BMRB Entry 15636

Name: Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines
Published: 2008-11-06

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PDB ID: 2k04
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15636
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines PubMed: 18799424

Deposition date: 2008-01-24 Original release date: 2008-11-06

Authors: Volkman, B.; Veldkamp, C.; Peterson, F.

Citation: Veldkamp, Christopher; Seibert, Christoph; Peterson, Francis; De la Cruz, Noberto; Haugner, John; Basnet, Harihar; Sakmar, Thomas; Volkman, Brian. "Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12" Sci. Signal. 1, ra4-ra4 (2008).

Assembly members:
CXCL12/SDF1-alpha, polymer, 70 residues, 8188.810 Da.
CXCR4, polymer, 40 residues, 4518.798 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo Sapiens

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

Entity Sequences (FASTA):
CXCL12/SDF1-alpha: GMKPVSLSYRCPCRFFESHV ARANVKHLKILNTPNCACQI VARLKNNNRQVCIDPKLKWI QEYLEKCLNK
CXCR4: GSMEGISIYTSDNYTEEMGS GDYDSMKEPAFREENANFNK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	850
15N chemical shifts	212
1H chemical shifts	1416

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Entity Assembly ID	Entity Name	Entity ID
1	CXCL12/SDF1-alpha_1	1
2	CXCR4_1	2
3	CXCL12/SDF1-alpha_2	1
4	CXCR4_2	2

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-separated_NOESY (AROMATIC)	sample_1	isotropic	sample_conditions_1
3D_13C-F1-filtered_13C-F3-separateded_NOESY	sample_1	isotropic	sample_conditions_1
3D_15N-separated_NOESY	sample_2	isotropic	sample_conditions_1
3D_13C-separated_NOESY	sample_2	isotropic	sample_conditions_1
3D_13C-separated_NOESY (AROMATIC)	sample_2	isotropic	sample_conditions_1
3D_13C-F1-filtered_13C-F3-separateded_NOESY	sample_2	isotropic	sample_conditions_1

Related Database Links:

BMRB	15633 15635 15637 16142 16143 15635
PDB	1QG7 1SDF 2J7Z 2K01 2K03 2K04 2K05 2KEC 2KED 2SDF 3HP3 4UAI 2K03 2K04
DBJ	BAA28601 BAA28602 BAF85317 BAG11056 BAG34757 BAA01722 BAG35177
EMBL	CAG29279 CAA50641 CAA75034
GB	AAA97434 AAB39332 AAB39333 AAB40516 AAH39893 AAA03209 AAA16594 AAA16617 AAB81970 AAB93982
REF	NP_000600 NP_001009847 NP_001028106 NP_001029058 NP_001171605 NP_001009047 NP_003458 XP_003822867
SP	O62657 P48061 P61072 P61073

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts

1	GLY	MET	LYS	PRO	VAL	SER	LEU	SER	TYR	ARG
2	CYS	PRO	CYS	ARG	PHE	PHE	GLU	SER	HIS	VAL
3	ALA	ARG	ALA	ASN	VAL	LYS	HIS	LEU	LYS	ILE
4	LEU	ASN	THR	PRO	ASN	CYS	ALA	CYS	GLN	ILE
5	VAL	ALA	ARG	LEU	LYS	ASN	ASN	ASN	ARG	GLN
6	VAL	CYS	ILE	ASP	PRO	LYS	LEU	LYS	TRP	ILE
7	GLN	GLU	TYR	LEU	GLU	LYS	CYS	LEU	ASN	LYS

1	GLY	SER	MET	GLU	GLY	ILE	SER	ILE	TYR	THR
2	SER	ASP	ASN	TYR	THR	GLU	GLU	MET	GLY	SER
3	GLY	ASP	TYR	ASP	SER	MET	LYS	GLU	PRO	ALA
4	PHE	ARG	GLU	GLU	ASN	ALA	ASN	PHE	ASN	LYS

Biological Magnetic Resonance Data Bank

BMRB Entry 15636

Title: Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines PubMed: 18799424

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

Related Database Links:

1	GLY	MET	LYS	PRO	VAL	SER	LEU	SER	TYR	ARG
2	CYS	PRO	CYS	ARG	PHE	PHE	GLU	SER	HIS	VAL
3	ALA	ARG	ALA	ASN	VAL	LYS	HIS	LEU	LYS	ILE
4	LEU	ASN	THR	PRO	ASN	CYS	ALA	CYS	GLN	ILE
5	VAL	ALA	ARG	LEU	LYS	ASN	ASN	ASN	ARG	GLN
6	VAL	CYS	ILE	ASP	PRO	LYS	LEU	LYS	TRP	ILE
7	GLN	GLU	TYR	LEU	GLU	LYS	CYS	LEU	ASN	LYS

1	GLY	SER	MET	GLU	GLY	ILE	SER	ILE	TYR	THR
2	SER	ASP	ASN	TYR	THR	GLU	GLU	MET	GLY	SER
3	GLY	ASP	TYR	ASP	SER	MET	LYS	GLU	PRO	ALA
4	PHE	ARG	GLU	GLU	ASN	ALA	ASN	PHE	ASN	LYS

1	GLY	MET	LYS	PRO	VAL	SER	LEU	SER	TYR	ARG
2	CYS	PRO	CYS	ARG	PHE	PHE	GLU	SER	HIS	VAL
3	ALA	ARG	ALA	ASN	VAL	LYS	HIS	LEU	LYS	ILE
4	LEU	ASN	THR	PRO	ASN	CYS	ALA	CYS	GLN	ILE
5	VAL	ALA	ARG	LEU	LYS	ASN	ASN	ASN	ARG	GLN
6	VAL	CYS	ILE	ASP	PRO	LYS	LEU	LYS	TRP	ILE
7	GLN	GLU	TYR	LEU	GLU	LYS	CYS	LEU	ASN	LYS

1	GLY	SER	MET	GLU	GLY	ILE	SER	ILE	TYR	THR
2	SER	ASP	ASN	TYR	THR	GLU	GLU	MET	GLY	SER
3	GLY	ASP	TYR	ASP	SER	MET	LYS	GLU	PRO	ALA
4	PHE	ARG	GLU	GLU	ASN	ALA	ASN	PHE	ASN	LYS

1	GLY	MET	LYS	PRO	VAL	SER	LEU	SER	TYR	ARG
2	CYS	PRO	CYS	ARG	PHE	PHE	GLU	SER	HIS	VAL
3	ALA	ARG	ALA	ASN	VAL	LYS	HIS	LEU	LYS	ILE
4	LEU	ASN	THR	PRO	ASN	CYS	ALA	CYS	GLN	ILE
5	VAL	ALA	ARG	LEU	LYS	ASN	ASN	ASN	ARG	GLN
6	VAL	CYS	ILE	ASP	PRO	LYS	LEU	LYS	TRP	ILE
7	GLN	GLU	TYR	LEU	GLU	LYS	CYS	LEU	ASN	LYS

1	GLY	SER	MET	GLU	GLY	ILE	SER	ILE	TYR	THR
2	SER	ASP	ASN	TYR	THR	GLU	GLU	MET	GLY	SER
3	GLY	ASP	TYR	ASP	SER	MET	LYS	GLU	PRO	ALA
4	PHE	ARG	GLU	GLU	ASN	ALA	ASN	PHE	ASN	LYS