BMRB Entry 18720

Name: The solution structure of the Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide
Published: 2012-10-15

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PDB ID: 2lyd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18720
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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:

The solution structure of the Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide

Deposition date:

2012-09-17

Original release date:

2012-10-15

Authors:

Truffault, Vincent

Citation:

Citation: Braun, Joerg; Truffault, Vincent; Boland, Andreas; Huntzinger, Eric; Chang, Chung-Te; Haas, Gabrielle; Weichenrieder, Oliver; Coles, Murray; Izaurralde, Elisa. "A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation." Nat. Struct. Mol. Biol. 19, 1324-1331 (2012).
PubMed: 23142987

Assembly members:

Assembly members:
Dm_DCP1_EVH1_domain, polymer, 133 residues, 15361.304 Da.
XRN1_DBM, polymer, 38 residues, 4355.992 Da.

Natural source:

Natural source: Common Name: Fruit fly Taxonomy ID: 7227 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Drosophila melanogaster

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dm_DCP1_EVH1_domain: GPHMADLMADESITRMNLAA IKKIDPYAKEIVDSSSHVAF YTFNSSQNEWEKTDVEGAFF IYHRNAEPFHSIFINNRLNT TSFVEPITGSLELQSQPPFL LYRNERSRIRGFWFYNSEEC DRISGLVNGLLKSK
XRN1_DBM: GPQDPLLQQQRAPFPGQMPN LPKPPLFWQQEAQKQEAL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	524
15N chemical shifts	123
1H chemical shifts	18

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Dm DCP1 EVH1 domain	1
2	XRN1 DBM peptide	2

Entities:

Entity 1, Dm DCP1 EVH1 domain 133 residues - 15361.304 Da.

1

GLY

PRO

HIS

MET

ALA

ASP

LEU

MET

ALA

ASP

2

GLU

SER

ILE

THR

ARG

MET

ASN

LEU

ALA

3

ILE

LYS

ILE

ASP

PRO

TYR

ALA

LYS

GLU

4

ILE

VAL

ASP

SER

HIS

VAL

ALA

PHE

5

TYR

THR

PHE

ASN

SER

GLN

ASN

GLU

TRP

6

GLU

LYS

THR

ASP

VAL

GLU

GLY

ALA

PHE

7

ILE

TYR

HIS

ARG

ASN

ALA

GLU

PRO

PHE

HIS

8

SER

ILE

PHE

ILE

ASN

ARG

LEU

ASN

THR

9

THR

SER

PHE

VAL

GLU

PRO

ILE

THR

GLY

SER

10

LEU

GLU

LEU

GLN

SER

GLN

PRO

PHE

LEU

11

LEU

TYR

ARG

ASN

GLU

ARG

SER

ARG

ILE

ARG

12

GLY

PHE

TRP

PHE

TYR

ASN

SER

GLU

CYS

13

ASP

ARG

ILE

SER

GLY

LEU

VAL

ASN

GLY

LEU

14

LEU

LYS

SER

LYS

Entity 2, XRN1 DBM peptide 38 residues - 4355.992 Da.

1

GLY

PRO

GLN

ASP

PRO

LEU

GLN

2

ARG

ALA

PRO

PHE

PRO

GLY

GLN

MET

PRO

ASN

3

LEU

PRO

LYS

PRO

LEU

PHE

TRP

GLN

4

GLU

ALA

GLN

LYS

GLN

GLU

ALA

LEU

Samples:

sample_1: Dm_DCP1_EVH1_domain, [U-100% 15N], 0.4 mM; Dm_DCP1_EVH1_domain, [U-100% 13C; U-100% 15N], 0.7 mM; XRN1_DBM, [U-100% 15N], 0.4 mM; XRN1_DBM, [U-100% 13C; U-100% 15N], 0.7 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 300 mM; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	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
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
2D NOESYnoN	sample_1	isotropic	sample_conditions_1
2D PLUSH-TACSY	sample_1	isotropic	sample_conditions_1
3D NNH NOESY	sample_1	isotropic	sample_conditions_1
3D CNH NOESY	sample_1	isotropic	sample_conditions_1
3D CCH NOESY	sample_1	isotropic	sample_conditions_1
4D CCANH	sample_1	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

PDB	2LYD 2LYD
GB	AAF47089 AAX94785 ACL88332 ACZ94554 EDV56888 AAF48958 AAK93099 ACZ95330
REF	NP_001163282 NP_611842 XP_001976488 XP_002040166 XP_002045212 NP_001162796 NP_523408
EMBL	CAB43711