BMRB Entry 30201

Name: solution structure of nysgrc-2016
Published: 2017-02-16

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PDB ID: 5tvz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30201
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: solution structure of nysgrc-2016 PubMed: 28162953

Deposition date: 2016-11-10 Original release date: 2017-02-16

Authors: Dutta, K.; Sampathkumar, P.; Cowburn, D.; Almo, S.; Rout, M.; Fernandez-Martinez, J.

Citation: Upla, P.; Kim, S.; Dutta, K.; Sampathkumar, P.; Cahill, S.; Chemmama, I.; Williams, R.; Bonanno, J.; Rice, W.; Stokes, D.; Cowburn, D.; Almo, S.; Sali, A.; Rout, M.; Fernandez-Martinez, J.. "Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex" Structure 25, 434-445 (2017).

Assembly members:
Nucleoporin POM152, polymer, 114 residues, 12741.649 Da.

Natural source: Common Name: Baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

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

Entity Sequences (FASTA):
Nucleoporin POM152: MSLRVKPSASLKLHHDLKLC LGDHSSVPVALKGQGPFTLT YDIIETFSSKRKTFEIKEIK TNEYVIKTPVFTTGGDYILS LVSIKDSTGCVVGLSQPDAK IQVRRDEGHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	471
15N chemical shifts	106
1H chemical shifts	760

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 114 residues - 12741.649 Da.

1

MET

SER

LEU

ARG

VAL

LYS

PRO

SER

ALA

SER

2

LEU

LYS

LEU

HIS

ASP

LEU

LYS

LEU

CYS

3

LEU

GLY

ASP

HIS

SER

VAL

PRO

VAL

ALA

4

LEU

LYS

GLY

GLN

GLY

PRO

PHE

THR

LEU

THR

5

TYR

ASP

ILE

GLU

THR

PHE

SER

LYS

6

ARG

LYS

THR

PHE

GLU

ILE

LYS

GLU

ILE

LYS

7

THR

ASN

GLU

TYR

VAL

ILE

LYS

THR

PRO

VAL

8

PHE

THR

GLY

ASP

TYR

ILE

LEU

SER

9

LEU

VAL

SER

ILE

LYS

ASP

SER

THR

GLY

CYS

10

VAL

GLY

LEU

SER

GLN

PRO

ASP

ALA

LYS

11

ILE

GLN

VAL

ARG

ASP

GLU

GLY

HIS

12

HIS

Samples:

sample_1: POM152, [U-100% 13C; U-100% 15N], 235 uM; H2O 90%; D2O 10%; NaCl 150 mM

sample_2: POM152, [U-100% 13C; U-100% 15N], 402 uM; H2O 90%; D2O 10%; NaCl 150 mM

sample_3: POM152, [U-100% 13C; U-100% 15N], 300 uM; H2O 90%; D2O 10%; NaCl 150 mM

sample_4: POM152, [U-100% 13C; U-100% 15N], 1.2 mM; H2O 90%; D2O 10%; NaCl 150 mM

sample_5: POM152, [U-100% 13C; U-100% 15N], 324 uM; D2O 100%; NaCl 150 mM

sample_conditions_1: ionic strength: 160 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3d HNCACO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_3	isotropic	sample_conditions_1
3D C(CO)NH	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_5	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_5	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_5	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_5	isotropic	sample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

Bruker DRX 600 MHz
Varian INOVA 600 MHz
Bruker DRX 900 MHz

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