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- EMDB-1219: Crystal structure of a soluble CD28-Fab complex. -

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Basic information

Entry
Database: EMDB / ID: EMD-1219
TitleCrystal structure of a soluble CD28-Fab complex.
Map dataThis is a twofold-averaged map of the complex formed between dimeric CD28 and the mitogenic antibody 5.11A1.
Sample
  • Sample: CD28-Fc fusion complexed with 5.11A1 monoclonal antibody
  • Protein or peptide: CD28Fc fusion
  • Protein or peptide: Antibody 5.11A1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 28.0 Å
AuthorsEvans EJ / Esnouf RM / Manso-Sancho R / Gilbert RJC / James JR / Yu C / Fennely JA / Vowles C / Hanke T / Walse B ...Evans EJ / Esnouf RM / Manso-Sancho R / Gilbert RJC / James JR / Yu C / Fennely JA / Vowles C / Hanke T / Walse B / Hunig T / Sorensen P / Stuart DI / Davis SJ
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
DepositionMay 2, 2006-
Header (metadata) releaseMay 3, 2006-
Map releaseMay 3, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 98.059940608
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 98.059940608
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1219.gif

Downloads & links

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Map

FileDownload / File: emd_1219.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a twofold-averaged map of the complex formed between dimeric CD28 and the mitogenic antibody 5.11A1.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 128 pix.
= 332.88 Å		2.6 Å/pix.
x 128 pix.
= 332.88 Å		2.6 Å/pix.
x 128 pix.
= 332.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.60063 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 14.1 / Movie #1: 98.0599406
Minimum - Maximum-29.77 - 176.780000000000001
Average (Standard dev.)1.70765 (±12.410299999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 332.88 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.6006252.6006252.600625
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z332.880332.880332.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-29.770176.7801.708

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Supplemental data

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Sample components

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Entire : CD28-Fc fusion complexed with 5.11A1 monoclonal antibody

EntireName: CD28-Fc fusion complexed with 5.11A1 monoclonal antibody
Components
  • Sample: CD28-Fc fusion complexed with 5.11A1 monoclonal antibody
  • Protein or peptide: CD28Fc fusion
  • Protein or peptide: Antibody 5.11A1

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Supramolecule #1000: CD28-Fc fusion complexed with 5.11A1 monoclonal antibody

SupramoleculeName: CD28-Fc fusion complexed with 5.11A1 monoclonal antibody
type: sample / ID: 1000
Details: The monoclonal antibody 5.11A1 cross links CD28Fc dimers resulting in the formation of filaments. The assymetric unit of the filament is therefore one molecule of CD28Fc and one of Ab 5.11A1. ...Details: The monoclonal antibody 5.11A1 cross links CD28Fc dimers resulting in the formation of filaments. The assymetric unit of the filament is therefore one molecule of CD28Fc and one of Ab 5.11A1. The whole structure presented is the twofold averaged dimer Fab5.11A1-CD28Fc-CD28Fc-Fab5.11A1.
Oligomeric state: Filaments of the repeating unit -5.11A1-CD28Fc-
Number unique components: 2
Molecular weightExperimental: 80 KDa / Theoretical: 80 KDa / Method: By sequence and knowledge of oligomeric assembly.

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Macromolecule #1: CD28Fc fusion

MacromoleculeName: CD28Fc fusion / type: protein_or_peptide / ID: 1 / Name.synonym: CD28Fc / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane
Molecular weightExperimental: 20 KDa / Theoretical: 20 KDa
Recombinant expressionOrganism: Lec3.2.8.1

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Macromolecule #2: Antibody 5.11A1

MacromoleculeName: Antibody 5.11A1 / type: protein_or_peptide / ID: 2 / Name.synonym: 5.11A1 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 60 KDa / Theoretical: 60 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.04 mg/mL
BufferpH: 7 / Details: HBS
GridDetails: 200 mesh lacey carbon film
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Alignment procedureLegacy - Astigmatism: Corrected at 100,000 X magnification
DateJan 2, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 8.322 µm / Number real images: 10 / Od range: 5 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: FREALIGN and GAP
Details: 3D reconstructions were carried out in FREALIGN without symmetry being imposed and subsequently the twofold symmetry was determined and refined in GAP.
Number images used: 529

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Atomic model buiding 1

Initial modelPDB ID:

1yjd

SoftwareName: URO
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: CC and R-factor

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