BMRB Entry 30388

Name: Solution NMR structure of cysteine-rich calcium bound domains of very low density lipoprotein receptor
Published: 2018-07-10

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PDB ID: 6byv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30388
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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:

Solution NMR structure of cysteine-rich calcium bound domains of very low density lipoprotein receptor

Deposition date:

2017-12-21

Original release date:

2018-07-10

Authors:

Banerjee, K.; Gruschus, J.; Tjandra, N.; Yakovlev, S.; Medved, L.

Citation:

Citation: Banerjee, Koyeli; Yakovlev, Sergiy; Gruschus, James; Medved, Leonid; Tjandra, Nico. "Nuclear Magnetic Resonance Solution Structure of the Recombinant Fragment Containing Three Fibrin-Binding Cysteine-Rich Domains of the Very Low Density Lipoprotein Receptor" Biochemistry 57, 4395-4403 (2018).
PubMed: 29965730

Assembly members:

Assembly members:
entity_1, polymer, 121 residues, 13175.093 Da.
entity_CA, non-polymer, 40.078 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KTCAESDFVCNNGQCVPSRW KCDGDPDCEDGSDESPEQCH MRTCRIHEISCGAHSTQCIP VSWRCDGENDCDSGEDEENC GNITCSPDEFTCSSGRCISR NFVCNGQDDCSDGSDELDCA P

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	403
15N chemical shifts	125
1H chemical shifts	647

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, 1	2
3	entity_2, 2	2
4	entity_2, 3	2

Entities:

Entity 1, entity_1 121 residues - 13175.093 Da.

1

LYS

THR

CYS

ALA

GLU

SER

ASP

PHE

VAL

CYS

2

ASN

GLY

GLN

CYS

VAL

PRO

SER

ARG

TRP

3

LYS

CYS

ASP

GLY

ASP

PRO

ASP

CYS

GLU

ASP

4

GLY

SER

ASP

GLU

SER

PRO

GLU

GLN

CYS

HIS

5

MET

ARG

THR

CYS

ARG

ILE

HIS

GLU

ILE

SER

6

CYS

GLY

ALA

HIS

SER

THR

GLN

CYS

ILE

PRO

7

VAL

SER

TRP

ARG

CYS

ASP

GLY

GLU

ASN

ASP

8

CYS

ASP

SER

GLY

GLU

ASP

GLU

ASN

CYS

9

GLY

ASN

ILE

THR

CYS

SER

PRO

ASP

GLU

PHE

10

THR

CYS

SER

GLY

ARG

CYS

ILE

SER

ARG

11

ASN

PHE

VAL

CYS

ASN

GLY

GLN

ASP

CYS

12

SER

ASP

GLY

SER

ASP

GLU

LEU

ASP

CYS

ALA

13

PRO

Entity 2, entity_2, 1 - Ca - 40.078 Da.

1

CA

Samples:

sample_1: VLDLR, [U-99% 15N], 350 uM

sample_2: VLDLR, [U-99% 13C; U-99% 15N], 250 uM

sample_3: VLDLR, [U-99% 13C; U-99% 15N], 250 uM

sample_conditions_1: ionic strength: 100 mM; pH: 6.2; pressure: 760 mmHg; temperature: 306.5 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.2; pressure: 760 mmHg; temperature: 306.5 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_2
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_2
3D HNCA	sample_2	isotropic	sample_conditions_2
3D HNCO	sample_2	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

Analysis, CCPN - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks