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BMRB: 19766

2MKC

Cooperative Structure of the Heterotrimeric pre-mRNA Retention and Splicing Complex

Authors

Wysoczanski, P., Schneider, C., Xiang, S., Munari, F., Trowitzsch, S., Wahl, M.C., Luhrmann, R., Becker, S., Zweckstetter, M.

Assembly

Heterotrimeric pre-mRNA Retention and Splicing Complex

Entity

1. Snu17p (polymer, Thiol state: not present), 118 monomers, 13478.84 Da Detail

GAMGNEYKDN AYIYIGNLNR ELTEGDILTV FSEYGVPVDV ILSRDENTGE SQGFAYLKYE DQRSTILAVD NLNGFKIGGR ALKIDHTFYR PKRSLQKYYE AVKEELDRDI VSKNNAEK

2. Pml1p (polymer, Thiol state: not present), 23 monomers, 2513.772 Da Detail

GSKSQYIDIM PDFSPSGLLE LES

3. Bud13p (polymer, Thiol state: not present), 33 monomers, 3822.141 Da Detail

GSYDKPAPEN RFAIMPGSRW DGVHRSNGFE EKW

Total weight

19814.752 Da

Max. entity weight

13478.84 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.2 %, Completeness (bb): 92.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.2 % (1902 of 2040)	94.9 % (1013 of 1068)	90.4 % (712 of 788)	96.2 % (177 of 184)
Backbone	92.9 % (957 of 1030)	98.3 % (351 of 357)	87.5 % (443 of 506)	97.6 % (163 of 167)
Sidechain	94.3 % (1102 of 1168)	93.1 % (662 of 711)	96.8 % (426 of 440)	82.4 % (14 of 17)
Aromatic	92.1 % (175 of 190)	92.6 % (88 of 95)	91.4 % (85 of 93)	100.0 % (2 of 2)
Methyl	100.0 % (156 of 156)	100.0 % (78 of 78)	100.0 % (78 of 78)

1. Snu17p

GAMGNEYKDN AYIYIGNLNR ELTEGDILTV FSEYGVPVDV ILSRDENTGE SQGFAYLKYE DQRSTILAVD NLNGFKIGGR ALKIDHTFYR PKRSLQKYYE AVKEELDRDI VSKNNAEK

2. Pml1p

GSKSQYIDIM PDFSPSGLLE LES

3. Bud13p

GSYDKPAPEN RFAIMPGSRW DGVHRSNGFE EKW

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 160-180 uL, 3 mm tube

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	NaCl	natural abundance	250 mM
3	sodium azide	natural abundance	1 mM
4	Snu17p	[U-13C; U-15N]	0.9 ~ 1.3 mM
5	Bud13p	natural abundance	1.1 ~ 1.5 mM
6	Pml1p	natural abundance	1.4 ~ 19.0 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 160-180 uL, 3 mm tube

#	Name	Isotope labeling	Concentration
9	sodium phosphate	natural abundance	25 mM
10	NaCl	natural abundance	250 mM
11	sodium azide	natural abundance	1 mM
12	Snu17p	natural abundance	1.0 ~ 1.3 mM
13	Bud13p	natural abundance	1.2 ~ 1.5 mM
14	Pml1p	[U-13C; U-15N]	0.8 ~ 1.0 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 160-180 uL, 3 mm tube

#	Name	Isotope labeling	Concentration
17	sodium phosphate	natural abundance	25 mM
18	NaCl	natural abundance	250 mM
19	sodium azide	natural abundance	1 mM
20	Snu17p	natural abundance	1.0 ~ 1.3 mM
21	Bud13p	[U-10% 13C; U-99% 15N]	0.8 ~ 1.0 mM
22	Pml1p	natural abundance	1.5 ~ 1.9 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 160-180 uL, 3 mm tube

#	Name	Isotope labeling	Concentration
25	sodium phosphate	natural abundance	25 mM
26	NaCl	natural abundance	250 mM
27	sodium azide	natural abundance	1 mM
28	Snu17p	[U-13C; U-15N; U-2H]	0.9 ~ 1.3 mM
29	Bud13p	natural abundance	1.1 ~ 1.5 mM
30	Pml1p	natural abundance	1.4 ~ 1.9 mM
31	H2O	natural abundance	90 %
32	D2O	natural abundance	10 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 160-180 uL, 3 mm tube

#	Name	Isotope labeling	Concentration
33	sodium phosphate	natural abundance	25 mM
34	NaCl	natural abundance	250 mM
35	sodium azide	natural abundance	1 mM
36	Snu17p	[U-13C; U-15N; U-2H]	1.0 ~ 1.3 mM
37	Bud13p	[U-10% 13C; U-99% 15N]	0.8 ~ 1.0 mM
38	Pml1p	natural abundance	1.5 ~ 1.9 mM
39	H2O	natural abundance	90 %
40	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: 0.15 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MKC, Strand ID: A, B, C Detail

Release date

2014-08-26

Citation

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex
Wysoczanski, P., Schneider, C., Xiang, S., Munari, F., Trowitzsch, S., Wahl, M.C., Luhrmann, R., Becker, S., Zweckstetter, M.
Nat. Struct. Mol. Biol. (2014), 21, 911-918, PubMed 25218446 , DOI 10.1038/nsmb.2889 , Abstract

Related entities 1. Snu17p, : 15 entities Detail

Related entities 2. Pml1p, : 1 : 1 : 5 : 1 entities Detail

Related entities 3. Bud13p, : 1 : 5 : 32 entities Detail

Interaction partners 2. Pml1p, : 9 interactors Detail

More details for 9 interactors identified by 5 citations

Interaction partners 3. Bud13p, : 19 interactors Detail

More details for 19 interactors identified by 6 citations

Experiments performed 41 experiments Detail

1 2D 1H-15N HSQC