BMRB Entry 19014

Name: Solution structure of the putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans
Published: 2013-03-04

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PDB ID: 2m4n
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19014
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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 the putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans

Deposition date:

2013-02-07

Original release date:

2013-03-04

Authors:

Harris, R.; Hillerich, B.; Ahmed, M.; Bonanno, J.; Chamala, S.; Evans, B.; Lafleur, J.; Hammonds, J.; Washington, E.; Stead, M.; Love, J.; Attonito, J.; Seidel, R.; Liddington, R.; Weis, W.; Nelson, W.; Girvin, M.; Almo, S.

Citation:

Citation: Harris, R.; Hillerich, B.; Ahmed, M.; Bonanno, J.; Chamala, S.; Evans, B.; Lafleur, J.; Hammonds, J.; Washington, E.; Stead, M.; Love, J.; Attonito, J.; Seidel, R.; Chook, Y.; Rout, M.; Liddington, R.; Weis, W.; Nelson, W.; Girvin, M.; Almo, S.. "Solution structure of the putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans" To be published ., .-..

Assembly members:

Assembly members:
putative_Ras_interaction_domain_of_AFD-1_isoform_a, polymer, 108 residues, 11972.540 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: modified pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
putative_Ras_interaction_domain_of_AFD-1_isoform_a: SMFGGSLKVYGGEIVPTRPY VSILAEINENADRILGAALE KYGLEHSKDDFILVEVSNDD DRKSMSDLREIDGRPIPPTE CPLFEMTARSGNGENGFDSF LAIKRKPH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	478
15N chemical shifts	108
1H chemical shifts	751

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans	1

Entities:

Entity 1, putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans 108 residues - 11972.540 Da.

1

SER

MET

PHE

GLY

SER

LEU

LYS

VAL

TYR

2

GLY

GLU

ILE

VAL

PRO

THR

ARG

PRO

TYR

3

VAL

SER

ILE

LEU

ALA

GLU

ILE

ASN

GLU

ASN

4

ALA

ASP

ARG

ILE

LEU

GLY

ALA

LEU

GLU

5

LYS

TYR

GLY

LEU

GLU

HIS

SER

LYS

ASP

6

PHE

ILE

LEU

VAL

GLU

VAL

SER

ASN

ASP

7

ASP

ARG

LYS

SER

MET

SER

ASP

LEU

ARG

GLU

8

ILE

ASP

GLY

ARG

PRO

ILE

PRO

THR

GLU

9

CYS

PRO

LEU

PHE

GLU

MET

THR

ALA

ARG

SER

10

GLY

ASN

GLY

GLU

ASN

GLY

PHE

ASP

SER

PHE

11

LEU

ALA

ILE

LYS

ARG

LYS

PRO

HIS

Samples:

sample_1: putative Ras interaction domain of AFD-1, isoform a, [U-100% 13C; U-100% 15N], 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 1 mM; EDTA 0.1 mM

sample_2: putative Ras interaction domain of AFD-1, isoform a, [U-100% 13C; U-100% 15N], 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 1 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 70 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
15N HSQC	sample_1	isotropic	sample_conditions_1
15N NOESY-HSQC	sample_1	isotropic	sample_conditions_1
13C HSQC	sample_2	isotropic	sample_conditions_1
aromatic 13C HSQC	sample_2	isotropic	sample_conditions_1
13C NOESY-HSQC	sample_2	isotropic	sample_conditions_1
13C aromatic NOESY-HSQC	sample_2	isotropic	sample_conditions_1
HNCO	sample_1	isotropic	sample_conditions_1
HNCACO	sample_1	isotropic	sample_conditions_1
HNCA	sample_1	isotropic	sample_conditions_1
HNCOCA	sample_1	isotropic	sample_conditions_1
HNCACB	sample_1	isotropic	sample_conditions_1
CBCACONH	sample_1	isotropic	sample_conditions_1

Software:

CNS v1.21, Brunger A. T. et.al. - refinement

VNMRJ v2.2D, Varian - collection

TOPSPIN v1.3 & 2.1, Bruker Biospin - collection

NMRPipe v7.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

MDDNMR v2.2, (MDDNMR) Orekhov, Jaravine, Kazimierczuk - collection, processing

MDDGUI v1.0, (MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmith - collection, processing

CCPN_Analysis, CCPN - data analysis

ARIA v2.3, Linge, O'Donoghue and Nilges - data analysis

SIDER, Hansen - data analysis

X-PLOR NIH v2.32, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Varian Inova 600 MHz
Bruker Avance 600 MHz
Bruker Avance 700 MHz

UNP	Q9BIC1
PDB	2M4N
EMBL	CCD69313 CCD69315 CCD69316 CDO41086
GB	AAD20441
REF	NP_001021660 NP_001021661 NP_001293329 NP_490938
AlphaFold	Q9N400