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- PDB-8xlc: Clamda1 domain of human immunoglobulin -

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Basic information

Entry
Database: PDB / ID: 8xlc
TitleClamda1 domain of human immunoglobulin
ComponentsImmunoglobulin lambda constant 2
KeywordsIMMUNE SYSTEM / STRUCTURE FROM CYANA 3.98.15
Function / homology
Function and homology information


CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma ...CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin lambda constant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsYanaka, S. / Kodama, A. / Miyanoiri, Y. / Kato, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22H02755 Japan
Japan Agency for Medical Research and Development (AMED)JP21ae0121020h0001 Japan
Japan Agency for Medical Research and Development (AMED)JP21ae0121013h0301 Japan
CitationJournal: Int.Immunol. / Year: 2024
Title: Identification of potential C1-binding sites in the immunoglobulin CL domains.
Authors: Yanaka, S. / Kodama, A. / Nishiguchi, S. / Fujita, R. / Shen, J. / Boonsri, P. / Sung, D. / Isono, Y. / Yagi, H. / Miyanoiri, Y. / Uchihashi, T. / Kato, K.
History
DepositionDec 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin lambda constant 2


Theoretical massNumber of molelcules
Total (without water)12,0261
Polymers12,0261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Immunoglobulin lambda constant 2 / Ig lambda chain C region Kern / Ig lambda chain C region NIG-64 / Ig lambda chain C region SH / Ig ...Ig lambda chain C region Kern / Ig lambda chain C region NIG-64 / Ig lambda chain C region SH / Ig lambda chain C region X / Ig lambda-2 chain C region


Mass: 12026.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DOY2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D HNCA
151isotropic13D HNCO
1101isotropic13D HN(CO)CA
191isotropic13D HN(CA)CO
181isotropic13D 1H-13C NOESY
171isotropic13D 1H-15N NOESY
161isotropic13D 1H-15N TOCSY
1121isotropic13D HBHA(CO)NH
1111isotropic13D C(CO)NH
1131isotropic13D CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.6 mM [U-100% 13C; U-100% 15N] Clamda1 domain of human immunoglobulin, 5 mM NaPi, 50 mM sodium chloride, 95% H2O/5% D2O
Label: 13C, 15N / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.6 mMClamda1 domain of human immunoglobulin[U-100% 13C; U-100% 15N]1
5 mMNaPinone1
50 mMsodium chloridenone1
Sample conditionsIonic strength: Not defined Not defined / Label: condition_! / pH: 6 / Pressure: 1 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
ARTINAKlukowski, P., Riek, R. and Guntert, P.refinement
ARTINAKlukowski, P., Riek, R. and Guntert, P.structure calculation
ARTINAKlukowski, P., Riek, R. and Guntert, P.chemical shift assignment
ARTINAKlukowski, P., Riek, R. and Guntert, P.peak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 20

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