BMRB Entry 15215

Name: Solution structure of the alternative conformation of XCL1/Lymphotactin
Published: 2007-10-29

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PDB ID: 2jp1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15215
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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 structure of the alternative conformation of XCL1/Lymphotactin

Deposition date:

2007-04-17

Original release date:

2007-10-29

Authors:

Volkman, B.; Tuinstra, R.; Peterson, F.

Citation:

Citation: Tuinstra, R.; Peterson, F.; Elgin, E.; Pelzek, A.; Volkman, B.. "An engineered second disulfide bond restricts lymphotactin/XCL1 to a chemokine-like conformation with XCR1 agonist activity" Biochemistry 46, 2564-2573 (2007).
PubMed: 17302442

Assembly members:

Assembly members:
XCL1, polymer, 93 residues, 10289.896 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 Vector: pQE30-8HT

Entity Sequences (FASTA):

Entity Sequences (FASTA):
XCL1: VGSEVSDKRTCVSLTTQRLP VSRIKTYTITEGSLRAVIFI TKRGLKVCADPQATWVRDVV RSMDRKSNTRNNMIQTKPTG TQQSTNTAVTLTG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	344
15N chemical shifts	85
1H chemical shifts	461

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	XCL1	1

Entities:

Entity 1, XCL1 93 residues - 10289.896 Da.

1

VAL

GLY

SER

GLU

VAL

SER

ASP

LYS

ARG

THR

2

CYS

VAL

SER

LEU

THR

GLN

ARG

LEU

PRO

3

VAL

SER

ARG

ILE

LYS

THR

TYR

THR

ILE

THR

4

GLU

GLY

SER

LEU

ARG

ALA

VAL

ILE

PHE

ILE

5

THR

LYS

ARG

GLY

LEU

LYS

VAL

CYS

ALA

ASP

6

PRO

GLN

ALA

THR

TRP

VAL

ARG

ASP

VAL

7

ARG

SER

MET

ASP

ARG

LYS

SER

ASN

THR

ARG

8

ASN

MET

ILE

GLN

THR

LYS

PRO

THR

GLY

9

THR

GLN

SER

THR

ASN

THR

ALA

VAL

THR

10

LEU

THR

GLY

Samples:

sample_1: XCL1, [U-100% 13C; U-100% 15N], 1.0 mM; sodium phosphate 20 mM

sample_2: XCL1, [U-100% 13C; U-100% 15N], 0.6 mM; XCL1 0.6 mM; sodium phosphate 20 mM

sample_conditions_1: ionic strength: 22 mM; pH: 6.0; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-separated NOESY	sample_1	isotropic	sample_conditions_1
3D 13C-separated NOESY	sample_1	isotropic	sample_conditions_1
3D 13C-F1-filtered 13C-F3-separateded NOESY	sample_2	isotropic	sample_conditions_1

Software:

X-PLOR NIH v2.9.3, SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. - refinement

xwinnmr v3.5, Bruker - collection

NMRPipe v2004, Delagio,F. et al. - processing

XEASY v1.3, Eccles, C., Guntert, P., Billeter, M., Wuthrich, K. - data analysis

SPSCAN v1.1.0, R.W. Glaser - data analysis

GARANT v2.1, C. Bartels - data analysis

CYANA v2.1, Guntert, P. - structural calculation

NMR spectrometers:

Bruker DRX 600 MHz

BMRB	15110 25693
PDB	1J8I 1J9O 2HDM 2JP1 2N54 2NYZ
DBJ	BAA07825 BAA09858 BAA09859 BAJ20778
EMBL	CAA60198
GB	AAC50164 AAH69360 AAH69817 AAH70308 AAH70309
REF	NP_002986 NP_003166 XP_003824662 XP_004027907 XP_009436138
SP	P47992 Q9UBD3
AlphaFold	P47992 Q9UBD3