BMRB Entry 19766
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19766
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Title: Cooperative Structure of the Heterotrimeric pre-mRNA Retention and Splicing Complex
Deposition date: 2014-02-04 Original release date: 2014-08-27
Authors: Wysoczanski, Piotr; Schneider, Cornelius; Xiang, ShengQi; Munari, Francesca; Trowitzsch, Simon; Wahl, Markus; Luhrmann, Reinhard; Becker, Stefan; Zweckstetter, Markus
Citation: Wysoczanski, Piotr; Schneider, Cornelius; Xiang, ShengQi; Munari, Francesca; Trowitzsch, Simon; Wahl, Markus; Luhrmann, Reinhard; Becker, Stefan; Zweckstetter, Markus. "Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex" Nat. Struct. Mol. Biol. ., .-..
Assembly members:
Snu17p, polymer, 118 residues, 13496.103 Da.
Pml1p, polymer, 23 residues, 2514.800 Da.
Bud13p, polymer, 33 residues, 3828.226 Da.
Natural source: Common Name: baker Taxonomy ID: 4932 Superkingdom: not available Kingdom: not available Genus/species: Eukaryota Fungi
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Snu17p: GAMGNEYKDNAYIYIGNLNR
ELTEGDILTVFSEYGVPVDV
ILSRDENTGESQGFAYLKYE
DQRSTILAVDNLNGFKIGGR
ALKIDHTFYRPKRSLQKYYE
AVKEELDRDIVSKNNAEK
Pml1p: GSKSQYIDIMPDFSPSGLLE
LES
Bud13p: GSYDKPAPENRFAIMPGSRW
DGVHRSNGFEEKW
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 705 |
| 15N chemical shifts | 180 |
| 1H chemical shifts | 1188 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Snu17p | 1 |
| 2 | Pml1p | 2 |
| 3 | Bud13p | 3 |
Entities:
Entity 1, Snu17p 118 residues - 13496.103 Da.
as above
| 1 | GLY | ALA | MET | GLY | ASN | GLU | TYR | LYS | ASP | ASN | ||||
| 2 | ALA | TYR | ILE | TYR | ILE | GLY | ASN | LEU | ASN | ARG | ||||
| 3 | GLU | LEU | THR | GLU | GLY | ASP | ILE | LEU | THR | VAL | ||||
| 4 | PHE | SER | GLU | TYR | GLY | VAL | PRO | VAL | ASP | VAL | ||||
| 5 | ILE | LEU | SER | ARG | ASP | GLU | ASN | THR | GLY | GLU | ||||
| 6 | SER | GLN | GLY | PHE | ALA | TYR | LEU | LYS | TYR | GLU | ||||
| 7 | ASP | GLN | ARG | SER | THR | ILE | LEU | ALA | VAL | ASP | ||||
| 8 | ASN | LEU | ASN | GLY | PHE | LYS | ILE | GLY | GLY | ARG | ||||
| 9 | ALA | LEU | LYS | ILE | ASP | HIS | THR | PHE | TYR | ARG | ||||
| 10 | PRO | LYS | ARG | SER | LEU | GLN | LYS | TYR | TYR | GLU | ||||
| 11 | ALA | VAL | LYS | GLU | GLU | LEU | ASP | ARG | ASP | ILE | ||||
| 12 | VAL | SER | LYS | ASN | ASN | ALA | GLU | LYS |
Entity 2, Pml1p 23 residues - 2514.800 Da.
as above
| 1 | GLY | SER | LYS | SER | GLN | TYR | ILE | ASP | ILE | MET | ||||
| 2 | PRO | ASP | PHE | SER | PRO | SER | GLY | LEU | LEU | GLU | ||||
| 3 | LEU | GLU | SER |
Entity 3, Bud13p 33 residues - 3828.226 Da.
as above
| 1 | GLY | SER | TYR | ASP | LYS | PRO | ALA | PRO | GLU | ASN | ||||
| 2 | ARG | PHE | ALA | ILE | MET | PRO | GLY | SER | ARG | TRP | ||||
| 3 | ASP | GLY | VAL | HIS | ARG | SER | ASN | GLY | PHE | GLU | ||||
| 4 | GLU | LYS | TRP |
Samples:
Snu17p_13C15N: sodium phosphate 25 mM; NaCl 250 mM; sodium azide 1 mM; Snu17p, [U-13C; U-15N], 0.9 – 1.3 mM; Bud13p1.1 – 1.5 mM; Pml1p1.4 – 19 mM; H2O 90%; D2O 10%
Pml1p_13C15N: sodium phosphate 25 mM; NaCl 250 mM; sodium azide 1 mM; Snu17p1.0 – 1.3 mM; Bud13p1.2 – 1.5 mM; Pml1p, [U-13C; U-15N], 0.8 – 1.0 mM; H2O 90%; D2O 10%
Bud13p_13C15N: sodium phosphate 25 mM; NaCl 250 mM; sodium azide 1 mM; Snu17p1.0 – 1.3 mM; Bud13p, [U-10% 13C; U-99% 15N], 0.8 – 1.0 mM; Pml1p1.5 – 1.9 mM; H2O 90%; D2O 10%
Snu17p_2H13C15N: sodium phosphate 25 mM; NaCl 250 mM; sodium azide 1 mM; Snu17p, [U-13C; U-15N; U-2H], 0.9 – 1.3 mM; Bud13p1.1 – 1.5 mM; Pml1p1.4 – 1.9 mM; H2O 90%; D2O 10%
Bud13p_13C15N_Snu17p_2H: sodium phosphate 25 mM; NaCl 250 mM; sodium azide 1 mM; Snu17p, [U-13C; U-15N; U-2H], 1.0 – 1.3 mM; Bud13p, [U-10% 13C; U-99% 15N], 0.8 – 1.0 mM; Pml1p1.5 – 1.9 mM; H2O 90%; D2O 10%
CONDITIONS: pH: 6.8; pressure: 1 atm; temperature: 308 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | Snu17p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Snu17p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Snu17p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Snu17p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Pml1p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Pml1p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Pml1p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Pml1p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Bud13p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Bud13p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Bud13p_13C15N | isotropic | CONDITIONS |
| 2D 1H-15N HSQC | Bud13p_13C15N | isotropic | CONDITIONS |
| 3D HNCO | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D HNCA | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D HNCA | Pml1p_13C15N | isotropic | CONDITIONS |
| 3D HNCA | Bud13p_13C15N | isotropic | CONDITIONS |
| 3D HNCACB | Snu17p_2H13C15N | isotropic | CONDITIONS |
| 3D HN(CO)CA | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D HN(CO)CA | Pml1p_13C15N | isotropic | CONDITIONS |
| 3D HN(CO)CA | Bud13p_13C15N | isotropic | CONDITIONS |
| 3D HCCH-TOCSY | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D HCCH-TOCSY | Pml1p_13C15N | isotropic | CONDITIONS |
| 3D HCCH-TOCSY | Bud13p_13C15N | isotropic | CONDITIONS |
| 3D 1H-15N NOESY | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D 1H-15N NOESY | Pml1p_13C15N | isotropic | CONDITIONS |
| 3D 1H-15N NOESY | Bud13p_13C15N | isotropic | CONDITIONS |
| 3D 1H-15N NOESY | Bud13p_13C15N_Snu17p_2H | isotropic | CONDITIONS |
| 3D 1H-13C NOESY aliphatic | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D 1H-13C NOESY aliphatic | Pml1p_13C15N | isotropic | CONDITIONS |
| 3D 1H-13C NOESY aliphatic | Bud13p_13C15N | isotropic | CONDITIONS |
| 3D 1H-13C NOESY aliphatic | Bud13p_13C15N_Snu17p_2H | isotropic | CONDITIONS |
| 3D 1H-13C NOESY aromatic | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D 1H-13C NOESY aromatic | Pml1p_13C15N | isotropic | CONDITIONS |
| 3D 1H-13C NOESY aromatic | Bud13p_13C15N | isotropic | CONDITIONS |
| 3D HCCH-TOCSY | Bud13p_13C15N_Snu17p_2H | isotropic | CONDITIONS |
| 3D 1H-13C NOESY filtered/edited | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D 1H-13C NOESY filtered/edited | Pml1p_13C15N | isotropic | CONDITIONS |
| HBCBCGCDHD | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D CCH-TOCSY | Snu17p_13C15N | isotropic | CONDITIONS |
| 3D CBCA(CO)NH | Bud13p_13C15N | isotropic | CONDITIONS |
| 3D 1H-15N NOESY ARG-centered | Bud13p_13C15N | isotropic | CONDITIONS |
Software:
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution
CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
TOPSPIN v3.1, Bruker Biospin - processing
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
Analysis_CCPN, CCPN - data analysis
NMR spectrometers:
- Bruker Avance 900 MHz
- Bruker Avance 800 MHz
- Bruker Avance 700 MHz
- Bruker Avance 600 MHz
- Bruker Avance 800 MHz
Related Database Links:
| UNP | P40565 Q07930 P46947 |
| BMRB | 25047 |
| PDB | |
| DBJ | GAA24120 GAA24903 GAA23224 |
| EMBL | CAA86207 CAY80517 CAA62157 CAA97538 CAY81254 CAA59179 CAA96886 CAY79593 |
| GB | AAS56407 AEO21093 AHY76002 AJP39470 AJR36763 AAS56260 AHY78422 EDN59562 EDV09324 EDZ70737 AAS56830 AHY79214 EDN61950 EDV10384 EDZ72293 |
| REF | NP_012270 NP_013116 NP_011341 |
| SP | P40565 Q07930 P46947 |
| TPG | DAA08551 DAA09334 DAA07939 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts