BMRB Entry 15986
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15986
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
Citation: Erat, Michele; Slatte, David; Lowe, Edward; Millard, Christopher; Farndale, Richard; Campbell, Iain; Vakonakis, Ioannis. "Identification and structural analysis of type-I collagen sites in complex with fibronectin fragments" Proc. Natl. Acad. Sci., U.S.A. 106, 4195-4200 (2009).
PubMed: 19251642
Assembly members:
89FnI, polymer, 93 residues, 10829.9 Da.
collagen_peptide, polymer, 23 residues, 2366.69 Da.
N-ACETYL-D-GLUCOSAMINE, non-polymer, 221.208 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: Pichia pastoris Vector: Genomic integration
Entity Sequences (FASTA):
89FnI: DQCIVDDITYNVQDTFHKKH
EEGHMLNCTCFGQGRGRWKC
DPVDQCQDSETGTFYQIGDS
WEKYVHGVRYQCYCYGRGIG
EWHCQPLQTYPSS
collagen_peptide: IAGQRGVVGLXGQRGERGFX
GLX
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 174 |
| 15N chemical shifts | 86 |
| 1H chemical shifts | 86 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | 89FnI | 1 |
| 2 | collagen peptide | 2 |
| 3 | NAG | 3 |
Entities:
Entity 1, 89FnI 93 residues - 10829.9 Da.
N542 is glycosylated with a single N-Acetylglucosamine (NAG) residue
| 1 | ASP | GLN | CYS | ILE | VAL | ASP | ASP | ILE | THR | TYR | ||||
| 2 | ASN | VAL | GLN | ASP | THR | PHE | HIS | LYS | LYS | HIS | ||||
| 3 | GLU | GLU | GLY | HIS | MET | LEU | ASN | CYS | THR | CYS | ||||
| 4 | PHE | GLY | GLN | GLY | ARG | GLY | ARG | TRP | LYS | CYS | ||||
| 5 | ASP | PRO | VAL | ASP | GLN | CYS | GLN | ASP | SER | GLU | ||||
| 6 | THR | GLY | THR | PHE | TYR | GLN | ILE | GLY | ASP | SER | ||||
| 7 | TRP | GLU | LYS | TYR | VAL | HIS | GLY | VAL | ARG | TYR | ||||
| 8 | GLN | CYS | TYR | CYS | TYR | GLY | ARG | GLY | ILE | GLY | ||||
| 9 | GLU | TRP | HIS | CYS | GLN | PRO | LEU | GLN | THR | TYR | ||||
| 10 | PRO | SER | SER |
Entity 2, collagen peptide 23 residues - 2366.69 Da.
a 23 aminoacid long peptide of the sequence C-terminal to the collagenase cleavage site in collagen I alpha1 chain, O is 4-hydroxyproline
| 1 | ILE | ALA | GLY | GLN | ARG | GLY | VAL | VAL | GLY | LEU | ||||
| 2 | HYP | GLY | GLN | ARG | GLY | GLU | ARG | GLY | PHE | HYP | ||||
| 3 | GLY | LEU | HYP |
Entity 3, NAG - C8 H15 N O6 - 221.208 Da.
| 1 | NAG |
Samples:
sample_1: 89FnI, [U-100% 13C; U-100% 15N], 1.4 mM; collagen peptide 1.5 mM; potassium phosphate 20 mM; sodium chloride 150 mM; D2O, [U-2H], 5%; H2O 95%
sample_2: 89FnI, [U-15N], 1.1 mM; collagen peptide 1.2 mM; potassium phosphate 20 mM; sodium chloride 150 mM; D2O, [U-2H], 5%; H2O 95%
sample_conditions_1: ionic strength: 0.255 M; pH: 7.2; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCANH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
NMRPipe v2.4 Rev 2006.095.11.35, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
PIPP v4.3.7, Garrett - chemical shift assignment
TOPSPIN v1.3, Bruker Biospin - collection
SPARKY v3.110, Goddard - chemical shift assignment
Omega Spectrometer Operating Software vBeta 6.03b2, GE/Bruker - collection
NMR spectrometers:
- home built OMEGA 950 MHz
- home built OMEGA 600 MHz
- Bruker Avance 500 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated peaks
SPARKY: Backbone
or all simulated peaks