BMRB Entry 34260

Name: Structure of Nrd1 CID - Sen1 NIM complex
Published: 2020-01-31

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34260

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Structure of Nrd1 CID - Sen1 NIM complex

Deposition date: 2018-04-17 Original release date: 2020-01-31

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

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

Assembly members:
entity_1, polymer, 161 residues, 18315.674 Da.
entity_2, polymer, 12 residues, 1371.274 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: MQQDDDFQNFVATLESFKDL KSGISGSRIKKLTTYALDHI DIESKIISLIIDYSRLCPDS HKLGSLYIIDSIGRAYLDET RSNSNSSSNKPGTCAHAINT LGEVIQELLSDAIAKSNQDH KEKIRMLLDIWDRSGLFQKS YLNAIRSKCFAMDLEHHHHH H
entity_2: DDDEDDYTPSIS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	470
15N chemical shifts	150
1H chemical shifts	972

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_1 161 residues - 18315.674 Da.

1

MET

GLN

ASP

PHE

GLN

ASN

PHE

2

VAL

ALA

THR

LEU

GLU

SER

PHE

LYS

ASP

LEU

3

LYS

SER

GLY

ILE

SER

GLY

SER

ARG

ILE

LYS

4

LYS

LEU

THR

TYR

ALA

LEU

ASP

HIS

ILE

5

ASP

ILE

GLU

SER

LYS

ILE

SER

LEU

ILE

6

ILE

ASP

TYR

SER

ARG

LEU

CYS

PRO

ASP

SER

7

HIS

LYS

LEU

GLY

SER

LEU

TYR

ILE

ASP

8

SER

ILE

GLY

ARG

ALA

TYR

LEU

ASP

GLU

THR

9

ARG

SER

ASN

SER

ASN

SER

ASN

LYS

10

PRO

GLY

THR

CYS

ALA

HIS

ALA

ILE

ASN

THR

11

LEU

GLY

GLU

VAL

ILE

GLN

GLU

LEU

SER

12

ASP

ALA

ILE

ALA

LYS

SER

ASN

GLN

ASP

HIS

13

LYS

GLU

LYS

ILE

ARG

MET

LEU

ASP

ILE

14

TRP

ASP

ARG

SER

GLY

LEU

PHE

GLN

LYS

SER

15

TYR

LEU

ASN

ALA

ILE

ARG

SER

LYS

CYS

PHE

16

ALA

MET

ASP

LEU

GLU

HIS

17

HIS

Entity 2, entity_2 12 residues - 1371.274 Da.

1

ASP

GLU

ASP

TYR

THR

PRO

SER

2

ILE

SER

Samples:

sample_1: CTD-interacting domain of Nrd1, [U-99% 13C; U-99% 15N], 1.0 ± 0.1 mM; ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER 1.5 ± 0.1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 8.0; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_1	isotropic	sample_conditions_1
HCCCONH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
4D HCCH TOCSY	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 - processing

NMR spectrometers:

Bruker AvanceIII 950 MHz
Bruker AvanceIII 850 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