BMRB Entry 7194

Name: Transcription Factor IIIA zinc fingers 4-6 bound to 5S rRNA 55mer
Published: 2006-08-12

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PDB ID: 2hgh
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR7194
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Transcription Factor IIIA zinc fingers 4-6 bound to 5S rRNA 55mer

Deposition date:

2006-06-27

Original release date:

2006-08-12

Authors:

Lee, Brian

Citation:

Citation: Lee, Brian; Xu, Jing; Clarkson, Bryan; Martinez-Yamout, Maria; Dyson, H.; Case, Dave; Gottesfeld, Joel; Wright, Peter. "Induced Fit and 'Lock and Key' Recognition of 5 S RNA by Zinc Fingers of Transcription Factor IIIA" J. Mol. Biol. 357, 275-291 (2006).
PubMed: 16405997

Assembly members:

Assembly members:
5S rRNA 55mer, polymer, 55 residues, Formula weight is not available
TFIIIA zf46, polymer, 87 residues, Formula weight is not available
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: African clawed frog Taxonomy ID: 8355 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Xenopus laevis

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
5S rRNA 55mer: GGGCCACACCUCUUGGGCCU GGUUAGUACCUGUUCGCUGG GAAUACCAGGUGCCC
TFIIIA zf46: MYVCHFENCGKAFKKHNQLK VHQFSHTQQLPYECPHEGCD KRFSLPSRLKRHEKVHAGYP CKKDDSCSFVGKTWTLYLKH VAECHQD

Data sets:

assigned_chemical_shifts
- chem_shift_list_1
RDCs
- RDC_list_1

Data type	Count
13C chemical shifts	297
15N chemical shifts	97
1H chemical shifts	583
residual dipolar couplings	98

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	5S rRNA	1
2	TFIIIA zf46	2
3	ZINC (II) ION, 1	3
4	ZINC (II) ION, 2	3
5	ZINC (II) ION, 3	3

Entities:

Entity 1, 5S rRNA 55 residues - Formula weight is not available

1

G

C

A

C

A

C

2

U

C

U

G

C

U

3

G

U

A

G

U

A

C

4

U

G

U

C

G

C

U

G

5

G

A

U

A

C

A

G

6

U

G

C

Entity 2, TFIIIA zf46 87 residues - Formula weight is not available

1

MET

TYR

VAL

CYS

HIS

PHE

GLU

ASN

CYS

GLY

2

LYS

ALA

PHE

LYS

HIS

ASN

GLN

LEU

LYS

3

VAL

HIS

GLN

PHE

SER

HIS

THR

GLN

LEU

4

PRO

TYR

GLU

CYS

PRO

HIS

GLU

GLY

CYS

ASP

5

LYS

ARG

PHE

SER

LEU

PRO

SER

ARG

LEU

LYS

6

ARG

HIS

GLU

LYS

VAL

HIS

ALA

GLY

TYR

PRO

7

CYS

LYS

ASP

SER

CYS

SER

PHE

VAL

8

GLY

LYS

THR

TRP

THR

LEU

TYR

LEU

LYS

HIS

9

VAL

ALA

GLU

CYS

HIS

GLN

ASP

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

1

ZN

Samples:

sample_1: 5S rRNA 55mer0.6 – 2.0 mM; TFIIIA zf46, [U-15N], 0.6 – 2.0 mM; ZINC (II) ION1.8 – 6.0 mM; KH2PO4 10 mM; DTT 20 mM

sample_2: 5S rRNA 55mer0.6 – 2.0 mM; TFIIIA zf46, [U-13; U-15N], 0.6 – 2.0 mM; ZINC (II) ION1.8 – 6.0 mM; KH2PO4 10 mM; DTT 20 mM

sample_3: 5S rRNA 55mer0.6 – 2.0 mM; TFIIIA zf46, [U-2H; U-13; U-15N], 0.6 – 2.0 mM; ZINC (II) ION1.8 – 6.0 mM; KH2PO4 10 mM; DTT 20 mM

sample_4: 5S rRNA 55mer, [U-15N], 0.6 – 2.0 mM; TFIIIA zf46, [U-15N], 0.6 – 2.0 mM; ZINC (II) ION1.8 – 6.0 mM; KH2PO4 10 mM; DTT 20 mM

sample_5: 5S rRNA 55mer, [U-15N], 0.6 – 2.0 mM; TFIIIA zf460.6 – 2.0 mM; ZINC (II) ION1.8 – 6.0 mM; KH2PO4 10 mM; DTT 20 mM

sample_6: 5S rRNA 55mer, [U-13C; U-15N], 0.6 – 2.0 mM; TFIIIA zf460.6 – 2.0 mM; ZINC (II) ION1.8 – 6.0 mM; KH2PO4 10 mM; DTT 20 mM

conditions_1: ionic strength: 10 mM; pH: 6.5; temperature: 291 K

Experiments:

Name	Sample	Sample state	Sample conditions
HNCO	not available	not available	conditions_1
HNCA	not available	not available	conditions_1
(HCA)CO(CA)NH	not available	not available	conditions_1
CBCA(CO)NH	not available	not available	conditions_1
HCACO	not available	not available	conditions_1
13C-HSQC	not available	not available	conditions_1
(H)C(CO)NH-TOCSY	not available	not available	conditions_1
(H)CCH-COSY	not available	not available	conditions_1
HCCH-TOCSY	not available	not available	conditions_1
(HB)CB(CGCD)HD	not available	not available	conditions_1
TROSY based HNCO	not available	not available	conditions_1
TROSY based HNCA	not available	not available	conditions_1
TROSY based HN(CA)CO	not available	not available	conditions_1
3D 15N NOESY HSQC	not available	not available	conditions_1
3D shared-time 15N/13C NOESY HSQC	not available	not available	conditions_1
3D 13C HMQC-NOESY	not available	not available	conditions_1
15N HMQC	not available	not available	conditions_1
water flip-back 2D NOESY	not available	not available	conditions_1
TROSY based HNN-COSY	not available	not available	conditions_1
13C HMQC	not available	not available	conditions_1
2JHN 15N HMQC	not available	not available	conditions_1
3D 13C HMQC NOESY	not available	not available	conditions_1
2D double half filtered NOESY	not available	not available	conditions_1
3D 13C edit/filter NOESY	not available	not available	conditions_1

Software:

No software information available

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 800 MHz
Bruker DMX 750 MHz
Bruker DRX 600 MHz
Bruker AMX-II 500 MHz
Bruker AMX 500 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks