BMRB Entry 34103

Name: Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex B)
Published: 2018-02-19

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PDB ID: 5n8l
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34103
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex B)

Deposition date:

2017-02-23

Original release date:

2018-02-19

Authors:

Masliah, G.; Maris, C.; Allain, H.

Citation:

Citation: Masliah, G.; Maris, C.; Koenig, L.; Yulikov, M.; Aeschimann, F.; Malinowska, A.; Mabille, J.; Weiler, J.; Holla, A.; Meisner-Kober, N.; Meisner-Kober, N.; Schuler, B.; Jeschke, G.; Allain, H.. "Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains" Embo J. 37, e97089-e97089 (2018).
PubMed: 29449323

Assembly members:

Assembly members:
entity_1, polymer, 215 residues, 23012.332 Da.
entity_2, polymer, 21 residues, 6534.828 Da.
entity_3, polymer, 21 residues, 6747.062 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGSLPSIEQMLAANPGKTPI SLLQEYGTRIGKTPVYDLLK AEGQAHQPNFTFRVTVGDTS CTGQGPSKKAAKHKAAEVAL KHLKGGSMLEPALEDSSSFS PLDSSLPEDIPVFTAAAAAT PVPSVVLTRSPPMELQPPVS PQQSECNPVGALQELVVQKG WRLPEYTVTQESGPAHRKEF TMTCRVERFIEIGSGTSKKL AKRNAAAKMLLRVHT
entity_2: UUAAUUAUCUAUUCCGUACU U
entity_3: GUACGGAAUAGAUAAUUAAU U

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	484
15N chemical shifts	182
1H chemical shifts	1076

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	entity_3	3

Entities:

Entity 1, entity_1 215 residues - 23012.332 Da.

1

GLY

SER

LEU

PRO

SER

ILE

GLU

GLN

MET

2

LEU

ALA

ASN

PRO

GLY

LYS

THR

PRO

ILE

3

SER

LEU

GLN

GLU

TYR

GLY

THR

ARG

ILE

4

GLY

LYS

THR

PRO

VAL

TYR

ASP

LEU

LYS

5

ALA

GLU

GLY

GLN

ALA

HIS

GLN

PRO

ASN

PHE

6

THR

PHE

ARG

VAL

THR

VAL

GLY

ASP

THR

SER

7

CYS

THR

GLY

GLN

GLY

PRO

SER

LYS

ALA

8

ALA

LYS

HIS

LYS

ALA

GLU

VAL

ALA

LEU

9

LYS

HIS

LEU

LYS

GLY

SER

MET

LEU

GLU

10

PRO

ALA

LEU

GLU

ASP

SER

PHE

SER

11

PRO

LEU

ASP

SER

LEU

PRO

GLU

ASP

ILE

12

PRO

VAL

PHE

THR

ALA

THR

13

PRO

VAL

PRO

SER

VAL

LEU

THR

ARG

SER

14

PRO

MET

GLU

LEU

GLN

PRO

VAL

SER

15

PRO

GLN

SER

GLU

CYS

ASN

PRO

VAL

GLY

16

ALA

LEU

GLN

GLU

LEU

VAL

GLN

LYS

GLY

17

TRP

ARG

LEU

PRO

GLU

TYR

THR

VAL

THR

GLN

18

GLU

SER

GLY

PRO

ALA

HIS

ARG

LYS

GLU

PHE

19

THR

MET

THR

CYS

ARG

VAL

GLU

ARG

PHE

ILE

20

GLU

ILE

GLY

SER

GLY

THR

SER

LYS

LEU

21

ALA

LYS

ARG

ASN

ALA

LYS

MET

LEU

22

LEU

ARG

VAL

HIS

THR

Entity 2, entity_2 21 residues - 6534.828 Da.

1

U

A

U

A

U

C

U

2

A

U

C

G

U

A

C

U

3

U

Entity 3, entity_3 21 residues - 6747.062 Da.

1

G

U

A

C

G

A

U

A

2

G

A

U

A

U

A

U

3

U

Samples:

sample_1: dsRBD1, [U-100% 13C; U-100% 15N], 1 mM; EL86 1 mM

sample_2: EL86 1 mM; dsRBD2, [U-100% 13C; U-100% 15N], 1 mM

sample_3: EL86 1 mM; dsRBD12, [U-100% 13C; U-100% 15N; U-80% 2H], 1 mM

sample_4: EL86 1 mM; dsRBD12, [U-100% 13C; U-100% 15N; U-80% 2H], 1 mM

sample_5: EL86 1 mM; dsRBD12, [U-100% 13C; U-100% 15N; U-80% 2H], 1 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
hCccoNH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D f1-13C-filtered,f2-13C-edited NOESY aliphatic-HMQC	sample_3	isotropic	sample_conditions_1
TROSY IPAP	sample_4	isotropic	sample_conditions_1
TROSY IPAP	sample_5	anisotropic	sample_conditions_1

Software:

AMBER v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment

TOPSPIN v3.0, Bruker Biospin - collection

NMR spectrometers:

Bruker AvanceIII 750 MHz
Bruker AvanceIII 900 MHz
Bruker AvanceIII 600 MHz
Bruker AvanceIII 500 MHz

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