BMRB Entry 25265

Name: Structural insight into an essential assembly factor network on the pre-ribosome
Published: 2014-12-01

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PDB ID: 2mvf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25265
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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:

Structural insight into an essential assembly factor network on the pre-ribosome

Deposition date:

2014-10-02

Original release date:

2014-12-01

Authors:

Lee, Woonghee; BaBler, Jochen; Paternoga, Helge; Holdermann, Iris; Thomas, Matthias; Granneman, Sander; Barrio-Garcia, Clara; Nyarko, Afua; Stier, Gunter; Clark, Sarah; Schraivogel, Daniel; Kallas, Martina; Beckmann, Roland; Tollervey, David; Barbar, Elisar; Sinning, Irmi; Hurt, Ed

Citation:

Citation: Lee, Woonghee; BaBler, Jochen; Paternoga, Helge; Holdermann, Iris; Thomas, Matthias; Granneman, Sander; Barrio-Garcia, Clara; Nyarko, Afua; Stier, Gunter; Clark, Sarah; Schraivogel, Daniel; Kallas, Martina; Beckmann, Roland; Tollervey, David; Barbar, Elisar; Sinning, Irmi; Hurt, Ed. "A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation" J. Cell Biol. 207, 481-498 (2014).
PubMed: 25404745

Assembly members:

Assembly members:
entity, polymer, 188 residues, 20618.100 Da.

Natural source:

Natural source: Common Name: ascomycetes Taxonomy ID: 209285 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Chaetomium thermophilum

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: YERFIRPMGLRYKKANVTHP TLNVTVQLPILSVKKNPSNP LYTQLGVLTKGTIIEVNVSD LGIVTASGKIAWGRYAQITN NPENDGCVNAVLLVYERFIR PMGLRYKKANVTHPTLNVTV QLPILSVKKNPSNPLYTQLG VLTKGTIIEVNVSDLGIVTA SGKIAWGRYAQITNNPENDG CVNAVLLV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	365
15N chemical shifts	86
1H chemical shifts	636

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1

Entities:

Entity 1, entity 188 residues - 20618.100 Da.

1

TYR

GLU

ARG

PHE

ILE

ARG

PRO

MET

GLY

LEU

2

ARG

TYR

LYS

ALA

ASN

VAL

THR

HIS

PRO

3

THR

LEU

ASN

VAL

THR

VAL

GLN

LEU

PRO

ILE

4

LEU

SER

VAL

LYS

ASN

PRO

SER

ASN

PRO

5

LEU

TYR

THR

GLN

LEU

GLY

VAL

LEU

THR

LYS

6

GLY

THR

ILE

GLU

VAL

ASN

VAL

SER

ASP

7

LEU

GLY

ILE

VAL

THR

ALA

SER

GLY

LYS

ILE

8

ALA

TRP

GLY

ARG

TYR

ALA

GLN

ILE

THR

ASN

9

ASN

PRO

GLU

ASN

ASP

GLY

CYS

VAL

ASN

ALA

10

VAL

LEU

VAL

TYR

GLU

ARG

PHE

ILE

ARG

11

PRO

MET

GLY

LEU

ARG

TYR

LYS

ALA

ASN

12

VAL

THR

HIS

PRO

THR

LEU

ASN

VAL

THR

VAL

13

GLN

LEU

PRO

ILE

LEU

SER

VAL

LYS

ASN

14

PRO

SER

ASN

PRO

LEU

TYR

THR

GLN

LEU

GLY

15

VAL

LEU

THR

LYS

GLY

THR

ILE

GLU

VAL

16

ASN

VAL

SER

ASP

LEU

GLY

ILE

VAL

THR

ALA

17

SER

GLY

LYS

ILE

ALA

TRP

GLY

ARG

TYR

ALA

18

GLN

ILE

THR

ASN

PRO

GLU

ASN

ASP

GLY

19

CYS

VAL

ASN

ALA

VAL

LEU

VAL

Samples:

sample_1: D2O 10%; TRIS 10 mM; H2O 90%; sodium chloride 5 mM; DSS 1 uM; TCEP 2 mM; entity, [U-99% 13C; U-99% 15N], 450 mM

sample_conditions_1: ionic strength: 5 mM; pH: 7.4; pressure: 1 atm; temperature: 280 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	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 HBHA(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich, PONDEROSA-C/S and NMRFAM-SPARKY - peak picking, structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 850 MHz
Bruker Avance 950 MHz

PDB	2MVF
GB	AEO54371 AEO65388 EGS23242
REF	XP_003651724 XP_003659616 XP_006691433