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- EMDB-22423: Structure of an endocytic receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-22423
TitleStructure of an endocytic receptor
Map datahalf1
Sample
  • Organelle or cellular component: Lymphocyte antigen 75, DEC205, CD205
    • Protein or peptide: Lymphocyte antigen 75
Function / homology
Function and homology information


endocytosis / signaling receptor activity / carbohydrate binding / inflammatory response / immune response / external side of plasma membrane / extracellular exosome / plasma membrane
Similarity search - Function
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. ...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 / Resolution: 5.0 Å
AuthorsGully BS / Rossjohn J / Berry R
Funding support Australia, 2 items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL160100049 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1109901 Australia
CitationJournal: J Biol Chem / Year: 2021
Title: The cryo-EM structure of the endocytic receptor DEC-205.
Authors: Benjamin S Gully / Hariprasad Venugopal / Alex J Fulcher / Zhihui Fu / Jessica Li / Felix A Deuss / Carmen Llerena / William R Heath / Mireille H Lahoud / Irina Caminschi / Jamie Rossjohn / Richard Berry /
Abstract: DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine ...DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine oligonucleotides, a motif often seen in bacterial or viral DNA. However, despite growing biological and clinical significance, little is known about the structural arrangement of this receptor or any of its family members. Here, we describe the 3.2 Å cryo-EM structure of human DEC-205, thereby illuminating the structure of the mannose receptor protein family. The DEC-205 monomer forms a compact structure comprising two intercalated rings of C-type lectin-like domains, where the N-terminal cysteine-rich and fibronectin domains reside at the central intersection. We establish a pH-dependent oligomerization pathway forming tetrameric DEC-205 using solution-based techniques and ultimately solved the 4.9 Å cryo-EM structure of the DEC-205 tetramer to identify the unfurling of the second lectin ring which enables tetramer formation. Furthermore, we suggest the relevance of this oligomerization pathway within a cellular setting, whereby cytosine-guanosine binding appeared to disrupt this cell-surface oligomer. Accordingly, we provide insight into the structure and oligomeric assembly of the DEC-205 receptor.
History
DepositionAug 9, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jpu
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22423.png

Downloads & links

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Map

FileDownload / File: emd_22423.map.gz / Format: CCP4 / Size: 48.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhalf1
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.013
Minimum - Maximum-0.032895893 - 0.07060371
Average (Standard dev.)0.0007745162 (±0.00356172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions234234234
Spacing234234234
CellA=B=C: 248.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z234234234
origin x/y/z0.0000.0000.000
length x/y/z248.040248.040248.040
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS234234234
D min/max/mean-0.0330.0710.001

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Supplemental data

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Mask #1

Fileemd_22423_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_22423_half_map_1.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_22423_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lymphocyte antigen 75, DEC205, CD205

EntireName: Lymphocyte antigen 75, DEC205, CD205
Components
  • Organelle or cellular component: Lymphocyte antigen 75, DEC205, CD205
    • Protein or peptide: Lymphocyte antigen 75

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Supramolecule #1: Lymphocyte antigen 75, DEC205, CD205

SupramoleculeName: Lymphocyte antigen 75, DEC205, CD205 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 200 KDa

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Macromolecule #1: Lymphocyte antigen 75

MacromoleculeName: Lymphocyte antigen 75 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 198.553172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRTGWATPRR PAGLLMLLFW FFDLAEPSGR AANDPFTIVH GNTGKCIKPV YGWIVADDCD ETEDKLWKWV SQHRLFHLHS QKCLGLDIT KSVNELRMFS CDSSAMLWWK CEHHSLYGAA RYRLALKDGH GTAISNASDV WKKGGSEESL CDQPYHEIYT R DGNSYGRP ...String:
MRTGWATPRR PAGLLMLLFW FFDLAEPSGR AANDPFTIVH GNTGKCIKPV YGWIVADDCD ETEDKLWKWV SQHRLFHLHS QKCLGLDIT KSVNELRMFS CDSSAMLWWK CEHHSLYGAA RYRLALKDGH GTAISNASDV WKKGGSEESL CDQPYHEIYT R DGNSYGRP CEFPFLIDGT WHHDCILDED HSGPWCATTL NYEYDRKWGI CLKPENGCED NWEKNEQFGS CYQFNTQTAL SW KEAYVSC QNQGADLLSI NSAAELTYLK EKEGIAKIFW IGLNQLYSAR GWEWSDHKPL NFLNWDPDRP SAPTIGGSSC ARM DAESGL WQSFSCEAQL PYVCRKPLNN TVELTDVWTY SDTRCDAGWL PNNGFCYLLV NESNSWDKAH AKCKAFSSDL ISIH SLADV EVVVTKLHNE DIKEEVWIGL KNINIPTLFQ WSDGTEVTLT YWDENEPNVP YNKTPNCVSY LGELGQWKVQ SCEEK LKYV CKRKGEKLND ASSDKMCPPD EGWKRHGETC YKIYEDEVPF GTNCNLTITS RFEQEYLNDL MKKYDKSLRK YFWTGL RDV DSCGEYNWAT VGGRRRAVTF SNWNFLEPAS PGGCVAMSTG KSVGKWEVKD CRSFKALSIC KKMSGPLGPE EASPKPD DP CPEGWQSFPA SLSCYKVFHA ERIVRKRNWE EAERFCQALG AHLSSFSHVD EIKEFLHFLT DQFSGQHWLW IGLNKRSP D LQGSWQWSDR TPVSTIIMPN EFQQDYDIRD CAAVKVFHRP WRRGWHFYDD REFIYLRPFA CDTKLEWVCQ IPKGRTPKT PDWYNPDRAG IHGPPLIIEG SEYWFVADLH LNYEEAVLYC ASNHSFLATI TSFVGLKAIK NKIANISGDG QKWWIRISEW PIDDHFTYS RYPWHRFPVT FGEECLYMSA KTWLIDLGKP TDCSTKLPFI CEKYNVSSLE KYSPDSAAKV QCSEQWIPFQ N KCFLKIKP VSLTFSQASD TCHSYGGTLP SVLSQIEQDF ITSLLPDMEA TLWIGLRWTA YEKINKWTDN RELTYSNFHP LL VSGRLRI PENFFEEESR YHCALILNLQ KSPFTGTWNF TSCSERHFVS LCQKYSEVKS RQTLQNASET VKYLNNLYKI IPK TLTWHS AKRECLKSNM QLVSITDPYQ QAFLSVQALL HNSSLWIGLF SQDDELNFGW SDGKRLHFSR WAETNGQLED CVVL DTDGF WKTVDCNDNQ PGAICYYSGN ETEKEVKPVD SVKCPSPVLN TPWIPFQNCC YNFIITKNRH MATTQDEVHT KCQKL NPKS HILSIRDEKE NNFVLEQLLY FNYMASWVML GITYRNKSLM WFDKTPLSYT HWRAGRPTIK NEKFLAGLST DGFWDI QTF KVIEEAVYFH QHSILACKIE MVDYKEEYNT TLPQFMPYED GIYSVIQKKV TWYEALNMCS QSGGHLASVH NQNGQLF LE DIVKRDGFPL WVGLSSHDGS ESSFEWSDGS TFDYIPWKGQ TSPGNCVLLD PKGTWKHEKC NSVKDGAICY KPTKSKKL S RLTYSSRCPA AKENGSRWIQ YKGHCYKSDQ ALHSFSEAKK LCSKHDHSAT IVSIKDEDEN KFVSRLMREN NNITMRVWL GLSQHSVDQS WSWLDGSEVT FVKWENKSKS GVGRCSMLIA SNETWKKVEC EHGFGRVVCK VPLGPDYTAI AIIVATLSIL VLMGGLIWF LFQRHRLHLA GFSSVRYAQG VNEDEIMLPS FHD

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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

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationName
20.0 mMTris
150.0 mMsodium chloride

Details: 20 mM Tris-HCl at pH 8.0, 150 mM NaCl buffer
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II
Details3 microlitres of sample in 20 mM Tris-HCl at pH 8.0, 150 mM NaCl buffer

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 63.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 185187
Startup modelType of model: OTHER / Details: Cryosparc V2 ab initio model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 102569
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

1dqo

,

2v5p

,

1qdd

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7jpu:
Structure of an endocytic receptor

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