BMRB Entry 6005

Click here to enlarge.

PDB ID: 1rgo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR6005
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Structural Basis for Recognition of the mRNA Class II AU-Rich Element by the Tandem Zinc Finger Domain of TIS11d

Deposition date:

2003-11-13

Original release date:

2005-11-14

Authors:

Hudson, Brian; Martinez-Yamout, Maria; Dyson, H.; Wright, Peter

Citation:

Citation: Hudson, Brian; Martinez-Yamout, Maria; Dyson, H.; Wright, Peter. "Recognition of the mRNA AU-Rich Element by the Zinc Finger Domain of TIS11d" Nat. Struct. Biol. 11, 257-264 (2004).
PubMed: 14981510

Assembly members:

Assembly members:
TIS11d TZF, polymer, 70 residues, 8298 Da.
5'-UUAUUUAUU-3', polymer, 7 residues, 2830 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
TIS11d TZF: STRYKTELCRPFEESGTCKY GEKCQFAHGFHELRSLTRHP KYKTELCRTFHTIGFCPYGP RCHFIHNADE
5'-UUAUUUAUU-3': UUAUUUAUU

Data sets:

assigned_chemical_shifts
- protein_shifts
- rna_shifts

Data type	Count
13C chemical shifts	282
15N chemical shifts	70
1H chemical shifts	483

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	TIS11d TZF	1
2	5'-UUAUUUAUU-3'	2
3	ZINC (II) ION 1	3
4	ZINC (II) ION 2	3

Entities:

Entity 1, TIS11d TZF 70 residues - 8298 Da.

1	SER	THR	ARG	TYR	LYS	THR	GLU	LEU	CYS	ARG
2	PRO	PHE	GLU	GLU	SER	GLY	THR	CYS	LYS	TYR
3	GLY	GLU	LYS	CYS	GLN	PHE	ALA	HIS	GLY	PHE
4	HIS	GLU	LEU	ARG	SER	LEU	THR	ARG	HIS	PRO
5	LYS	TYR	LYS	THR	GLU	LEU	CYS	ARG	THR	PHE
6	HIS	THR	ILE	GLY	PHE	CYS	PRO	TYR	GLY	PRO
7	ARG	CYS	HIS	PHE	ILE	HIS	ASN	ALA	ASP	GLU

Entity 2, 5'-UUAUUUAUU-3' 7 residues - 2830 Da.

1

U

A

U

A

U

Entity 3, ZINC (II) ION 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: TIS11d TZF, [U-15N], 0.5 mM; 5'-UUAUUUAUU-3' 0.5 mM; TrisHCl 10 mM; KCl 20 mM; DTT 2.5 mM; ZnSO4 25 uM; H20 95%; D2O 5%

sample_2: TIS11d TZF, [U-13C; U-15N], 0.5 mM; 5'-UUAUUUAUU-3' 0.5 mM; TrisHCl 10 mM; KCl 20 mM; DTT 2.5 mM; ZnSO4 25 uM; H20 95%; D2O 5%

sample_3: TIS11d TZF, [U-13C; U-15N], 0.5 mM; 5'-UUAUUUAUU-3' 0.5 mM; Tris-HCl 10 mM; KCl 20 mM; DTT 2.5 mM; ZnSO4 25 uM; D2O 100%

sample_4: TIS11d TZF, [U-13C; U-15N], 0.5 mM; 5'-UUAUUUAUU-3' 0.5 mM; TrisHCl 10 mM; KCl 20 mM; DTT 2.5 mM; ZnSO4 25 uM; Pf1 filamentous phage 12 mg/mL; D2O 100%

Conditions_1: ionic strength: 0.02 M; pH: 6.2; temperature: 298 K

Conditions_2: ionic strength: 0.02 M; pH: 6.2; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-15N HSQC	not available	not available	not available
1H-15N-HMQC	not available	not available	not available
1H-13C-HSQC	not available	not available	not available
1H-13C-CT-HSQC	not available	not available	not available
HNCACB	not available	not available	not available
CBCA(CO)NH	not available	not available	not available
HNCO	not available	not available	not available
C(CO)NH-TOCSY	not available	not available	not available
H(CCO)NH-TOCSY	not available	not available	not available
CCH-COSY	not available	not available	not available
CCH-TOCSY	not available	not available	not available
H(C)CH-COSY	not available	not available	not available
H(C)CH-TOCSY	not available	not available	not available
(HB)CB(CGCD)HD	not available	not available	not available
(HB)CB(CGCDCE)HE	not available	not available	not available
3D 15N-separated NOESY	not available	not available	not available
3D 13C-separated NOESY	not available	not available	not available
3D 13C F1-edited, F3-separated NOESY	not available	not available	not available
2D 13C double-half-filtered NOESY	not available	not available	not available
2D 13C double-half-filtered TOCSY	not available	not available	not available
HNHA	not available	not available	not available
HNHB	not available	not available	not available
HACAHB-COSY	not available	not available	not available
13C-{13CO} spin-echo difference CT-HSQC	not available	not available	not available
13C-{15N} spin-echo difference CT-HSQC	not available	not available	not available
IPAP-[1H,15N]-HSQC	not available	not available	not available
IPAP-HNCO	not available	not available	not available

BMRB Entry 6005

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

Related Database Links:

1	SER	THR	ARG	TYR	LYS	THR	GLU	LEU	CYS	ARG
2	PRO	PHE	GLU	GLU	SER	GLY	THR	CYS	LYS	TYR
3	GLY	GLU	LYS	CYS	GLN	PHE	ALA	HIS	GLY	PHE
4	HIS	GLU	LEU	ARG	SER	LEU	THR	ARG	HIS	PRO
5	LYS	TYR	LYS	THR	GLU	LEU	CYS	ARG	THR	PHE
6	HIS	THR	ILE	GLY	PHE	CYS	PRO	TYR	GLY	PRO
7	ARG	CYS	HIS	PHE	ILE	HIS	ASN	ALA	ASP	GLU

1	SER	THR	ARG	TYR	LYS	THR	GLU	LEU	CYS	ARG
2	PRO	PHE	GLU	GLU	SER	GLY	THR	CYS	LYS	TYR
3	GLY	GLU	LYS	CYS	GLN	PHE	ALA	HIS	GLY	PHE
4	HIS	GLU	LEU	ARG	SER	LEU	THR	ARG	HIS	PRO
5	LYS	TYR	LYS	THR	GLU	LEU	CYS	ARG	THR	PHE
6	HIS	THR	ILE	GLY	PHE	CYS	PRO	TYR	GLY	PRO
7	ARG	CYS	HIS	PHE	ILE	HIS	ASN	ALA	ASP	GLU

1	SER	THR	ARG	TYR	LYS	THR	GLU	LEU	CYS	ARG
2	PRO	PHE	GLU	GLU	SER	GLY	THR	CYS	LYS	TYR
3	GLY	GLU	LYS	CYS	GLN	PHE	ALA	HIS	GLY	PHE
4	HIS	GLU	LEU	ARG	SER	LEU	THR	ARG	HIS	PRO
5	LYS	TYR	LYS	THR	GLU	LEU	CYS	ARG	THR	PHE
6	HIS	THR	ILE	GLY	PHE	CYS	PRO	TYR	GLY	PRO
7	ARG	CYS	HIS	PHE	ILE	HIS	ASN	ALA	ASP	GLU