complex
Entity
1. TIS11d TZF (polymer, Thiol state: all other bound), 70 monomers, 8298.309 Da Detail

STRYKTELCR PFEESGTCKY GEKCQFAHGF HELRSLTRHP KYKTELCRTF HTIGFCPYGP RCHFIHNADE


2. 5'-UUAUUUAUU-3' (polymer, Thiol state: not present), 9 monomers, 2819.587 Da Detail

UUAUUUAUU


3. ZN (non-polymer), 65.409 × 2 Da
Total weight
11248.714 Da
Max. entity weight
8298.309 Da
Entity Connection
na 8 Detail

IDTypeValue orderAtom ID 1Atom ID 2
1nasing1:CYS9:SG3:ZN1:ZN
2nasing1:CYS18:SG3:ZN1:ZN
3nasing1:CYS24:SG3:ZN1:ZN
4nasing1:HIS28:NE23:ZN1:ZN
5nasing1:CYS47:SG3:ZN1:ZN
6nasing1:CYS56:SG3:ZN1:ZN
7nasing1:CYS62:SG3:ZN1:ZN
8nasing1:HIS66:NE23:ZN1:ZN

Source organism
Homo sapiens
Exptl. method
NMR
Refine. method
Individual zinc finger domains were created in DYANA and docked to UAUU (finger I) and UUAUU (finger II) using five rounds of simulated annealing in AMBER using distance and torsional restraints. Finger I/UAUU and Finger II/UUAUU complexes were connected to form TZF/UUAUUUAUU complexes and refined in AMBER with residual dipolar coupling restraints added. Calculations were then switched from in vacuo to Generalized Born continuum solvent model and one additional round of simulated annealing was performed.
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 87.3 %, Completeness: 78.4 %, Completeness (bb): 77.5 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C15N
All78.4 % (775 of 989)81.3 % (423 of 520)72.6 % (286 of 394)88.0 % (66 of 75)
Backbone77.5 % (396 of 511)70.8 % (138 of 195)77.6 % (194 of 250)97.0 % (64 of 66)
Sidechain81.4 % (442 of 543)87.7 % (285 of 325)74.2 % (155 of 209)22.2 % (2 of 9)
Aromatic42.8 % (71 of 166)55.4 % (46 of 83)32.9 % (25 of 76) 0.0 % (0 of 7)
Methyl100.0 % (42 of 42)100.0 % (21 of 21)100.0 % (21 of 21)

1. TIS11d TZF

STRYKTELCR PFEESGTCKY GEKCQFAHGF HELRSLTRHP KYKTELCRTF HTIGFCPYGP RCHFIHNADE

2. 5'-UUAUUUAUU-3'

UUAUUUAUU

Sample #1

Temperature 298 (±0.5) K, pH 6.2 (±0.1)


#NameIsotope labelingTypeConcentration
1TIS11d TZF[U-15N]0.5 mM
25'-UUAUUUAUU-3'0.5 mM
3TrisHCl10 mM
4KCl20 mM
5DTT2.5 mM
6ZnSO425 uM
7H2095 %
8D2O5 %
Sample #2

Temperature 298 (±0.5) K, pH 6.2 (±0.1)


#NameIsotope labelingTypeConcentration
17TIS11d TZF[U-13C; U-15N]0.5 mM
185'-UUAUUUAUU-3'0.5 mM
19Tris-HCl10 mM
20KCl20 mM
21DTT2.5 mM
22ZnSO425 uM
23D2O100 %

Chem. Shift Complete2
Sequence coverage: 27.8 %, Completeness: 46.9 %, Completeness (bb): 46.2 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C15N
All46.9 % (928 of 1978)49.5 % (515 of 1040)42.4 % (334 of 788)52.7 % (79 of 150)
Backbone46.2 % (472 of 1022)43.8 % (171 of 390)44.8 % (224 of 500)58.3 % (77 of 132)
Sidechain48.9 % (531 of 1086)52.9 % (344 of 650)44.3 % (185 of 418)11.1 % (2 of 18)
Aromatic29.2 % (97 of 332)40.4 % (67 of 166)19.7 % (30 of 152) 0.0 % (0 of 14)
Methyl64.3 % (54 of 84)64.3 % (27 of 42)64.3 % (27 of 42)

1. TIS11d TZF

STRYKTELCR PFEESGTCKY GEKCQFAHGF HELRSLTRHP KYKTELCRTF HTIGFCPYGP RCHFIHNADE

2. 5'-UUAUUUAUU-3'

UUAUUUAUU

Sample #1

Temperature 298 (±0.5) K, pH 6.2 (±0.1)


#NameIsotope labelingTypeConcentration
1TIS11d TZF[U-15N]0.5 mM
25'-UUAUUUAUU-3'0.5 mM
3TrisHCl10 mM
4KCl20 mM
5DTT2.5 mM
6ZnSO425 uM
7H2095 %
8D2O5 %
Sample #2

Temperature 298 (±0.5) K, pH 6.2 (±0.1)


#NameIsotope labelingTypeConcentration
17TIS11d TZF[U-13C; U-15N]0.5 mM
185'-UUAUUUAUU-3'0.5 mM
19Tris-HCl10 mM
20KCl20 mM
21DTT2.5 mM
22ZnSO425 uM
23D2O100 %

LACS Plot; CA
Referencing offset: -0.01 ppm, Outliers: 1 Detail
LACS Plot; CB
Referencing offset: -0.01 ppm, Outliers: 1 Detail
LACS Plot; HA
Referencing offset: 0.12 ppm, Outliers: 1 Detail
LACS Plot; CO
Referencing offset: 0.05 ppm, Outliers: 1 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 1RGO, Strand ID: A Detail


Release date
2005-11-13
Citation 1
Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d
Hudson, B.P., Martinez-Yamout, M.A., Dyson, H.JANE., Wright, P.E.
Nat. Struct. Mol. Biol. (2004), 11, 257-264, PubMed 14981510 , DOI 10.1038/nsmb738 ,
Citation 2
ERF-2, the human homologue of the murine Tis11d early response gene
Nie, X.F., Maclean, K.N., Kumar, V., McKay, I.A., Bustin, S.A.
Gene (1995), 152, 285-286, PubMed 7835719 , DOI: ,
Citation 3
Characteristics of the interaction of a synthetic human tristetraprolin tandem zinc finger peptide with AU-rich element-containing RNA substrates
Blackshear, P.J., Lai, W.S., Kennington, E.A., Brewer, G., Wilson, G.M., Guan, X., Zhou, P.
J. Biol. Chem. (2003), 278, 19947-19955, PubMed 12639954 , DOI 10.1074/jbc.M301290200 ,
Entries sharing articles Swiss-Prot: 1 entries Detail
  Swiss-Prot: P47974 released on 1996-10-01
    Title TISD_HUMAN Entity Zinc finger protein 36, C3H1 type-like 2
Related entities 1. TIS11d TZF, : 1 : 6 : 164 entities Detail
Experiments performed 27 experiments Detail
nullKeywords butyrate, complex, degradation ARE UTR Nup475, ERF, intercalate, intercalation, response factor, single-stranded, TIS11, TTP tristetraprolin RNA