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- PDB-7jpu: Structure of an endocytic receptor -

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Basic information

Entry
Database: PDB / ID: 7jpu
TitleStructure of an endocytic receptor
ComponentsLymphocyte antigen 75
KeywordsIMMUNE SYSTEM / Cell-surface receptor / Immune receptor / mannose receptor family
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsGully, B.S. / Rossjohn, J. / Berry, R.
Funding support Australia, 2items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Lymphocyte antigen 75
B: Lymphocyte antigen 75
C: Lymphocyte antigen 75
D: Lymphocyte antigen 75


Theoretical massNumber of molelcules
Total (without water)794,2134
Polymers794,2134
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, analytical centrifugation, light scattering, multi-angle light scattering and SEC
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15490 Å2
ΔGint-112 kcal/mol
Surface area237940 Å2

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Components

#1: Protein
Lymphocyte antigen 75 / Ly-75 / C-type lectin domain family 13 member B / DEC-205 / gp200-MR6


Mass: 198553.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LY75, CD205, CLEC13B / Cell line (production host): HEK293s / Production host: Homo sapiens (human) / References: UniProt: O60449

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Lymphocyte antigen 75, DEC205, CD205 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.2 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl at pH 8.0, 150 mM NaCl buffer
Buffer component
IDConc.NameBuffer-ID
120 mMTris1
2150 mMsodium chloride1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 3 microlitres of sample in 20 mM Tris-HCl at pH 8.0, 150 mM NaCl buffer
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 63 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategory
7Coot1model fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.17.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 185187
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102569 / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-ID
11DQO

1dqo

1
22V5P

2v5p

1
31QDD

1qdd

1
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00236980
ELECTRON MICROSCOPYf_angle_d0.5450309
ELECTRON MICROSCOPYf_dihedral_angle_d13.2744859
ELECTRON MICROSCOPYf_chiral_restr0.0415422
ELECTRON MICROSCOPYf_plane_restr0.0036299

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