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- PDB-2klu: NMR structure of the transmembrane and cytoplasmic domains of hum... -

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Basic information

Entry
Database: PDB / ID: 2klu
TitleNMR structure of the transmembrane and cytoplasmic domains of human CD4
ComponentsT-cell surface glycoprotein CD4
KeywordsImmune System / Membrane Protein / Protein / Cell membrane / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Immunoglobulin domain / Lipoprotein / Membrane / Palmitate / Polymorphism / Transmembrane
Function / homology
Function and homology information


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / positive regulation of interleukin-2 production / protein tyrosine kinase binding / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / early endosome / cell adhesion / positive regulation of protein phosphorylation / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / lipid binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
transmembrane domain of human cd4 / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain ...transmembrane domain of human cd4 / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
T-cell surface glycoprotein CD4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWittlich, M. / Willbold, D.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: NMR structure of the transmembrane and cytoplasmic domains of human CD4 in micelles.
Authors: Wittlich, M. / Thiagarajan, P. / Koenig, B.W. / Hartmann, R. / Willbold, D.
History
DepositionJul 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD4


Theoretical massNumber of molelcules
Total (without water)7,8661
Polymers7,8661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 7866.364 Da / Num. of mol.: 1 / Fragment: UNP residues 397-458 / Mutation: C394S,C397S,C420S,C422S,C430H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Escherichia coli (E. coli) / Strain (production host): c43 DE3 / References: UniProt: P01730

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D (H)CCH-COSY
11013D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] CD4 coreceptor polypeptide, 200 mM [U-100% 2H] DPC, 150 mM sodium chloride, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCD4 coreceptor polypeptide[U-100% 13C; U-100% 15N]1
200 mMDPC[U-100% 2H]1
150 mMsodium chloride1
20 mMsodium phosphate1
0.02 %sodium azide1
Sample conditionsIonic strength: 150 / pH: 6.2 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4a.5Keller and Wuthrichchemical shift assignment
CARA1.8.4a.5Keller and Wuthrichdata analysis
CARA1.8.4a.5Keller and Wuthrichprocessing
CARA1.8.4a.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
CARA1.8.4a.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CARA1.8.4a.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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