BMRB Entry 11597

Name: Solution NMR structure of Monosiga brevicollis CRK/CRKL homolog (crka1) SH2 domain
Published: 2016-09-19

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PDB ID: 2rvf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11597
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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:

Solution NMR structure of Monosiga brevicollis CRK/CRKL homolog (crka1) SH2 domain

Deposition date:

2015-09-24

Original release date:

2016-09-19

Authors:

Kasai, Takuma; Pawlak, Jana; Imamoto, Akira; Kigawa, Takanori

Citation:

Citation: Shigeno-Nakazawa, Yoko; Kasai, Takuma; Kostyanovskaya, Elina; Pawlak, Jana; Yamagishi, Junya; Okimoto, Noriaki; Taiji, Makoto; Okada, Mariko; Sauka-Spengler, Tatjana; Westbrook, Jody; Satta, Yoko; Kigawa, Takanori; Imamoto, Akira. "A premetazoan origin of the CRK gene family and co-opted signaling network" Sci. Rep. ., .-..

Assembly members:

Assembly members:
crka1_SH2_domain, polymer, 104 residues, 11482.751 Da.

Natural source:

Natural source: Common Name: Monosiga brevicollis Taxonomy ID: 81824 Superkingdom: Eukaryota Kingdom: not available Genus/species: Monosiga brevicollis

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: E. coli - cell free Vector: P100927-01

Entity Sequences (FASTA):

Entity Sequences (FASTA):
crka1_SH2_domain: GSSGSSGMAEAAAPWYHGPL SRTDAENSLLRMPEGTFLVR DSTSSPGDYVLSCSENGKVT HYKLSAEEGKIRIDTHLFDN LDAAITFYMEHELEYSSLKQ PLQR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	440
15N chemical shifts	101
1H chemical shifts	685

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Monosiga brevicollis CRK/CRKL homolog (crka1) SH2 domain	1

Entities:

Entity 1, Monosiga brevicollis CRK/CRKL homolog (crka1) SH2 domain 104 residues - 11482.751 Da.

Residues -6 to 0 are cloning artifacts. GenBank entry KT795324 which corresponds to mRNA sequence of Monosiga brevicollis crka1 is not released yet. The nucleotide sequence of KT795324 is: TGCGCCTCGATCATTTTGAGCCCCAGGGCCTTTGTTGTGCATCATGGCGGAAGCCGCAGCACCCTGGTATCATGGGCCGC TGAGCCGCACCGATGCAGAAAACAGTCTCTTGCGTATGCCCGAAGGGACTTTCTTGGTCCGCGACAGCACCTCGTCCCCC GGAGATTATGTCCTCTCATGCAGCGAGAATGGCAAGGTGACGCACTACAAGCTCTCGGCCGAAGAGGGCAAGATTCGTAT CGATACACACCTCTTTGACAACCTGGATGCTGCCATCACCTTTTACATGGAGCACGAGTTGGAATACAGTTCGCTCAAAC AGCCCCTGCAACGGCAATCATCATGGCGCGATGACGAGCTTGTCGCCACGGTCATGTTCTCTGCAGAAGGGCTGTACAAG TTTGTCGGCCGCAATGAAAACGATTTACCCTTTGACAAGGGGGAGCTTCTCAATGTCTTGCAGCTAACACAGGACAATTG GTGGATGGCCCAGAGTCAGAAAACGCTCAAGATTGGCTACGTTCCCGTCAATTATGTCCGGGCGCTAGAGCAGCCAGCTG CCCCGCCACCGCGCCCTGCTCCACGTCCTGCCGAGGAGGAGTCTTCCAGGCTTGAGCGAACCGAATCCCGTCGTACGCCG GCCAGCCACCATCGACCCAAGGAACCCATGCCGGCAGGTGCCGTCATGACACGAGCTCCGGCTCGACATCACCAAGAGGC AAAGGCACCCCCTGCACGGCCTCAGCCGACTGGGCCTTCTGCCGCGGGTCCGATAGCCGCTGCTGCTCCGCCTCCACGTC CCAAAACATCAAAGCCCACGACCGACTTTAGTGCGCTCAAGGCTCAACTGCAGGAGCCAATTGTTTCCAATCCCACGCCC ACCTCGACGGCCCCAGAGCAGGCGGCTTTGCCCGCCGAAACCACGGCAGAAGTCTCAACACCAACGCAGCCGCTCGCATC TGCTCCGCCCACTTCTACGGCCTCGCATGAAGCGCCGGCAAGCTCTGCCGCACCCGCTACTCAGCACGGCGCAGGGTCAG AGGATCACGCTACCGCTCCCGACTCGGAGCCTCCCATCACTTTGGTCCGCGCCATCACCGCCATCATCCCCAACGCCTAT GACAATGATGCCTTGGTCTTGGAGGAAAATGATTTGGTTCACGTGCTGGATGGCGGCGAAGGCGCACTGGAGCGGGGCCG CGTTCTCAGAACTGGACAGATCGGCTTGTATCCCTTTGCAAAGACTGAGGATATTGAGAGCCACAACTACGATGCCGAAG TGAAGGCAGCCGTCGCTGACTACCTGAAGCGGTTTCCAGATGCATGCTAGCAAACCATAGGTGGCTATTGGCGACGGTCG TGAGATACGT And the translated protein sequence is: MAEAAAPWYHGPLSRTDAENSLLRMPEGTFLVRDSTSSPGDYVLSCSENGKVTHYKLSAEEGKIRIDTHLFDNLDAAITF YMEHELEYSSLKQPLQRQSSWRDDELVATVMFSAEGLYKFVGRNENDLPFDKGELLNVLQLTQDNWWMAQSQKTLKIGYV PVNYVRALEQPAAPPPRPAPRPAEEESSRLERTESRRTPASHHRPKEPMPAGAVMTRAPARHHQEAKAPPARPQPTGPSA AGPIAAAAPPPRPKTSKPTTDFSALKAQLQEPIVSNPTPTSTAPEQAALPAETTAEVSTPTQPLASAPPTSTASHEAPAS SAAPATQHGAGSEDHATAPDSEPPITLVRAITAIIPNAYDNDALVLEENDLVHVLDGGEGALERGRVLRTGQIGLYPFAK TEDIESHNYDAEVKAAVADYLKRFPDAC

1

GLY

SER

GLY

SER

GLY

MET

ALA

GLU

2

ALA

PRO

TRP

TYR

HIS

GLY

PRO

LEU

3

SER

ARG

THR

ASP

ALA

GLU

ASN

SER

LEU

4

ARG

MET

PRO

GLU

GLY

THR

PHE

LEU

VAL

ARG

5

ASP

SER

THR

SER

PRO

GLY

ASP

TYR

VAL

6

LEU

SER

CYS

SER

GLU

ASN

GLY

LYS

VAL

THR

7

HIS

TYR

LYS

LEU

SER

ALA

GLU

GLY

LYS

8

ILE

ARG

ILE

ASP

THR

HIS

LEU

PHE

ASP

ASN

9

LEU

ASP

ALA

ILE

THR

PHE

TYR

MET

GLU

10

HIS

GLU

LEU

GLU

TYR

SER

LEU

LYS

GLN

11

PRO

LEU

GLN

ARG

Samples:

sample_1: crka1 SH2 domain, [U-13C; U-15N], 1.1 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; sodium azide 0.02%; DTT, [U-2H], 1 mM; D2O, [U-2H], 10%; H2O 90%

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 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
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	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 HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCD)HD	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:

xwinnmr v3.6, Bruker Biospin - collection

TOPSPIN v2.1, Bruker Biospin - collection

NMRPipe v20110801, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5.2.2_01, Johnson, One Moon Scientific - data analysis

Kujira v0.9843, Kobayashi, Iwahara, Koshiba, Tomizawa, Tochio, G ntert, Kigawa, Yokoyama - chemical shift assignment, data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

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

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz