BMRB Entry 19609

Name: Solution Structure of Protein-RNA Ternary Complex
Published: 2014-08-11

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PDB ID: 2mgz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19609
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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:

Solution Structure of Protein-RNA Ternary Complex

Deposition date:

2013-11-12

Original release date:

2014-08-11

Authors:

Takahashi, Mari; Kuwasako, Kanako; Unzai, Satoru; Tsuda, Kengo; Yoshikawa, Seiko; He, Fahu; Kobayashi, Naohiro; Guntert, Peter; Shirouzu, Mikako; Ito, Takuhiro; Tanaka, Akiko; Yokoyama, Shigeyuki; Hagiwara, Masatoshi; Kuroyanagi, Hidehito; Muto, Yutaka

Citation:

Citation: Kuwasako, Kanako; Takahashi, Mari; Unzai, Satoru; Tsuda, Kengo; Yoshikawa, Seiko; He, Fahu; Kobayashi, Naohiro; Guntert, Peter; Shirouzu, Mikako; Ito, Takuhiro; Tanaka, Akiko; Yokoyama, Shigeyuki; Hagiwara, Masatoshi; Kuroyanagi, Hidehito; Muto, Yutaka. "Solution Structure of Protein-RNA Ternary Complex" .

Assembly members:

Assembly members:
entity_1, polymer, 94 residues, 10588.121 Da.
entity_2, polymer, 105 residues, 11611.109 Da.
RNA, polymer, 12 residues, Formula weight is not available

Natural source:

Natural source: Common Name: nematode Taxonomy ID: 6239 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Caenorhabditis elegans

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX6p-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GDGPRRLHVSNIPFKYREPD LTAMFEKVGPVVDVEIIFNE RGSKGFGFVTMQNPDDADRA RAEFNGTTIEGRRVEVNLAT QRVHNKKAKPLMSV
entity_2: GSTNAEPVVGSRDTMFTKIF VGGLPYHTSDKTLHEYFEQF GDIEEAVVITDRNTQKSRGY GFVTMKDRASAERACKDPNP IIDGRKANVNLAYLGAKPRT NVQLA
RNA: UGCAUGGUGUGC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	575
15N chemical shifts	184
1H chemical shifts	1157

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	RNA	3

Entities:

Entity 1, entity_1 94 residues - 10588.121 Da.

1

GLY

ASP

GLY

PRO

ARG

LEU

HIS

VAL

SER

2

ASN

ILE

PRO

PHE

LYS

TYR

ARG

GLU

PRO

ASP

3

LEU

THR

ALA

MET

PHE

GLU

LYS

VAL

GLY

PRO

4

VAL

ASP

VAL

GLU

ILE

PHE

ASN

GLU

5

ARG

GLY

SER

LYS

GLY

PHE

GLY

PHE

VAL

THR

6

MET

GLN

ASN

PRO

ASP

ALA

ASP

ARG

ALA

7

ARG

ALA

GLU

PHE

ASN

GLY

THR

ILE

GLU

8

GLY

ARG

VAL

GLU

VAL

ASN

LEU

ALA

THR

9

GLN

ARG

VAL

HIS

ASN

LYS

ALA

LYS

PRO

10

LEU

MET

SER

VAL

Entity 2, entity_2 105 residues - 11611.109 Da.

1

GLY

SER

THR

ASN

ALA

GLU

PRO

VAL

GLY

2

SER

ARG

ASP

THR

MET

PHE

THR

LYS

ILE

PHE

3

VAL

GLY

LEU

PRO

TYR

HIS

THR

SER

ASP

4

LYS

THR

LEU

HIS

GLU

TYR

PHE

GLU

GLN

PHE

5

GLY

ASP

ILE

GLU

ALA

VAL

ILE

THR

6

ASP

ARG

ASN

THR

GLN

LYS

SER

ARG

GLY

TYR

7

GLY

PHE

VAL

THR

MET

LYS

ASP

ARG

ALA

SER

8

ALA

GLU

ARG

ALA

CYS

LYS

ASP

PRO

ASN

PRO

9

ILE

ASP

GLY

ARG

LYS

ALA

ASN

VAL

ASN

10

LEU

ALA

TYR

LEU

GLY

ALA

LYS

PRO

ARG

THR

11

ASN

VAL

GLN

LEU

ALA

Entity 3, RNA 12 residues - Formula weight is not available

1

U

G

C

A

U

G

U

G

U

2

G

C

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.7 mM; entity_2, [U-99% 13C; U-99% 15N], 0.7 mM; RNA 0.7 mM; H2O 90%; D2O 10%; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%

sample_conditions_1: ionic strength: 0.1 M; pH: 6; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 700 MHz
Bruker Avance 600 MHz

BMRB	19680 19686 11541 18845 18846 19653
PDB	2MGZ 2MGZ 2RU3 4CH0 4CH1 4CIO
EMBL	CAA85276 CAD82915 CCU83325 CCD71425 CCD71429
GB	ABF22491 EFO82252 EGT29982 ETN82682 KHJ75674 KIH66793
REF	NP_001293646 NP_497841 NP_871667 NP_001129938 NP_508674 XP_003117654 XP_006219866