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
MolProbity Validation Chart

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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:

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:

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:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pETM-11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Snu17p: GAMGNEYKDNAYIYIGNLNR ELTEGDILTVFSEYGVPVDV ILSRDENTGESQGFAYLKYE DQRSTILAVDNLNGFKIGGR ALKIDHTFYRPKRSLQKYYE AVKEELDRDIVSKNNAEK
Pml1p: GSKSQYIDIMPDFSPSGLLE LES
Bud13p: GSYDKPAPENRFAIMPGSRW DGVHRSNGFEEKW

Data sets:
Data typeCount
13C chemical shifts705
15N chemical shifts180
1H chemical shifts1188

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Snu17p1
2Pml1p2
3Bud13p3

Entities:

Entity 1, Snu17p 118 residues - 13496.103 Da.

as above

1   GLYALAMETGLYASNGLUTYRLYSASPASN
2   ALATYRILETYRILEGLYASNLEUASNARG
3   GLULEUTHRGLUGLYASPILELEUTHRVAL
4   PHESERGLUTYRGLYVALPROVALASPVAL
5   ILELEUSERARGASPGLUASNTHRGLYGLU
6   SERGLNGLYPHEALATYRLEULYSTYRGLU
7   ASPGLNARGSERTHRILELEUALAVALASP
8   ASNLEUASNGLYPHELYSILEGLYGLYARG
9   ALALEULYSILEASPHISTHRPHETYRARG
10   PROLYSARGSERLEUGLNLYSTYRTYRGLU
11   ALAVALLYSGLUGLULEUASPARGASPILE
12   VALSERLYSASNASNALAGLULYS

Entity 2, Pml1p 23 residues - 2514.800 Da.

as above

1   GLYSERLYSSERGLNTYRILEASPILEMET
2   PROASPPHESERPROSERGLYLEULEUGLU
3   LEUGLUSER

Entity 3, Bud13p 33 residues - 3828.226 Da.

as above

1   GLYSERTYRASPLYSPROALAPROGLUASN
2   ARGPHEALAILEMETPROGLYSERARGTRP
3   ASPGLYVALHISARGSERASNGLYPHEGLU
4   GLULYSTRP

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCSnu17p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCSnu17p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCSnu17p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCSnu17p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCPml1p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCPml1p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCPml1p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCPml1p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCBud13p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCBud13p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCBud13p_13C15NisotropicCONDITIONS
2D 1H-15N HSQCBud13p_13C15NisotropicCONDITIONS
3D HNCOSnu17p_13C15NisotropicCONDITIONS
3D HNCASnu17p_13C15NisotropicCONDITIONS
3D HNCAPml1p_13C15NisotropicCONDITIONS
3D HNCABud13p_13C15NisotropicCONDITIONS
3D HNCACBSnu17p_2H13C15NisotropicCONDITIONS
3D HN(CO)CASnu17p_13C15NisotropicCONDITIONS
3D HN(CO)CAPml1p_13C15NisotropicCONDITIONS
3D HN(CO)CABud13p_13C15NisotropicCONDITIONS
3D HCCH-TOCSYSnu17p_13C15NisotropicCONDITIONS
3D HCCH-TOCSYPml1p_13C15NisotropicCONDITIONS
3D HCCH-TOCSYBud13p_13C15NisotropicCONDITIONS
3D 1H-15N NOESYSnu17p_13C15NisotropicCONDITIONS
3D 1H-15N NOESYPml1p_13C15NisotropicCONDITIONS
3D 1H-15N NOESYBud13p_13C15NisotropicCONDITIONS
3D 1H-15N NOESYBud13p_13C15N_Snu17p_2HisotropicCONDITIONS
3D 1H-13C NOESY aliphaticSnu17p_13C15NisotropicCONDITIONS
3D 1H-13C NOESY aliphaticPml1p_13C15NisotropicCONDITIONS
3D 1H-13C NOESY aliphaticBud13p_13C15NisotropicCONDITIONS
3D 1H-13C NOESY aliphaticBud13p_13C15N_Snu17p_2HisotropicCONDITIONS
3D 1H-13C NOESY aromaticSnu17p_13C15NisotropicCONDITIONS
3D 1H-13C NOESY aromaticPml1p_13C15NisotropicCONDITIONS
3D 1H-13C NOESY aromaticBud13p_13C15NisotropicCONDITIONS
3D HCCH-TOCSYBud13p_13C15N_Snu17p_2HisotropicCONDITIONS
3D 1H-13C NOESY filtered/editedSnu17p_13C15NisotropicCONDITIONS
3D 1H-13C NOESY filtered/editedPml1p_13C15NisotropicCONDITIONS
HBCBCGCDHDSnu17p_13C15NisotropicCONDITIONS
3D CCH-TOCSYSnu17p_13C15NisotropicCONDITIONS
3D CBCA(CO)NHBud13p_13C15NisotropicCONDITIONS
3D 1H-15N NOESY ARG-centeredBud13p_13C15NisotropicCONDITIONS

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
AlphaFold D6VVT5 P40565 Q06901 Q07930 D6VTX8 P46947

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks