BMRB Entry 18490

Name: TDRD3 complex
Published: 2012-11-02

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PDB ID: 2lto
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18490
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:

TDRD3 complex

Deposition date:

2012-05-30

Original release date:

2012-11-02

Authors:

Sikorsky, Tomas

Citation:

Citation: Sikorsky, Tomas; Hobor, Fruzsina; Krizanova, Eva; Pasulka, Josef; Kubicek, Karel; Stefl, Richard. "Recognition of asymmetrically dimethylated arginine by TDRD3." Nucleic Acids Res. 40, 11748-11755 (2012).
PubMed: 23066109

Assembly members:

Assembly members:
entity_1, polymer, 58 residues, 6827.864 Da.
TDRD3_2, polymer, 13 residues, 1494.620 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: pET22b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MKMWKPGDECFALYWEDNKF YRAEVEALHSSGMTAVVKFI DYGNYEEVLLSNIKPILE
TDRD3_2: YSPSSPXYTPQSP

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	176
15N chemical shifts	53
1H chemical shifts	346

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	TDRD3, chain 1	1
2	TDRD3, chain 2	2

Entities:

Entity 1, TDRD3, chain 1 58 residues - 6827.864 Da.

1

MET

LYS

MET

TRP

LYS

PRO

GLY

ASP

GLU

CYS

2

PHE

ALA

LEU

TYR

TRP

GLU

ASP

ASN

LYS

PHE

3

TYR

ARG

ALA

GLU

VAL

GLU

ALA

LEU

HIS

SER

4

SER

GLY

MET

THR

ALA

VAL

LYS

PHE

ILE

5

ASP

TYR

GLY

ASN

TYR

GLU

VAL

LEU

6

SER

ASN

ILE

LYS

PRO

ILE

LEU

GLU

Entity 2, TDRD3, chain 2 13 residues - 1494.620 Da.

1

TYR

SER

PRO

SER

PRO

DA2

TYR

THR

PRO

2

GLN

SER

PRO

Samples:

sample_1: TDRD3_1, [U-99% 13C; U-99% 15N], 1.7 mM; sodium phosphate 50 mM; beta-mercaptoethanol 10 mM; sodium chloride 150 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 150 mM; pH: 8; pressure: 1 atm; temperature: 293.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 MHz

PDB	2LTO 3PMT 3PNW 3S6W
DBJ	BAB14950 BAJ17879 BAK63800
EMBL	CAD97894 CAL37786
GB	AAH30514 AAH60876 ACC94142 AIC52422 EAW52079
REF	NP_001139542 NP_001139543 NP_110421 XP_003257452 XP_003257453
SP	Q9H7E2
AlphaFold	Q9H7E2 Q6NX41