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- PDB-2nan: NMR structure of human DCL-1 (CD302) extracellular domain -

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Basic information

Entry
Database: PDB / ID: 2nan
TitleNMR structure of human DCL-1 (CD302) extracellular domain
ComponentsCD302 antigen
KeywordsIMMUNE SYSTEM / C-type lectin like receptor
Function / homology
Function and homology information


microvillus / phagocytosis / filopodium / signaling receptor activity / carbohydrate binding / cell cortex / membrane
Similarity search - Function
: / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
Model detailslowest energy, model1
AuthorsPospisilova, E. / Kukacka, Z. / Kavan, D. / Novak, P. / Chmelik, J.
CitationJournal: To be Published
Title: NMR structure of human DCL-1 (CD302) extracellular domain
Authors: Pospisilova, E. / Kukacka, Z. / Kavan, D. / Novak, P. / Chmelik, J.
History
DepositionJan 6, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD302 antigen


Theoretical massNumber of molelcules
Total (without water)16,2281
Polymers16,2281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CD302 antigen / C-type lectin BIMLEC / C-type lectin domain family 13 member A / DEC205-associated C-type lectin 1 ...C-type lectin BIMLEC / C-type lectin domain family 13 member A / DEC205-associated C-type lectin 1 / Type I transmembrane C-type lectin receptor DCL-1


Mass: 16227.978 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 23-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD302, CLEC13A, DCL1, KIAA0022 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q8IX05
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CO
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D CBCA(CO)NH
1812D 1H-13C HSQC aliphatic
1912D 1H-13C HSQC aromatic
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11313D 1H-15N TOCSY
11413D H(CC)(CO)NH
11513D (H)CC(CO)NH
11612D (HB)CB(CGCD)HD
11713D (H)CCH-TOCSY
11813D (H)CCH-TOCSY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] CD302, 25 mM PIPES, 50 mM sodium chloride, 1 mM sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCD302-1[U-100% 13C; U-100% 15N]1
25 mMPIPES-21
50 mMsodium chloride-31
1 mMsodium azide-41
90 %H2O-51
10 %D2O-61
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 303.15 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardstructure solution
SparkyGoddardrefinement
SparkyBrunger, Adams, Clore, Gros, Nilges and Readchemical shift assignment
SparkyBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardstructure solution
SparkyGoddardrefinement
SparkyBrunger, Adams, Clore, Gros, Nilges and Readchemical shift assignment
SparkyBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 4588 / NOE intraresidue total count: 1504 / NOE long range total count: 1555 / NOE medium range total count: 624 / NOE sequential total count: 905 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 114 / Protein psi angle constraints total count: 114
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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