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- EMDB-6333: Structure of DEC205 at acidic pH -

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Basic information

Entry
Database: EMDB / ID: EMD-6333
TitleStructure of DEC205 at acidic pH
Map dataReconstruction of DEC205 at acidic pH
Sample
  • Sample: DEC205 ectodomain at pH 6.0
  • Protein or peptide: CD205, Lymphocyte antigen 75
Keywordsdendritic cell receptor / apoptosis / cryoEM / mannose receptor family
Function / homology
Function and homology information


endocytosis / signaling receptor activity / carbohydrate binding / immune response / inflammatory response / external side of plasma membrane / extracellular exosome / plasma membrane
Similarity search - Function
MRC2-like, N-terminal cysteine-rich domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / : / C-type lectin, conserved site / C-type lectin domain signature. ...MRC2-like, N-terminal cysteine-rich domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Kringle-like fold
Similarity search - Domain/homology
Lymphocyte antigen 75
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.6 Å
AuthorsCao L / Shi X / Chang H / Zhang Q / Wah C / He Y
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: pH-Dependent recognition of apoptotic and necrotic cells by the human dendritic cell receptor DEC205.
Authors: Longxing Cao / Xiangyi Shi / Haishuang Chang / Qinfen Zhang / Yongning He /
Abstract: Dendritic cells play important roles in regulating innate and adaptive immune responses. DEC205 (CD205) is one of the major endocytotic receptors on dendritic cells and has been widely used for ...Dendritic cells play important roles in regulating innate and adaptive immune responses. DEC205 (CD205) is one of the major endocytotic receptors on dendritic cells and has been widely used for vaccine generation against viruses and tumors. However, little is known about its structure and functional mechanism. Here we determine the structure of the human DEC205 ectodomain by cryoelectron microscopy. The structure shows that the 12 extracellular domains form a compact double ring-shaped conformation at acidic pH and become extended at basic pH. Biochemical data indicate that the pH-dependent conformational change of DEC205 is correlated with ligand binding and release. DEC205 only binds to apoptotic and necrotic cells at acidic pH, whereas live cells cannot be recognized by DEC205 at either acidic or basic conditions. These results suggest that DEC205 is an immune receptor that recognizes apoptotic and necrotic cells specifically through a pH-dependent mechanism.
History
DepositionMay 5, 2015-
Header (metadata) releaseMay 27, 2015-
Map releaseMay 27, 2015-
UpdateMay 25, 2016-
Current statusMay 25, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6333.gif

Downloads & links

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Map

FileDownload / File: emd_6333.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of DEC205 at acidic pH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 128 pix.
= 174.08 Å		1.36 Å/pix.
x 128 pix.
= 174.08 Å		1.36 Å/pix.
x 128 pix.
= 174.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-2.22418284 - 31.99729919
Average (Standard dev.)0.32514369 (±1.81212509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 174.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z174.080174.080174.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-2.22431.9970.325

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Supplemental data

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Sample components

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Entire : DEC205 ectodomain at pH 6.0

EntireName: DEC205 ectodomain at pH 6.0
Components
  • Sample: DEC205 ectodomain at pH 6.0
  • Protein or peptide: CD205, Lymphocyte antigen 75

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Supramolecule #1000: DEC205 ectodomain at pH 6.0

SupramoleculeName: DEC205 ectodomain at pH 6.0 / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 191.2 MDa

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Macromolecule #1: CD205, Lymphocyte antigen 75

MacromoleculeName: CD205, Lymphocyte antigen 75 / type: protein_or_peptide / ID: 1 / Name.synonym: DEC205 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane
Molecular weightTheoretical: 191.2 MDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: Human / Recombinant cell: HEK293 / Recombinant plasmid: pTT5
SequenceUniProtKB: Lymphocyte antigen 75

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.0 mg/mL
BufferpH: 6 / Details: 150mM NaCl, 50mM Bis-Tris
StainingType: NEGATIVE / Details: Cryo
GridDetails: Quantifoil Holey Carbon Film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK II / Method: Blot for 6 seconds before plunging

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Electron microscopy

MicroscopeJEOL 2100F
Specialist opticsEnergy filter - Name: in column filter
DateApr 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 153 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 11029 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: JEOL

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Image processing

CTF correctionDetails: whole micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.6 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2 / Number images used: 15723
Final two d classificationNumber classes: 20

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