BMRB Entry 16871
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16871
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Title: Solution structure of the second PDZ domain from human zonula occludens-1: A dimeric form with 3D domain swapping PubMed: 21387411
Deposition date: 2010-04-15 Original release date: 2011-05-05
Authors: Ji, Peng; wu, Jiawen; Zhang, Jiahai; Yang, Yinshan; wu, Jihui; Shi, Yunyu
Citation: Ji, Peng; Yang, Guang; Zhang, Jiahai; Wu, Jiawen; Chen, Zhengjun; Gong, Qingguo; Wu, Jihui; Shi, Yunyu. "Solution structure of the second PDZ domain of Zonula Occludens 1." Proteins 79, 1342-1346 (2011).
Assembly members:
ZO-1 PDZ2, polymer, 88 residues, 2507.023 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):
ZO-1 PDZ2: TKVTLVKSRKNEEYGLRLAS
HIFVKEISQDSLAARDGNIQ
EGDVVLKINGTVTENMSLTD
AKTLIERSKGKLKMVVQRDE
LEHHHHHH
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 351 |
| 15N chemical shifts | 88 |
| 1H chemical shifts | 602 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | ZO-1 PDZ2 | 1 |
Entities:
Entity 1, ZO-1 PDZ2 88 residues - 2507.023 Da.
| 1 | THR | LYS | VAL | THR | LEU | VAL | LYS | SER | ARG | LYS | ||||
| 2 | ASN | GLU | GLU | TYR | GLY | LEU | ARG | LEU | ALA | SER | ||||
| 3 | HIS | ILE | PHE | VAL | LYS | GLU | ILE | SER | GLN | ASP | ||||
| 4 | SER | LEU | ALA | ALA | ARG | ASP | GLY | ASN | ILE | GLN | ||||
| 5 | GLU | GLY | ASP | VAL | VAL | LEU | LYS | ILE | ASN | GLY | ||||
| 6 | THR | VAL | THR | GLU | ASN | MET | SER | LEU | THR | ASP | ||||
| 7 | ALA | LYS | THR | LEU | ILE | GLU | ARG | SER | LYS | GLY | ||||
| 8 | LYS | LEU | LYS | MET | VAL | VAL | GLN | ARG | ASP | GLU | ||||
| 9 | LEU | GLU | HIS | HIS | HIS | HIS | HIS | HIS |
Samples:
sample_1: PDZ2, [U-99% 13C; U-99% 15N], 0.8 – 1 mM; H2O 90%; D2O 10%
sample_2: PDZ2, [U-99% 13C; U-99% 15N], 0.8 – 1 mM; D2O 100%
sample_3: PDZ2, [U-99% 13C; U-99% 15N], 0.4 – 0.5 mM; PDZ20.5 – 0.8 mM; D2O 100%
sample_4: PDZ20.5 – 0.8 mM; D2O 100%
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 310 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-1H 13C-Filtered NOESY | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_4 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_4 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
CNSSOLVE v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution
xwinnmr v3.5, Bruker Biospin - collection
NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY v3.112, Goddard - chemical shift assignment, data analysis, peak picking
TALOS v2003.027.13.05, Cornilescu, Delaglio and Bax - predicts angles from chemical shift homology
Molmol v2K.2, Koradi, Billeter and Wuthrich - data analysis
ProcheckNMR v3.5.4, Laskowski and MacArthur - data analysis
NMR spectrometers:
- Bruker DMX 600 MHz
Related Database Links:
| PDB | |
| GB | EAW51509 |
| REF | XP_004320454 XP_005193388 XP_009874121 XP_009922511 XP_010151333 |
| TPG | DAA17568 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts