BMRB Entry 18415

Name: Solution structure of human C-type lectin domain family 4 member D
Published: 2012-05-22

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PDB ID: 2ls8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18415
MolProbity Validation Chart

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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:

Solution structure of human C-type lectin domain family 4 member D

Deposition date:

2012-04-23

Original release date:

2012-05-22

Authors:

Harris, R.; Gaudette, J.; Bandaranayake, A.; Banu, R.; Bonanno, J.; Calarese, D.; Celikgil, A.; Chamala, S.; Chan, M.; Chaparro, R.; Evans, B.; Garforth, S.; Gizzi, A.; Hillerich, B.; Kar, A.; Lafleur, J.; Lim, S.; Love, J.; Matikainen, B.; Patel, H.; Seidel, R.; Smith, B.; Stead, M.; Girvin, M.; Almo, S.

Citation:

Citation: Harris, R.; Gaudette, J.; Bandaranayake, A.; Banu, R.; Bonanno, J.; Calarese, D.; Celikgil, A.; Chamala, S.; Chan, M.; Chaparro, R.; Evans, B.; Garforth, S.; Gizzi, A.; Hillerich, B.; Kar, A.; Lafleur, J.; Lim, S.; Love, J.; Matikainen, B.; Patel, H.; Seidel, R.; Smith, B.; Stead, M.; Girvin, M.; Almo, S.. "Solution structure of human C-type lectin domain family 4 member D" To be published ., .-..

Assembly members:

Assembly members:
C-type_lectin, polymer, 156 residues, 18610.879 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 Vector: modified pET23a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
C-type_lectin: MVCPIDWRAFQSNCYFPLTD NKTWAESERNCSGMGAHLMT ISTEAEQNFIIQFLDRRLSY FLGLRDENAKGQWRWVDQTP FNPRRVFWHKNEPDNSQGEN CVVLVYNQDKWAWNDVPCNF EASRICKIPGTTLNAENLYF QSHHHHHHWSHPQFEK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	673
15N chemical shifts	169
1H chemical shifts	1047

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	human C-type lectin domain family 4 member D	1

Entities:

Entity 1, human C-type lectin domain family 4 member D 156 residues - 18610.879 Da.

expressed sequence start-stop 84-215 (156 aa incl tag) N-term cloning artifact MV- C-term cloning artifact -AENLYFQSHHHHHHWSHPQFEK Only residues 1-142 included in structure calculations

1

MET

VAL

CYS

PRO

ILE

ASP

TRP

ARG

ALA

PHE

2

GLN

SER

ASN

CYS

TYR

PHE

PRO

LEU

THR

ASP

3

ASN

LYS

THR

TRP

ALA

GLU

SER

GLU

ARG

ASN

4

CYS

SER

GLY

MET

GLY

ALA

HIS

LEU

MET

THR

5

ILE

SER

THR

GLU

ALA

GLU

GLN

ASN

PHE

ILE

6

ILE

GLN

PHE

LEU

ASP

ARG

LEU

SER

TYR

7

PHE

LEU

GLY

LEU

ARG

ASP

GLU

ASN

ALA

LYS

8

GLY

GLN

TRP

ARG

TRP

VAL

ASP

GLN

THR

PRO

9

PHE

ASN

PRO

ARG

VAL

PHE

TRP

HIS

LYS

10

ASN

GLU

PRO

ASP

ASN

SER

GLN

GLY

GLU

ASN

11

CYS

VAL

LEU

VAL

TYR

ASN

GLN

ASP

LYS

12

TRP

ALA

TRP

ASN

ASP

VAL

PRO

CYS

ASN

PHE

13

GLU

ALA

SER

ARG

ILE

CYS

LYS

ILE

PRO

GLY

14

THR

LEU

ASN

ALA

GLU

ASN

LEU

TYR

PHE

15

GLN

SER

HIS

TRP

SER

16

HIS

PRO

GLN

PHE

GLU

LYS

Samples:

sample_1: C-type lectin, [U-13C; U-15N], 1 mM; sodium acetate 10 mM; EDTA 0.1 mM; H2O 90%; D2O 10%

sample_2: C-type lectin, [U-13C; U-15N], 1 mM; sodium acetate 10 mM; EDTA 0.1 mM; D2O 100%

sample_conditions_1: ionic strength: 10 mM; pH: 4.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
15N HSQC	sample_1	isotropic	sample_conditions_1
15N NOESY-HSQC	sample_1	isotropic	sample_conditions_1
13C CT-HSQC	sample_2	isotropic	sample_conditions_1
aromatic 13C CT-HSQC	sample_2	isotropic	sample_conditions_1
13C NOESY-HSQC	sample_2	isotropic	sample_conditions_1
13C aromatic NOESY-HSQC	sample_2	isotropic	sample_conditions_1
HNCO	sample_1	isotropic	sample_conditions_1
HNCACO	sample_1	isotropic	sample_conditions_1
HNCA	sample_1	isotropic	sample_conditions_1
HNCOCA	sample_1	isotropic	sample_conditions_1
HNCACB	sample_1	isotropic	sample_conditions_1
CBCACONH	sample_1	isotropic	sample_conditions_1

Software:

CCPN v2.1.5, CCPN - chemical shift assignment, peak picking

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

ARIA v2.3, Linge, O'Donoghue and Nilges - structure solution

NMRPipe v5.4, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMRJ v2.2D, Varian - collection

TOPSPIN, Bruker Biospin - collection

MDDNMR v2.0, (MDDNMR) Orekhov, Jaravine, Kazimierczuk - collection, processing

MDDGUI v1.0, (MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmith - collection, processing

NMR spectrometers:

Varian Inova 600 MHz
Bruker Avance 800 MHz

PDB	2LS8 3WHD
GB	AAH32313 AAL37713 AAM75389 AAQ63173 AAS59161
REF	NP_525126 XP_001134875 XP_003265492 XP_003808712 XP_004052704
SP	Q8WXI8
AlphaFold	Q8WXI8