BMRB Entry 34041

Name: Solution structure of Rtt103 CTD-interacting domain bound to a Thr4 phosphorylated CTD peptide
Published: 2017-05-08

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PDB ID: 5lvf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34041
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of Rtt103 CTD-interacting domain bound to a Thr4 phosphorylated CTD peptide PubMed: 28468956

Deposition date: 2016-09-14 Original release date: 2017-05-08

Authors: Jasnovidova, O.; Kubicek, K.; Krejcikova, M.; Stefl, R.

Citation: Jasnovidova, O.; Krejcikova, M.; Kubicek, K.; Stefl, R.. "Structural insight into recognition of phosphorylated threonine-4 of RNA polymerase II C-terminal domain by Rtt103p" Embo Rep. 18, 906-913 (2017).

Assembly members:
entity_1, polymer, 142 residues, 16569.100 Da.
entity_2, polymer, 16 residues, 1721.669 Da.

Natural source: Common Name: Baker's yeast Taxonomy ID: 559292 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: MAFSSEQFTTKLNTLEDSQE SISSASKWLLLQYRDAPKVA EMWKEYMLRPSVNTRRKLLG LYLMNHVVQQAKGQKIIQFQ DSFGKVAAEVLGRINQEFPR DLKKKLSRVVNILKERNIFS KQVVNDIERSLAAALEHHHH HH
entity_2: PSYSPXSPSYSPTSPS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	472
15N chemical shifts	144
1H chemical shifts	998

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 142 residues - 16569.100 Da.

1

MET

ALA

PHE

SER

GLU

GLN

PHE

THR

2

LYS

LEU

ASN

THR

LEU

GLU

ASP

SER

GLN

GLU

3

SER

ILE

SER

ALA

SER

LYS

TRP

LEU

4

LEU

GLN

TYR

ARG

ASP

ALA

PRO

LYS

VAL

ALA

5

GLU

MET

TRP

LYS

GLU

TYR

MET

LEU

ARG

PRO

6

SER

VAL

ASN

THR

ARG

LYS

LEU

GLY

7

LEU

TYR

LEU

MET

ASN

HIS

VAL

GLN

8

ALA

LYS

GLY

GLN

LYS

ILE

GLN

PHE

GLN

9

ASP

SER

PHE

GLY

LYS

VAL

ALA

GLU

VAL

10

LEU

GLY

ARG

ILE

ASN

GLN

GLU

PHE

PRO

ARG

11

ASP

LEU

LYS

LEU

SER

ARG

VAL

12

ASN

ILE

LEU

LYS

GLU

ARG

ASN

ILE

PHE

SER

13

LYS

GLN

VAL

ASN

ASP

ILE

GLU

ARG

SER

14

LEU

ALA

LEU

GLU

HIS

15

HIS

Entity 2, entity_2 16 residues - 1721.669 Da.

1

PRO

SER

TYR

SER

PRO

TPO

SER

PRO

SER

TYR

2

SER

PRO

THR

SER

PRO

SER

Samples:

sample_1: Rtt103 CID, [U-13C; U-15N], 1 ± 0.2 mM; pThr4-CTD 1.2 ± 0.2 mM; KH2PO4 35 mM; KCl 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.8; pressure: 760 mmHg; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
4D HCCH TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
F1-13C/15N-filtered NOESY-[13C,1H]-HSQC	sample_1	isotropic	sample_conditions_1

Software:

AMBER v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection, processing

NMR spectrometers:

Bruker AvanceIII 950 MHz
Bruker AvanceIII 700 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts