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- PDB-1yjd: Crystal structure of human CD28 in complex with the Fab fragment ... -

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Basic information

Entry
Database: PDB / ID: 1yjd
TitleCrystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1)
Components
  • Fab fragment of 5.11A1 antibody heavy chain
  • Fab fragment of 5.11A1 antibody light chain
  • T-cell-specific surface glycoprotein CD28
KeywordsIMMUNE SYSTEM/SIGNALING PROTEIN / IgSF / CD28 homodimer / IMMUNE SYSTEM-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / CD28 co-stimulation ...Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / CD28 co-stimulation / CD28 dependent Vav1 pathway / CD28 dependent PI3K/Akt signaling / positive regulation of interleukin-10 production / humoral immune response / immunological synapse / positive regulation of interleukin-4 production / positive regulation of viral genome replication / coreceptor activity / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / T cell activation / positive regulation of mitotic nuclear division / positive regulation of translation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / apoptotic signaling pathway / positive regulation of cytokine production / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / transcription by RNA polymerase II / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol
Similarity search - Function
T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell-specific surface glycoprotein CD28
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEvans, E.J. / Esnouf, R.M. / Manso-Sancho, R. / Gilbert, R.J.C. / James, J.R. / Sorensen, P. / Stuart, D.I. / Davis, S.J.
CitationJournal: Nat Immunol / Year: 2005
Title: Crystal structure of a soluble CD28-Fab complex.
Authors: Edward J Evans / Robert M Esnouf / Raquel Manso-Sancho / Robert J C Gilbert / John R James / Chao Yu / Janet A Fennelly / Cheryl Vowles / Thomas Hanke / Björn Walse / Thomas Hünig / Poul ...Authors: Edward J Evans / Robert M Esnouf / Raquel Manso-Sancho / Robert J C Gilbert / John R James / Chao Yu / Janet A Fennelly / Cheryl Vowles / Thomas Hanke / Björn Walse / Thomas Hünig / Poul Sørensen / David I Stuart / Simon J Davis /
Abstract: Naive T cell activation requires signaling by the T cell receptor and by nonclonotypic cell surface receptors. The most important costimulatory protein is the monovalent homodimer CD28, which ...Naive T cell activation requires signaling by the T cell receptor and by nonclonotypic cell surface receptors. The most important costimulatory protein is the monovalent homodimer CD28, which interacts with CD80 and CD86 expressed on antigen-presenting cells. Here we present the crystal structure of a soluble form of CD28 in complex with the Fab fragment of a mitogenic antibody. Structural comparisons redefine the evolutionary relationships of CD28-related proteins, antigen receptors and adhesion molecules and account for the distinct ligand-binding and stoichiometric properties of CD28 and the related, inhibitory homodimer CTLA-4. Cryo-electron microscopy-based comparisons of complexes of CD28 with mitogenic and nonmitogenic antibodies place new constraints on models of antibody-induced receptor triggering. This work completes the initial structural characterization of the CD28-CTLA-4-CD80-CD86 signaling system.
History
DepositionJan 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab fragment of 5.11A1 antibody light chain
H: Fab fragment of 5.11A1 antibody heavy chain
C: T-cell-specific surface glycoprotein CD28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9456
Polymers63,2823
Non-polymers6643
Water3,657203
1
L: Fab fragment of 5.11A1 antibody light chain
H: Fab fragment of 5.11A1 antibody heavy chain
C: T-cell-specific surface glycoprotein CD28
hetero molecules

L: Fab fragment of 5.11A1 antibody light chain
H: Fab fragment of 5.11A1 antibody heavy chain
C: T-cell-specific surface glycoprotein CD28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,89112
Polymers126,5646
Non-polymers1,3276
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)191.219, 47.417, 71.842
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: 1-x, y, 1-z.

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Components

#1: Antibody Fab fragment of 5.11A1 antibody light chain


Mass: 23388.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab fragment of 5.11A1 antibody heavy chain


Mass: 24108.939 Da / Num. of mol.: 1 / Fragment: IgV and IgC1 domains / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein T-cell-specific surface glycoprotein CD28 / TP44


Mass: 15784.077 Da / Num. of mol.: 1 / Fragment: Extracellular region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD28 / Plasmid: PEE14 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO Lec3.2.8.1 / References: UniProt: P10747
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: PEG 3350, magnesium formate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1.008 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 2, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 18408 / Num. obs: 17413 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.15
Reflection shellResolution: 2.7→2.8 Å / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.501data extraction
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→25 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 842 4.7 %RANDOM
Rwork0.239 ---
all0.239 17402 --
obs0.248 17402 96.7 %-
Displacement parametersBiso mean: 80 Å2
Baniso -1Baniso -2Baniso -3
1-18.538 Å20 Å2-4.28 Å2
2---3.91 Å20 Å2
3----14.629 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 42 203 4493
LS refinement shellResolution: 2.7→2.78 Å
RfactorNum. reflection
Rfree0.414 72
Rwork0.366 -
obs-1437

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