BMRBj - BMREntryMaster

Found 1 Document (0.96 seconds)

BMRB: 34058

5M9D

Solution structure of Rtt103 CTD-interacting domain bound to a Ser2Ser7 phosphorylated CTD peptide

Authors

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

Assembly

Regulator of Ty1 transposition protein 103, THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER

Entity

1. Regulator of Ty1 transposition protein 103, THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER, entity 1 (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

2. Regulator of Ty1 transposition protein 103, THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER, entity 2 (polymer, Thiol state: not present), 16 monomers, 1965.593 Da Detail

TSPXYXPTSP XYXPTS

Total weight

18505.443 Da

Max. entity weight

16539.85 Da

Source organism

Saccharomyces cerevisiae S288C , Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 86.7 %, Completeness: 79.6 %, Completeness (bb): 74.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.6 % (1497 of 1880)	85.2 % (841 of 987)	69.9 % (508 of 727)	89.2 % (148 of 166)
Backbone	74.1 % (674 of 910)	85.2 % (260 of 305)	62.0 % (284 of 458)	88.4 % (130 of 147)
Sidechain	84.3 % (944 of 1120)	84.5 % (576 of 682)	83.5 % (350 of 419)	94.7 % (18 of 19)
Aromatic	69.7 % (106 of 152)	69.7 % (53 of 76)	68.9 % (51 of 74)	100.0 % (2 of 2)
Methyl	93.4 % (155 of 166)	94.0 % (78 of 83)	92.8 % (77 of 83)

1. entity 1

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

2. entity 2

TSPXYXPTSP XYXPTS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 760 mmHg, Temperature 298 K, pH 6.8, Details 1 mM [U-13C; U-15N] CTD-interacting domain of Rtt103p, 1.5 mM THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	CTD-interacting domain of Rtt103p	[U-13C; U-15N]	1 (±0.2) mM
2	THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER	natural abundance	1.5 (±0.2) mM
3	KH2PO4	natural abundance	35 mM
4	KCl	natural abundance	100 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DMSO	methyl carbons	0.0 ppm	na	direct	1.0
¹H	water	protons	4.7 ppm	na	direct	1.0
¹⁵N	urea	nitrogen	75.0 ppm	na	direct	1.0

Referencing offset: 2.82 ppm, Outliers: 4 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DMSO	methyl carbons	0.0 ppm	na	direct	1.0
¹H	water	protons	4.7 ppm	na	direct	1.0
¹⁵N	urea	nitrogen	75.0 ppm	na	direct	1.0

Referencing offset: 2.82 ppm, Outliers: 4 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DMSO	methyl carbons	0.0 ppm	na	direct	1.0
¹H	water	protons	4.7 ppm	na	direct	1.0
¹⁵N	urea	nitrogen	75.0 ppm	na	direct	1.0

Referencing offset: 0.18 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5M9D, Strand ID: A, B Detail

Release date

2017-10-04

Citation

Structure and dynamics of the RNAPII CTDsome with Rtt103
Jasnovidova, O., Klumpler, T., Kubicek, K., Kalynych, S., Plevka, P., Stefl, R.
Proc. Natl. Acad. Sci. U. S. A. (2017), 114, 11133-11138, PubMed 29073019 , DOI 10.1073/pnas.1712450114 , Abstract

Related entities 1. Regulator of Ty1 transposition protein 103, THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER, entity 1, : 1 : 3 : 2 : 52 entities Detail

Related entities 2. Regulator of Ty1 transposition protein 103, THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER, entity 2, : 438 entities Detail

Experiments performed 6 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 950 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 760 mmHg, Temperature 298 K, pH 6.8, Details 1 mM [U-13C; U-15N] CTD-interacting domain of Rtt103p, 1.5 mM THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	CTD-interacting domain of Rtt103p	[U-13C; U-15N]	1 (±0.2) mM
2	THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER	natural abundance	1.5 (±0.2) mM
3	KH2PO4	natural abundance	35 mM
4	KCl	natural abundance	100 mM

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CTD-interacting domain of Rtt103p	[U-13C; U-15N]	1 (±0.2) mM
2	THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER	natural abundance	1.5 (±0.2) mM
3	KH2PO4	natural abundance	35 mM
4	KCl	natural abundance	100 mM

3 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CTD-interacting domain of Rtt103p	[U-13C; U-15N]	1 (±0.2) mM
2	THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER	natural abundance	1.5 (±0.2) mM
3	KH2PO4	natural abundance	35 mM
4	KCl	natural abundance	100 mM

4 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CTD-interacting domain of Rtt103p	[U-13C; U-15N]	1 (±0.2) mM
2	THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER	natural abundance	1.5 (±0.2) mM
3	KH2PO4	natural abundance	35 mM
4	KCl	natural abundance	100 mM

5 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CTD-interacting domain of Rtt103p	[U-13C; U-15N]	1 (±0.2) mM
2	THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER	natural abundance	1.5 (±0.2) mM
3	KH2PO4	natural abundance	35 mM
4	KCl	natural abundance	100 mM

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

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CTD-interacting domain of Rtt103p	[U-13C; U-15N]	1 (±0.2) mM
2	THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER	natural abundance	1.5 (±0.2) mM
3	KH2PO4	natural abundance	35 mM
4	KCl	natural abundance	100 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34058_5m9d.nef
Input source #2: Coordindates	5m9d.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:3:PRO:C	2:4:SEP:N	unknown	unknown	n/a
2:4:SEP:C	2:5:TYR:N	unknown	unknown	n/a
2:5:TYR:C	2:6:SEP:N	unknown	unknown	n/a
2:6:SEP:C	2:7:PRO:N	unknown	unknown	n/a
2:10:PRO:C	2:11:SEP:N	unknown	unknown	n/a
2:11:SEP:C	2:12:TYR:N	unknown	unknown	n/a
2:12:TYR:C	2:13:SEP:N	unknown	unknown	n/a
2:13:SEP:C	2:14:PRO:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	142	SEP	PHOSPHOSERINE	Coordinates
B	144	SEP	PHOSPHOSERINE	Coordinates
B	149	SEP	PHOSPHOSERINE	Coordinates
B	151	SEP	PHOSPHOSERINE	Coordinates

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

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

-140-----150----
TSPXYXPTSPXYXPTS
||||||||||||||||
TSPXYXPTSPXYXPTS
--------10------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	142	0	0	100.0
B	B	16	0	0	100.0

Content subtype: combined_34058_5m9d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1482		95.8 (chain: A, length: 142)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	5092 (1)	noe	94.4 (chain: A, length: 142)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 95.8%
- Total number of assignments
  - ¹H chemical shifts: 848
  - ¹³C chemical shifts: 487
  - ¹⁵N chemical shifts: 147
- 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	847	92.2
¹³C chemical shifts	672	487	72.5
¹⁵N chemical shifts	167	147	88.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	285	264	92.6
¹³C chemical shifts	284	136	47.9
¹⁵N chemical shifts	139	128	92.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	634	583	92.0
¹³C chemical shifts	388	351	90.5
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	53	77.9
¹³C chemical shifts	66	51	77.3
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

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: 94.4%
- Total number of restraints: 5092
- Weight of restraints: 1.0 (5092)
- Potential type of restraints: upper-bound-parabolic (5092)
- Range of distance target values: 2.35, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords CTD-interacting domain, RNAPII C-terminal domain, phosphorylation, transcription

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.96 seconds)

BMRB: 34058

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Regulator of Ty1 transposition protein 103, THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER, entity 1, : 1 : 3 : 2 : 52 entities Detail

Related entities 2. Regulator of Ty1 transposition protein 103, THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER, entity 2, : 438 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail