BMRB Entry 11076

Name: NMR based model structure of mesoderm development (MESD) in solution.
Published: 2011-06-03

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PDB ID: 2rqk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11076
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR based model structure of mesoderm development (MESD) in solution.

Deposition date:

2009-08-05

Original release date:

2011-06-03

Authors:

Koehler, Christian; Lighthouse, Janet; Werther, Tobias; Andersen, Olav; Diehl, Annette; Schmieder, Peter; Holdener, Bernadette; Oschkinat, Hartmut

Citation:

Citation: Kohler, Christian; Lighthouse, Janet; Werther, Tobias; Andersen, Olav; Diehl, Annette; Schmieder, Peter; Du, Jianguang; Holdener, Bernadette; Oschkinat, Hartmut. "The structure of MESD45-184 brings light into the mechanism of LDLR family folding." Structure 19, 337-348 (2011).
PubMed: 21397185

Assembly members:

Assembly members:
MESD polymer chain, polymer, 141 residues, Formula weight is not available

Natural source:

Natural source: Common Name: house mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-30 Xa/LIC

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MESD polymer chain: GDIRDYNDADMARLLEQWEK DDDIEEGDLPEHKRPSAPID FSKLDPGKPESILKMTKKGK TLMMFVTVSGNPTEKETEEI TSLWQGSLFNANYDVQRFIV GSDRAIFMLRDGSYAWEIKD FLVSQDRCAEVTLEGQMYPG K

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
RDCs
- RDC_list_1

Data type	Count
13C chemical shifts	460
15N chemical shifts	133
1H chemical shifts	863
residual dipolar couplings	36
T1 relaxation values	94
T2 relaxation values	94

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MESD polymer chain	1

Entities:

Entity 1, MESD polymer chain 141 residues - Formula weight is not available

1

GLY

ASP

ILE

ARG

ASP

TYR

ASN

ASP

ALA

ASP

2

MET

ALA

ARG

LEU

GLU

GLN

TRP

GLU

LYS

3

ASP

ILE

GLU

GLY

ASP

LEU

PRO

4

GLU

HIS

LYS

ARG

PRO

SER

ALA

PRO

ILE

ASP

5

PHE

SER

LYS

LEU

ASP

PRO

GLY

LYS

PRO

GLU

6

SER

ILE

LEU

LYS

MET

THR

LYS

GLY

LYS

7

THR

LEU

MET

PHE

VAL

THR

VAL

SER

GLY

8

ASN

PRO

THR

GLU

LYS

GLU

THR

GLU

ILE

9

THR

SER

LEU

TRP

GLN

GLY

SER

LEU

PHE

ASN

10

ALA

ASN

TYR

ASP

VAL

GLN

ARG

PHE

ILE

VAL

11

GLY

SER

ASP

ARG

ALA

ILE

PHE

MET

LEU

ARG

12

ASP

GLY

SER

TYR

ALA

TRP

GLU

ILE

LYS

ASP

13

PHE

LEU

VAL

SER

GLN

ASP

ARG

CYS

ALA

GLU

14

VAL

THR

LEU

GLU

GLY

GLN

MET

TYR

PRO

GLY

15

LYS

Samples:

sample_1: MESD, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.02%; EDTA 0.1 mM; H2O 90%; D2O 10%

sample_2: MESD, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.02%; EDTA 0.1 mM; D2O 100%

sample_3: MESD, [U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.02%; EDTA 0.1 mM; H2O 90%; D2O 10%

sample_4: MESD, [U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.02%; EDTA 0.1 mM; D2O 100%

sample_conditions_1: pH: 5.5; pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC No.1	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC No.2	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCANNH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D H(CCCO)NH-TOCSY	sample_1	isotropic	sample_conditions_1
3D (H)CC(CO)NH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC coupled	sample_3	anisotropic	sample_conditions_1
2D 1H-15N HSQC 15N_T1-edited	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC 15N_T2-edited	sample_3	isotropic	sample_conditions_1

Software:

xwinnmr v3.5, Bruker Biospin - collection, processing

SPARKY v3.10, Goddard - chemical shift assignment, peak picking

TOPSPIN v2.0, Bruker Biospin - collection, processing

CYANA v2.0, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR NIH v2.14, Schwieters, Kuszewski, Tjandra and Clore - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker AV 900 MHz
Bruker DRX 600 MHz
Bruker DMX 750 MHz

Entrez Gene	67943
UNP	Q9ERE7
BMRB	16213
PDB	2I9S 2KGL 2KMI 2RQK 2RQM 3OFH
DBJ	BAB25865 BAC27617 BAC36471 BAC36476
GB	AAG33621 AAH14742 AAH85892 EDL06865 EDL06866
REF	NP_001008346 NP_075892 XP_001928898 XP_003511746 XP_004658300
SP	Q5U2R7 Q9ERE7
AlphaFold	Q9CVB9 Q5U2R7 Q9ERE7