BMRB Entry 31138
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31138
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NMR-STAR v3 text file.
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Title: HADDOCK models of human alphaM I-domain bound to the the N-terminal domain of the cytokine pleiotrophin
Deposition date: 2024-01-15 Original release date: 2024-05-17
Authors: Wang, X.; Nguyen, H.
Citation: Wang, X.; Nguyen, H.. "NMR structure of alphaM I-domain of integrin Mac-1 in complex with the Cytokine Pleiotrophin" .
Assembly members:
entity_1, polymer, 194 residues, 22238.340 Da.
entity_2, polymer, 58 residues, 6431.449 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):
entity_1: EDSDIAFLIDGSGSIIPHDF
RRMKEFVSTVMEQLKKSKTL
FSLMQYSEEFRIHFTFKEFQ
NNPNPRSLVKPITQLLGRTH
TATGIRKVVRELFNITNGAR
KNAFKILVVITDGEKFGDPL
GYEDVIPEADREGVIRYVIG
VGDAFRSEKSRQELNTIASK
PPRDHVFQVNNFEALKTIQN
QLREKIFAIEGTQT
entity_2: GKKEKPEKKVKKSDCGEWQW
SVCVPTSGDCGLGTREGTRT
GAECKQTMKTQRCKIPCN
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 891 |
| 15N chemical shifts | 224 |
| 1H chemical shifts | 1111 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
Entities:
Entity 1, unit_1 194 residues - 22238.340 Da.
| 1 | GLU | ASP | SER | ASP | ILE | ALA | PHE | LEU | ILE | ASP | ||||
| 2 | GLY | SER | GLY | SER | ILE | ILE | PRO | HIS | ASP | PHE | ||||
| 3 | ARG | ARG | MET | LYS | GLU | PHE | VAL | SER | THR | VAL | ||||
| 4 | MET | GLU | GLN | LEU | LYS | LYS | SER | LYS | THR | LEU | ||||
| 5 | PHE | SER | LEU | MET | GLN | TYR | SER | GLU | GLU | PHE | ||||
| 6 | ARG | ILE | HIS | PHE | THR | PHE | LYS | GLU | PHE | GLN | ||||
| 7 | ASN | ASN | PRO | ASN | PRO | ARG | SER | LEU | VAL | LYS | ||||
| 8 | PRO | ILE | THR | GLN | LEU | LEU | GLY | ARG | THR | HIS | ||||
| 9 | THR | ALA | THR | GLY | ILE | ARG | LYS | VAL | VAL | ARG | ||||
| 10 | GLU | LEU | PHE | ASN | ILE | THR | ASN | GLY | ALA | ARG | ||||
| 11 | LYS | ASN | ALA | PHE | LYS | ILE | LEU | VAL | VAL | ILE | ||||
| 12 | THR | ASP | GLY | GLU | LYS | PHE | GLY | ASP | PRO | LEU | ||||
| 13 | GLY | TYR | GLU | ASP | VAL | ILE | PRO | GLU | ALA | ASP | ||||
| 14 | ARG | GLU | GLY | VAL | ILE | ARG | TYR | VAL | ILE | GLY | ||||
| 15 | VAL | GLY | ASP | ALA | PHE | ARG | SER | GLU | LYS | SER | ||||
| 16 | ARG | GLN | GLU | LEU | ASN | THR | ILE | ALA | SER | LYS | ||||
| 17 | PRO | PRO | ARG | ASP | HIS | VAL | PHE | GLN | VAL | ASN | ||||
| 18 | ASN | PHE | GLU | ALA | LEU | LYS | THR | ILE | GLN | ASN | ||||
| 19 | GLN | LEU | ARG | GLU | LYS | ILE | PHE | ALA | ILE | GLU | ||||
| 20 | GLY | THR | GLN | THR |
Entity 2, unit_2 58 residues - 6431.449 Da.
| 1 | GLY | LYS | LYS | GLU | LYS | PRO | GLU | LYS | LYS | VAL | ||||
| 2 | LYS | LYS | SER | ASP | CYS | GLY | GLU | TRP | GLN | TRP | ||||
| 3 | SER | VAL | CYS | VAL | PRO | THR | SER | GLY | ASP | CYS | ||||
| 4 | GLY | LEU | GLY | THR | ARG | GLU | GLY | THR | ARG | THR | ||||
| 5 | GLY | ALA | GLU | CYS | LYS | GLN | THR | MET | LYS | THR | ||||
| 6 | GLN | ARG | CYS | LYS | ILE | PRO | CYS | ASN |
Samples:
sample_1: human alphaM I-domain, [U-13C; U-15N], 0.2 mM; The N-terminal domain of pleiotrophin 1 mM
sample_2: human alphaM I-domain, [U-13C; U-15N], 0.5 mM
sample_3: The N-terminal domain of pleiotrophin, [U-13C; U-15N], 0.5 mM
sample_conditions_1: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D F1-13C-edited/F3-13C,15N-filtered HSQCNOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_3 | isotropic | sample_conditions_1 |
Software:
NMRViewJ, Bruce Johnson - chemical shift assignment
HADDOCK, Bonvin - structure calculation
NMR spectrometers:
- Bruker AVANCE III HD 850 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts