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BMRB: 34248

6G04

NMR Solution Structure of Yeast TSR2(1-152) in Complex with S26A(100-119)

Authors

Michel, E., Schuetz, S., Damberger, F.F., Allain, F.H.-T., Panse, V.G.

Assembly

Pre-rRNA-processing protein TSR2, 40S ribosomal protein S26-A

Entity

1. Pre-rRNA-processing protein TSR2, 40S ribosomal protein S26-A, entity 1 (polymer, Thiol state: all free), 156 monomers, 17919.90 Da Detail

SGSHMSTQYI DETAFVQAEQ GKTNLMFSDE KQQARFELGV SMVIYKWDAL DVAVENSWGG PDSAEKRDWI TGIVVDLFKN EKVVDAALIE ETLLYAMIDE FETNVEDDSA LPIAVEVINI YNDCFNLNYN KVEKLYLEWQ EKQRTKKSKR VVHIEG

2. Pre-rRNA-processing protein TSR2, 40S ribosomal protein S26-A, entity 2 (polymer, Thiol state: not present), 26 monomers, 2896.245 Da Detail

SGSQHMRPRF NRENKVSPAD AAKKAL

Total weight

20816.145 Da

Max. entity weight

17919.9 Da

Source organism

Saccharomyces cerevisiae S288C

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 40.7 %, Completeness: 31.1 %, Completeness (bb): 35.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	31.1 % (668 of 2150)	31.0 % (347 of 1118)	30.0 % (249 of 831)	35.8 % (72 of 201)
Backbone	35.1 % (380 of 1084)	36.1 % (133 of 368)	33.5 % (180 of 538)	37.6 % (67 of 178)
Sidechain	28.9 % (358 of 1240)	28.7 % (215 of 750)	29.6 % (138 of 467)	21.7 % (5 of 23)
Aromatic	7.9 % (14 of 178)	7.9 % (7 of 89)	7.1 % (6 of 85)	25.0 % (1 of 4)
Methyl	30.6 % (60 of 196)	31.6 % (31 of 98)	29.6 % (29 of 98)

1. entity 1

SGSHMSTQYI DETAFVQAEQ GKTNLMFSDE KQQARFELGV SMVIYKWDAL DVAVENSWGG PDSAEKRDWI TGIVVDLFKN EKVVDAALIE ETLLYAMIDE FETNVEDDSA LPIAVEVINI YNDCFNLNYN KVEKLYLEWQ EKQRTKKSKR VVHIEG

2. entity 2

SGSQHMRPRF NRENKVSPAD AAKKAL

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7, Details 0.5 mM [U-13C; U-15N] Tsr2(1-152), 0.5 mM S26A(100-119), 20 mM sodium phosphate, 1 mM [U-2H] DTT, 10 uM EDTA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	Tsr2(1-152)	[U-13C; U-15N]	0.5 mM
2	S26A(100-119)	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	[U-2H]	1 mM
5	EDTA	natural abundance	10 uM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7, Details 0.5 mM Tsr2(1-152), 0.5 mM [U-13C; U-15N] S26A(100-119), 20 mM sodium phosphate, 1 mM [U-2H] DTT, 10 uM EDTA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	Tsr2(1-152)	natural abundance	0.5 mM
7	S26A(100-119)	[U-13C; U-15N]	0.5 mM
8	sodium phosphate	natural abundance	20 mM
9	DTT	[U-2H]	1 mM
10	EDTA	natural abundance	10 uM

Chem. Shift Complete2

Sequence coverage: 86.3 %, Completeness: 55.2 %, Completeness (bb): 54.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	55.2 % (2375 of 4300)	57.7 % (1290 of 2236)	50.5 % (839 of 1662)	61.2 % (246 of 402)
Backbone	54.5 % (1181 of 2168)	60.6 % (446 of 736)	47.8 % (514 of 1076)	62.1 % (221 of 356)
Sidechain	57.0 % (1414 of 2480)	56.3 % (845 of 1500)	58.2 % (544 of 934)	54.3 % (25 of 46)
Aromatic	48.0 % (171 of 356)	47.8 % (85 of 178)	47.6 % (81 of 170)	62.5 % (5 of 8)
Methyl	61.0 % (239 of 392)	61.2 % (120 of 196)	60.7 % (119 of 196)

1. entity 1

SGSHMSTQYI DETAFVQAEQ GKTNLMFSDE KQQARFELGV SMVIYKWDAL DVAVENSWGG PDSAEKRDWI TGIVVDLFKN EKVVDAALIE ETLLYAMIDE FETNVEDDSA LPIAVEVINI YNDCFNLNYN KVEKLYLEWQ EKQRTKKSKR VVHIEG

2. entity 2

SGSQHMRPRF NRENKVSPAD AAKKAL

Show sample condition

Sample #1

#	Name	Isotope labeling	Concentration
1	Tsr2(1-152)	[U-13C; U-15N]	0.5 mM
2	S26A(100-119)	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	[U-2H]	1 mM
5	EDTA	natural abundance	10 uM

Sample #2

#	Name	Isotope labeling	Concentration
6	Tsr2(1-152)	natural abundance	0.5 mM
7	S26A(100-119)	[U-13C; U-15N]	0.5 mM
8	sodium phosphate	natural abundance	20 mM
9	DTT	[U-2H]	1 mM
10	EDTA	natural abundance	10 uM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	8.9960013E8 Hz	internal	indirect	0.2514495
¹H	water	protons	8.9960013E8 Hz	internal	direct	1.0
¹⁵N	water	protons	8.9960013E8 Hz	internal	indirect	0.1013291

Referencing offset: -0.19 ppm, Outliers: 4 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	8.9960013E8 Hz	internal	indirect	0.2514495
¹H	water	protons	8.9960013E8 Hz	internal	direct	1.0
¹⁵N	water	protons	8.9960013E8 Hz	internal	indirect	0.1013291

Referencing offset: -0.19 ppm, Outliers: 4 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	8.9960013E8 Hz	internal	indirect	0.2514495
¹H	water	protons	8.9960013E8 Hz	internal	direct	1.0
¹⁵N	water	protons	8.9960013E8 Hz	internal	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 3 Detail

Release date

2018-09-12

Citation

Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2
Schutz, S., Michel, E., Damberger, F.F., Oplova, M., Pena, C., Leitner, A., Aebersold, R., Allain, F.H., Panse, V.G.
Nat. Commun. (2018), 9, 3669-3669, PubMed 30201955 , DOI 10.1038/s41467-018-06160-x , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34247 released on 2018-09-10
Title NMR Solution Structure of yeast TSR2(1-152)

Related entities 1. Pre-rRNA-processing protein TSR2, 40S ribosomal protein S26-A, entity 1, : 1 : 1 : 2 : 3 entities Detail

Related entities 2. Pre-rRNA-processing protein TSR2, 40S ribosomal protein S26-A, entity 2, : 1 : 4 entities Detail

Interaction partners 1. Pre-rRNA-processing protein TSR2, 40S ribosomal protein S26-A, entity 1, : 17 interactors Detail

More details for 17 interactors identified by 5 citations

Experiments performed 14 experiments Detail

1 3D HNCA

Instrument

Bruker Avance - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7, Details 0.5 mM [U-13C; U-15N] Tsr2(1-152), 0.5 mM S26A(100-119), 20 mM sodium phosphate, 1 mM [U-2H] DTT, 10 uM EDTA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	Tsr2(1-152)	[U-13C; U-15N]	0.5 mM
2	S26A(100-119)	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	[U-2H]	1 mM
5	EDTA	natural abundance	10 uM

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Tsr2(1-152)	[U-13C; U-15N]	0.5 mM
2	S26A(100-119)	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	[U-2H]	1 mM
5	EDTA	natural abundance	10 uM

3 3D HBHA(CO)NH

Instrument

Bruker Avance - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Tsr2(1-152)	[U-13C; U-15N]	0.5 mM
2	S26A(100-119)	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	[U-2H]	1 mM
5	EDTA	natural abundance	10 uM

4 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Tsr2(1-152)	[U-13C; U-15N]	0.5 mM
2	S26A(100-119)	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	[U-2H]	1 mM
5	EDTA	natural abundance	10 uM

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Tsr2(1-152)	[U-13C; U-15N]	0.5 mM
2	S26A(100-119)	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	[U-2H]	1 mM
5	EDTA	natural abundance	10 uM

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Tsr2(1-152)	[U-13C; U-15N]	0.5 mM
2	S26A(100-119)	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	[U-2H]	1 mM
5	EDTA	natural abundance	10 uM

7 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Tsr2(1-152)	[U-13C; U-15N]	0.5 mM
2	S26A(100-119)	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	[U-2H]	1 mM
5	EDTA	natural abundance	10 uM

8 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7, Details 0.5 mM Tsr2(1-152), 0.5 mM [U-13C; U-15N] S26A(100-119), 20 mM sodium phosphate, 1 mM [U-2H] DTT, 10 uM EDTA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	Tsr2(1-152)	natural abundance	0.5 mM
7	S26A(100-119)	[U-13C; U-15N]	0.5 mM
8	sodium phosphate	natural abundance	20 mM
9	DTT	[U-2H]	1 mM
10	EDTA	natural abundance	10 uM

9 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Tsr2(1-152)	natural abundance	0.5 mM
7	S26A(100-119)	[U-13C; U-15N]	0.5 mM
8	sodium phosphate	natural abundance	20 mM
9	DTT	[U-2H]	1 mM
10	EDTA	natural abundance	10 uM

10 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Tsr2(1-152)	natural abundance	0.5 mM
7	S26A(100-119)	[U-13C; U-15N]	0.5 mM
8	sodium phosphate	natural abundance	20 mM
9	DTT	[U-2H]	1 mM
10	EDTA	natural abundance	10 uM

11 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Tsr2(1-152)	natural abundance	0.5 mM
7	S26A(100-119)	[U-13C; U-15N]	0.5 mM
8	sodium phosphate	natural abundance	20 mM
9	DTT	[U-2H]	1 mM
10	EDTA	natural abundance	10 uM

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Tsr2(1-152)	natural abundance	0.5 mM
7	S26A(100-119)	[U-13C; U-15N]	0.5 mM
8	sodium phosphate	natural abundance	20 mM
9	DTT	[U-2H]	1 mM
10	EDTA	natural abundance	10 uM

13 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Tsr2(1-152)	natural abundance	0.5 mM
7	S26A(100-119)	[U-13C; U-15N]	0.5 mM
8	sodium phosphate	natural abundance	20 mM
9	DTT	[U-2H]	1 mM
10	EDTA	natural abundance	10 uM

14 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Tsr2(1-152)	natural abundance	0.5 mM
7	S26A(100-119)	[U-13C; U-15N]	0.5 mM
8	sodium phosphate	natural abundance	20 mM
9	DTT	[U-2H]	1 mM
10	EDTA	natural abundance	10 uM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34248_6g04.nef
Input source #2: Coordindates	6g04.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
SGSHMSTQYIDETAFVQAEQGKTNLMFSDEKQQARFELGVSMVIYKWDALDVAVENSWGGPDSAEKRDWITGIVVDLFKNEKVVDAALIEETLLYAMIDE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SGSHMSTQYIDETAFVQAEQGKTNLMFSDEKQQARFELGVSMVIYKWDALDVAVENSWGGPDSAEKRDWITGIVVDLFKNEKVVDAALIEETLLYAMIDE

-------110-------120-------130-------140-------150------
FETNVEDDSALPIAVEVINIYNDCFNLNYNKVEKLYLEWQEKQRTKKSKRVVHIEG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FETNVEDDSALPIAVEVINIYNDCFNLNYNKVEKLYLEWQEKQRTKKSKRVVHIEG

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20------
SGSQHMRPRFNRENKVSPADAAKKAL
||||||||||||||||||||||||||
SGSQHMRPRFNRENKVSPADAAKKAL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	156	0	0	100.0
B	B	26	0	0	100.0

Content subtype: combined_34248_6g04.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	270		84.6 (chain: B, length: 26)
2	Assigned chemical shifts	assigned_chemical_shifts_2	Warning	1660		99.4 (chain: A, length: 156)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	7589 (1)	noe	98.7 (chain: A, length: 156), 96.2 (chain: B, length: 26)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 26, Sequence coverage: 84.6%
- Total number of assignments
  - ¹H chemical shifts: 158
  - ¹³C chemical shifts: 83
  - ¹⁵N chemical shifts: 29
- Completeness of assignments
  - Entity_assemble_ID: B
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: B
Saveframe: assigned_chemical_shifts_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 99.4%
- Total number of assignments
  - ¹H chemical shifts: 932
  - ¹³C chemical shifts: 555
  - ¹⁵N chemical shifts: 173
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
7	ARG	HH11	6.225
7	ARG	HH12	6.225
7	ARG	NH1	70.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	162	145	89.5
¹³C chemical shifts	112	76	67.9
¹⁵N chemical shifts	30	26	86.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	42	82.4
¹³C chemical shifts	52	22	42.3
¹⁵N chemical shifts	24	20	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	111	103	92.8
¹³C chemical shifts	60	54	90.0
¹⁵N chemical shifts	6	6	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	7	77.8
¹³C chemical shifts	9	7	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	6	85.7
¹³C chemical shifts	7	6	85.7

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
6	SER	HG	4.814
153	HIS	HD1	7.065
153	HIS	HE2	8.227

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	956	929	97.2
¹³C chemical shifts	719	555	77.2
¹⁵N chemical shifts	178	173	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	317	313	98.7
¹³C chemical shifts	312	155	49.7
¹⁵N chemical shifts	154	151	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	639	616	96.4
¹³C chemical shifts	407	400	98.3
¹⁵N chemical shifts	24	22	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	93	98.9
¹³C chemical shifts	94	94	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	78	95.1
¹³C chemical shifts	78	75	96.2
¹⁵N chemical shifts	4	4	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 98.7%
  - Entity_assembly_ID: B, Chain length: 26, Sequence coverage: 96.2%
- Total number of restraints: 7410
- Weight of restraints: 1.0 (7410)
- Potential type of restraints: upper-bound-parabolic (7410)
- Range of distance target values: 2.4, 5.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords TRANSPORT PROTEIN, alpha-helical protein, escortin, eukaryotic specific segments, nuclear unloading factor, nucleus, ribosome maturation, transport of ribosomal protein S26

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Found 1 Document (0.808 seconds)

BMRB: 34248

Sample #1

Sample #2

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Pre-rRNA-processing protein TSR2, 40S ribosomal protein S26-A, entity 1, : 1 : 1 : 2 : 3 entities Detail

Related entities 2. Pre-rRNA-processing protein TSR2, 40S ribosomal protein S26-A, entity 2, : 1 : 4 entities Detail

Interaction partners 1. Pre-rRNA-processing protein TSR2, 40S ribosomal protein S26-A, entity 1, : 17 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 4 contents Detail