BMRB Entry 31139
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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/BMR31139
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NMR-STAR v3 text file.
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Title: HADDOCK models of active human alphaM I-domain bound to the the C-terminal domain of the cytokine pleiotrophin
Deposition date: 2024-01-15 Original release date: 2024-05-15
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, 184 residues, 21148.152 Da.
entity_2, polymer, 57 residues, 6472.498 Da.
entity_MG, non-polymer, 24.305 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: DSDIAFLIDGSGSIIPHDFR
RMKEFVSTVMEQLKKSKTLF
SLMQYSEEFRIHFTFKEFQN
NPNPRSLVKPITQLLGRTHT
ATGIRKVVRELFNITNGARK
NAFKILVVITDGEKFGDPLG
YEDVIPEADREGVIRYVIGV
GDAFRSEKSRQELNTIASKP
PRDHVFQVNNFEALKTIQNQ
LREK
entity_2: NWKKQFGAECKYQFQAWGEC
DLNTALKTRTGSLKRALHNA
ECQKTVTISKPCGKLTK
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 432 |
| 15N chemical shifts | 129 |
| 1H chemical shifts | 367 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
| 3 | unit_3 | 3 |
Entities:
Entity 1, unit_1 184 residues - 21148.152 Da.
| 1 | ASP | SER | ASP | ILE | ALA | PHE | LEU | ILE | ASP | GLY | ||||
| 2 | SER | GLY | SER | ILE | ILE | PRO | HIS | ASP | PHE | ARG | ||||
| 3 | ARG | MET | LYS | GLU | PHE | VAL | SER | THR | VAL | MET | ||||
| 4 | GLU | GLN | LEU | LYS | LYS | SER | LYS | THR | LEU | PHE | ||||
| 5 | SER | LEU | MET | GLN | TYR | SER | GLU | GLU | PHE | ARG | ||||
| 6 | ILE | HIS | PHE | THR | PHE | LYS | GLU | PHE | GLN | ASN | ||||
| 7 | ASN | PRO | ASN | PRO | ARG | SER | LEU | VAL | LYS | PRO | ||||
| 8 | ILE | THR | GLN | LEU | LEU | GLY | ARG | THR | HIS | THR | ||||
| 9 | ALA | THR | GLY | ILE | ARG | LYS | VAL | VAL | ARG | GLU | ||||
| 10 | LEU | PHE | ASN | ILE | THR | ASN | GLY | ALA | ARG | LYS | ||||
| 11 | ASN | ALA | PHE | LYS | ILE | LEU | VAL | VAL | ILE | THR | ||||
| 12 | ASP | GLY | GLU | LYS | PHE | GLY | ASP | PRO | LEU | GLY | ||||
| 13 | TYR | GLU | ASP | VAL | ILE | PRO | GLU | ALA | ASP | ARG | ||||
| 14 | GLU | GLY | VAL | ILE | ARG | TYR | VAL | ILE | GLY | VAL | ||||
| 15 | GLY | ASP | ALA | PHE | ARG | SER | GLU | LYS | SER | ARG | ||||
| 16 | GLN | GLU | LEU | ASN | THR | ILE | ALA | SER | LYS | PRO | ||||
| 17 | PRO | ARG | ASP | HIS | VAL | PHE | GLN | VAL | ASN | ASN | ||||
| 18 | PHE | GLU | ALA | LEU | LYS | THR | ILE | GLN | ASN | GLN | ||||
| 19 | LEU | ARG | GLU | LYS |
Entity 2, unit_2 57 residues - 6472.498 Da.
| 1 | ASN | TRP | LYS | LYS | GLN | PHE | GLY | ALA | GLU | CYS | ||||
| 2 | LYS | TYR | GLN | PHE | GLN | ALA | TRP | GLY | GLU | CYS | ||||
| 3 | ASP | LEU | ASN | THR | ALA | LEU | LYS | THR | ARG | THR | ||||
| 4 | GLY | SER | LEU | LYS | ARG | ALA | LEU | HIS | ASN | ALA | ||||
| 5 | GLU | CYS | GLN | LYS | THR | VAL | THR | ILE | SER | LYS | ||||
| 6 | PRO | CYS | GLY | LYS | LEU | THR | LYS |
Entity 3, unit_3 - Mg - 24.305 Da.
| 1 | MG |
Samples:
sample_1: active human alphaM I-domain, [U-100% 13C; U-100% 15N], 0.3 mM
sample_2: The C-terminal Domain of Pleiotrophin, [U-100% 13C; U-100% 15N], 1.0 mM
sample_3: active human alphaM I-domain, [U-100% 13C; U-100% 15N; U-80% 2H], 0.2 mM; The C-terminal Domain of Pleiotrophin 1.0 mM
sample_conditions_1: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 4D 13C-HSQC-NOESY-15N-HMQC | sample_3 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(COCA)CB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | 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