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BMRB: 34260

6GC3

Structure of Nrd1 CID - Sen1 NIM complex

Authors

Jasnovidova, O., Kubicek, K., Stefl, R.

Assembly

Protein NRD1, Helicase SEN1 (E.C.3.6.4.-)

Entity

1. Protein NRD1, Helicase SEN1 (E.C.3.6.4.-), entity 1 (polymer), 161 monomers, 18286.42 Da Detail

MQQDDDFQNF VATLESFKDL KSGISGSRIK KLTTYALDHI DIESKIISLI IDYSRLCPDS HKLGSLYIID SIGRAYLDET RSNSNSSSNK PGTCAHAINT LGEVIQELLS DAIAKSNQDH KEKIRMLLDI WDRSGLFQKS YLNAIRSKCF AMDLEHHHHH H

2. Protein NRD1, Helicase SEN1 (E.C.3.6.4.-), entity 2 (polymer, Thiol state: not present), 12 monomers, 1371.273 Da Detail

DDDEDDYTPS IS

Total weight

19657.693 Da

Max. entity weight

18286.42 Da

Source organism

Saccharomyces cerevisiae S288C

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.9 %, Completeness: 72.6 %, Completeness (bb): 70.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.6 % (1451 of 1999)	77.4 % (803 of 1037)	63.9 % (497 of 778)	82.1 % (151 of 184)
Backbone	70.8 % (731 of 1032)	82.3 % (288 of 350)	58.2 % (298 of 512)	85.3 % (145 of 170)
Sidechain	75.3 % (853 of 1133)	75.0 % (515 of 687)	76.9 % (332 of 432)	42.9 % (6 of 14)
Aromatic	60.0 % (90 of 150)	72.0 % (54 of 75)	47.3 % (35 of 74)	100.0 % (1 of 1)
Methyl	94.4 % (170 of 180)	94.4 % (85 of 90)	94.4 % (85 of 90)

1. entity 1

MQQDDDFQNF VATLESFKDL KSGISGSRIK KLTTYALDHI DIESKIISLI IDYSRLCPDS HKLGSLYIID SIGRAYLDET RSNSNSSSNK PGTCAHAINT LGEVIQELLS DAIAKSNQDH KEKIRMLLDI WDRSGLFQKS YLNAIRSKCF AMDLEHHHHH H

2. entity 2

DDDEDDYTPS IS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 8.0, Details 1.0 mM [U-99% 13C; U-99% 15N] CTD-interacting domain of Nrd1, 1.5 mM ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6GC3, Strand ID: A, B Detail

Release date

2019-03-17

Citation

Structure of Nrd1 CID - Sen1 NIM complex
Jasnovidova, O., Kubicek, K., Stefl, R.

Related entities 1. Protein NRD1, Helicase SEN1 (E.C.3.6.4.-), entity 1, : 18 entities Detail

Related entities 2. Protein NRD1, Helicase SEN1 (E.C.3.6.4.-), entity 2, : 1 : 2 : 1 entities Detail

Interaction partners 2. Protein NRD1, Helicase SEN1 (E.C.3.6.4.-), entity 2, : 46 interactors Detail

More details for 46 interactors identified by 9 citations

Experiments performed 9 experiments Detail

1 3D HNCACB

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 8.0, Details 1.0 mM [U-99% 13C; U-99% 15N] CTD-interacting domain of Nrd1, 1.5 mM ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

2 HCCCONH

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

3 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

4 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

5 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

6 3D HNCA

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

7 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

8 4D HCCH TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

9 F1-13C/15N-filtered NOESY-[13C,1H]-HSQC

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CTD-interacting domain of Nrd1	[U-99% 13C; U-99% 15N]		1.0 (±0.1) mM
2	ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER	natural abundance		1.5 (±0.1) mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34260_3.str
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

Content subtype: bmr34260_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1592		92.5 (chain: 1, length: 161)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 161, Sequence coverage: 92.5%
- Total number of assignments
  - ¹H chemical shifts: 972
  - ¹³C chemical shifts: 470
  - ¹⁵N chemical shifts: 150
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	977	798	81.7
¹³C chemical shifts	731	470	64.3
¹⁵N chemical shifts	180	150	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	327	288	88.1
¹³C chemical shifts	322	142	44.1
¹⁵N chemical shifts	159	141	88.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	650	510	78.5
¹³C chemical shifts	409	328	80.2
¹⁵N chemical shifts	21	9	42.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	90	87	96.7
¹³C chemical shifts	90	87	96.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	54	76.1
¹³C chemical shifts	70	35	50.0
¹⁵N chemical shifts	1	1	100.0

Keywords CTD-interacting domain, TRANSCRIPTION, helicase, transcription termination

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Found 1 Document (1.383 seconds)

BMRB: 34260

Sample

Related entities 1. Protein NRD1, Helicase SEN1 (E.C.3.6.4.-), entity 1, : 18 entities Detail

Related entities 2. Protein NRD1, Helicase SEN1 (E.C.3.6.4.-), entity 2, : 1 : 2 : 1 entities Detail

Interaction partners 2. Protein NRD1, Helicase SEN1 (E.C.3.6.4.-), entity 2, : 46 interactors Detail

Experiments performed 9 experiments Detail

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Chemical shift validation 4 contents Detail