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BMRB: 16411

2KM4

Solution structure of Rtt103 CTD interacting domain

Authors

Lunde, B.M., Reichow, S., Kim, M., Leeper, T.C., Becker, R., Buratowski, S., Meinhart, A., Varani, G.

Assembly

Rtt103 CTD interacting domain

Entity

1. Rtt103 CTD interacting domain (polymer, Thiol state: not present), 142 monomers, 16539.85 Da Detail

MAFSSEQFTT KLNTLEDSQE SISSASKWLL LQYRDAPKVA EMWKEYMLRP SVNTRRKLLG LYLMNHVVQQ AKGQKIIQFQ DSFGKVAAEV LGRINQEFPR DLKKKLSRVV NILKERNIFS KQVVNDIERS LAAALEHHHH HH

Formula weight

16539.85 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 90.3 %, Completeness (bb): 94.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.3 % (1580 of 1749)	92.3 % (848 of 919)	86.0 % (578 of 672)	97.5 % (154 of 158)
Backbone	94.9 % (803 of 846)	95.1 % (271 of 285)	94.1 % (397 of 422)	97.1 % (135 of 139)
Sidechain	87.3 % (909 of 1041)	91.0 % (577 of 634)	80.7 % (313 of 388)	100.0 % (19 of 19)
Aromatic	39.7 % (54 of 136)	72.1 % (49 of 68)	4.5 % (3 of 66)	100.0 % (2 of 2)
Methyl	98.8 % (158 of 160)	98.8 % (79 of 80)	98.8 % (79 of 80)

1. Rtt103 CTD interacting domain

MAFSSEQFTT KLNTLEDSQE SISSASKWLL LQYRDAPKVA EMWKEYMLRP SVNTRRKLLG LYLMNHVVQQ AKGQKIIQFQ DSFGKVAAEV LGRINQEFPR DLKKKLSRVV NILKERNIFS KQVVNDIERS LAAALEHHHH HH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Rtt103	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	35 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	Rtt103	natural abundance	0.5 ~ 1.0 mM
7	potassium chloride	natural abundance	100 mM
8	potassium phosphate	natural abundance	35 mM
9	D2O	natural abundance	100 %

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

Referencing offset: 0.21 ppm, Outliers: 4 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

Referencing offset: 0.21 ppm, Outliers: 4 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

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.48 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KM4, Strand ID: A Detail

Release date

2010-09-16

Citation

Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain
Lunde, B.M., Reichow, S.L., Kim, M., Suh, H., Leeper, T.C., Yang, F., Mutschler, H., Buratowski, S., Meinhart, A., Varani, G.
Nat. Struct. Mol. Biol. (2010), 17, 1195-1201, PubMed 20818393 , DOI 10.1038/nsmb.1893 , Abstract

Related entities 1. Rtt103 CTD interacting domain, : 1 : 3 : 3 : 64 entities Detail

Interaction partners 1. Rtt103 CTD interacting domain, : 33 interactors Detail

More details for 33 interactors identified by 7 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Rtt103	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	35 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

2 3D 1H-15N NOESY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Rtt103	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	35 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

3 3D 1H-13C NOESY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Rtt103	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	35 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

4 3D HNCO

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Rtt103	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	35 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

5 3D CBCA(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Rtt103	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	35 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

6 2D 1H-13C HSQC

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Rtt103	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	35 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

7 2D 1H-1H NOESY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	Rtt103	natural abundance	0.5 ~ 1.0 mM
7	potassium chloride	natural abundance	100 mM
8	potassium phosphate	natural abundance	35 mM
9	D2O	natural abundance	100 %

8 3D HNCACB

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Rtt103	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	35 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

9 3D HCCH-TOCSY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Rtt103	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	35 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

10 2D 1H-1H TOCSY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	Rtt103	natural abundance	0.5 ~ 1.0 mM
7	potassium chloride	natural abundance	100 mM
8	potassium phosphate	natural abundance	35 mM
9	D2O	natural abundance	100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16411_2km4.nef
Input source #2: Coordindates	2km4.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
MAFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPR

-------110-------120-------130-------140--
DLKKKLSRVVNILKERNIFSKQVVNDIERSLAAALEHHHHHH
||||||||||||||||||||||||||||||||||||||||||
DLKKKLSRVVNILKERNIFSKQVVNDIERSLAAALEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	142	0	0	100.0

Content subtype: combined_16411_2km4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1570		96.5 (chain: A, length: 142)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3934 (1)	noe	93.7 (chain: A, length: 142)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 96.5%
- Total number of assignments
  - ¹H chemical shifts: 850
  - ¹³C chemical shifts: 570
  - ¹⁵N chemical shifts: 150
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	919	850	92.5
¹³C chemical shifts	672	570	84.8
¹⁵N chemical shifts	167	150	89.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	285	269	94.4
¹³C chemical shifts	284	262	92.3
¹⁵N chemical shifts	139	131	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	634	581	91.6
¹³C chemical shifts	388	308	79.4
¹⁵N chemical shifts	28	19	67.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	83	98.8
¹³C chemical shifts	84	82	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	49	72.1
¹³C chemical shifts	66	0	0.0
¹⁵N chemical shifts	2	2	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: 142, Sequence coverage: 93.7%
- Total number of restraints: 3934
- Weight of restraints: 1.0 (3934)
- Potential type of restraints: upper-bound-parabolic (3934)
- Range of distance target values: 2.32, 5.88 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords CTD-interacting domain, phosphoprotein, RNA polymerase II binding protein, transcription termination

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Found 1 Document (1.306 seconds)

BMRB: 16411

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Rtt103 CTD interacting domain, : 1 : 3 : 3 : 64 entities Detail

Interaction partners 1. Rtt103 CTD interacting domain, : 33 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail