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- PDB-5xf0: Solution structure of the IgI domain of CD147 -

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Basic information

Entry
Database: PDB / ID: 5xf0
TitleSolution structure of the IgI domain of CD147
ComponentsBasigin
KeywordsIMMUNE SYSTEM / IG-like Domain
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / neural retina development / endothelial tube morphogenesis / Pyruvate metabolism / photoreceptor cell maintenance / Basigin interactions ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / neural retina development / endothelial tube morphogenesis / Pyruvate metabolism / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / mannose binding / decidualization / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / Integrin cell surface interactions / embryo implantation / response to cAMP / photoreceptor inner segment / Degradation of the extracellular matrix / neutrophil chemotaxis / positive regulation of endothelial cell migration / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / virus receptor activity / signaling receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsJin, S.J. / Xia, B.
CitationJournal: Protein Cell / Year: 2018
Title: Zn(II) can mediate self-association of the extracellular C-terminal domain of CD147
Authors: Jin, S. / Ding, P. / Chu, P. / Li, H. / Sun, J. / Liang, D. / Song, F. / Xia, B.
History
DepositionApr 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basigin


Theoretical massNumber of molelcules
Total (without water)12,0081
Polymers12,0081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6760 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Basigin / / CD147 / 5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / ...CD147 / 5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / Leukocyte activation antigen M6 / OK blood group antigen / Tumor cell-derived collagenase stimulatory factor / TCSF


Mass: 12008.415 Da / Num. of mol.: 1 / Fragment: UNP residues 215-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BSG, UNQ6505/PRO21383 / Production host: Escherichia coli (E. coli) / Strain (production host): origami B(DE3) / References: UniProt: P35613

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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
121isotropic22D 1H-15N HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HNCO
181isotropic13D (H)CCH-TOCSY
171isotropic13D (H)CCH-COSY
161isotropic13D HBHA(CO)NH
191isotropic23D 1H-15N NOESY
1111isotropic23D 1H-13C NOESY
1101isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution / Contents: 0.5mM [U-13C; U-15N] CD147, 90% H2O/10% D2O / Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: CD147 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 50mM PBS 50mM NaCl 5mM EDTA / Ionic strength: 100 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance5001
Bruker AvanceBrukerAvance8002

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Processing

NMR software
NameDeveloperClassification
AMBERCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
DYANAGuntert, Braun and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are b5059 are NOE-derived distance constraints, 143 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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