[English] 日本語
Yorodumi
- EMDB-22422: Structure of an endocytic receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22422
TitleStructure of an endocytic receptor
Map dataFinal map
Sample
  • Organelle or cellular component: Lymphocyte antigen 75, DEC205, CD205
    • Protein or peptide: Lymphocyte antigen 75
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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: 3.2 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jpt
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22422.png

Downloads & links

-
Map

FileDownload / File: emd_22422.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.25616845 - 0.4359776
Average (Standard dev.)0.001403253 (±0.01532375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 169.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z169.600169.600169.600
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.2560.4360.001

-
Supplemental data

-
Mask #1

Fileemd_22422_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_22422_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_22422_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Lymphocyte antigen 75, DEC205, CD205

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

-
Macromolecule #1: Lymphocyte antigen 75

MacromoleculeName: Lymphocyte antigen 75 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 195.23025 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RAANDPFTIV HGNTGKCIKP VYGWIVADDC DETEDKLWKW VSQHRLFHLH SQKCLGLDIT KSVNELRMFS CDSSAMLWWK CEHHSLYGA ARYRLALKDG HGTAISNASD VWKKGGSEES LCDQPYHEIY TRDGNSYGRP CEFPFLIDGT WHHDCILDED H SGPWCATT ...String:
RAANDPFTIV HGNTGKCIKP VYGWIVADDC DETEDKLWKW VSQHRLFHLH SQKCLGLDIT KSVNELRMFS CDSSAMLWWK CEHHSLYGA ARYRLALKDG HGTAISNASD VWKKGGSEES LCDQPYHEIY TRDGNSYGRP CEFPFLIDGT WHHDCILDED H SGPWCATT LNYEYDRKWG ICLKPENGCE DNWEKNEQFG SCYQFNTQTA LSWKEAYVSC QNQGADLLSI NSAAELTYLK EK EGIAKIF WIGLNQLYSA RGWEWSDHKP LNFLNWDPDR PSAPTIGGSS CARMDAESGL WQSFSCEAQL PYVCRKPLNN TVE LTDVWT YSDTRCDAGW LPNNGFCYLL VNESNSWDKA HAKCKAFSSD LISIHSLADV EVVVTKLHNE DIKEEVWIGL KNIN IPTLF QWSDGTEVTL TYWDENEPNV PYNKTPNCVS YLGELGQWKV QSCEEKLKYV CKRKGEKLND ASSDKMCPPD EGWKR HGET CYKIYEDEVP FGTNCNLTIT SRFEQEYLND LMKKYDKSLR KYFWTGLRDV DSCGEYNWAT VGGRRRAVTF SNWNFL EPA SPGGCVAMST GKSVGKWEVK DCRSFKALSI CKKMSGPLGP EEASPKPDDP CPEGWQSFPA SLSCYKVFHA ERIVRKR NW EEAERFCQAL GAHLSSFSHV DEIKEFLHFL TDQFSGQHWL WIGLNKRSPD LQGSWQWSDR TPVSTIIMPN EFQQDYDI R DCAAVKVFHR PWRRGWHFYD DREFIYLRPF ACDTKLEWVC QIPKGRTPKT PDWYNPDRAG IHGPPLIIEG SEYWFVADL HLNYEEAVLY CASNHSFLAT ITSFVGLKAI KNKIANISGD GQKWWIRISE WPIDDHFTYS RYPWHRFPVT FGEECLYMSA KTWLIDLGK PTDCSTKLPF ICEKYNVSSL EKYSPDSAAK VQCSEQWIPF QNKCFLKIKP VSLTFSQASD TCHSYGGTLP S VLSQIEQD FITSLLPDME ATLWIGLRWT AYEKINKWTD NRELTYSNFH PLLVSGRLRI PENFFEEESR YHCALILNLQ KS PFTGTWN FTSCSERHFV SLCQKYSEVK SRQTLQNASE TVKYLNNLYK IIPKTLTWHS AKRECLKSNM QLVSITDPYQ QAF LSVQAL LHNSSLWIGL FSQDDELNFG WSDGKRLHFS RWAETNGQLE DCVVLDTDGF WKTVDCNDNQ PGAICYYSGN ETEK EVKPV DSVKCPSPVL NTPWIPFQNC CYNFIITKNR HMATTQDEVH TKCQKLNPKS HILSIRDEKE NNFVLEQLLY FNYMA SWVM LGITYRNKSL MWFDKTPLSY THWRAGRPTI KNEKFLAGLS TDGFWDIQTF KVIEEAVYFH QHSILACKIE MVDYKE EYN TTLPQFMPYE DGIYSVIQKK VTWYEALNMC SQSGGHLASV HNQNGQLFLE DIVKRDGFPL WVGLSSHDGS ESSFEWS DG STFDYIPWKG QTSPGNCVLL DPKGTWKHEK CNSVKDGAIC YKPTKSKKLS RLTYSSRCPA AKENGSRWIQ YKGHCYKS D QALHSFSEAK KLCSKHDHSA TIVSIKDEDE NKFVSRLMRE NNNITMRVWL GLSQHSVDQS WSWLDGSEVT FVKWENKSK SGVGRCSMLI ASNETWKKVE CEHGFGRVVC KVPLGPDYTA IAIIVATLSI LVLMGGLIWF LFQRHRLHLA GFSSVRYAQG VNEDEIMLP SFHD

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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
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

-
Electron microscopy

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

+
Image processing

Particle selectionNumber selected: 610069
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: Cryosparc V2 ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 310803
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model(PDB ID:

1dqo

,

2v5p

,

1qdd

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

PDB-7jpt:
Structure of an endocytic receptor

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more