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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Half spherical cluster of BAFF-BAFFR ectodomain complex | |||||||||
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![]() | BAFF receptor / Receptor / Receptor cluster / IMMUNE SYSTEM | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Lim CS / Lee JO | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Highly ordered clustering of TNFα and BAFF ligand-receptor-intracellular adaptor complexes on a lipid membrane. Authors: Chan Seok Lim / Jisun Lee / Ji Won Kim / Jie-Oh Lee / ![]() Abstract: The TNF family plays a critical role in immune regulation. Here, we present high-resolution structures of clusters formed by two TNF receptor family proteins, TNFR1 and BAFFR. Using a lipid monolayer ...The TNF family plays a critical role in immune regulation. Here, we present high-resolution structures of clusters formed by two TNF receptor family proteins, TNFR1 and BAFFR. Using a lipid monolayer method to mimic their membrane-bound state, we observe that the TNFα-TNFR1 complex forms highly ordered clusters of trimers on the lipid membrane. A non-competitive TNFR1 antagonist that inhibits receptor activation disrupted these clusters without blocking ligand binding or receptor trimerization. Furthermore, we find that the BAFF-BAFFR, BAFF-TACI, and BAFF-BCMA receptor-ligand complexes predominantly form pentagonal clusters of trimers on the lipid membrane. Notably, the binding of the intracellular adaptor TRAF3 to the BAFF-BAFFR complex induces a structural transition from a pentagonal to a flat hexagonal cluster. Mutations in BAFF that impair BAFFR activation prevented cluster formation. Our findings demonstrate that ligand binding induces the formation of highly ordered clusters of TNFR1 and BAFFR receptors on the lipid membrane, which is essential for their activation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 230.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
Images | ![]() | 110.6 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Others | ![]() ![]() | 226.4 MB 226.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 882.5 KB | Display | ![]() |
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Full document | ![]() | 882.1 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.088 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_60493_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60493_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Half spherical cluster of BAFF-BAFFR ectodomain 3:3 complex
Entire | Name: Half spherical cluster of BAFF-BAFFR ectodomain 3:3 complex |
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Components |
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-Supramolecule #1: Half spherical cluster of BAFF-BAFFR ectodomain 3:3 complex
Supramolecule | Name: Half spherical cluster of BAFF-BAFFR ectodomain 3:3 complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Chains: 1,2,6,7,8,A,B,C,G,H,I,M,N,O,S,T,V,Y,Z,a,e,f,g,k,l,m,q,r,v,w
Macromolecule | Name: Chains: 1,2,6,7,8,A,B,C,G,H,I,M,N,O,S,T,V,Y,Z,a,e,f,g,k,l,m,q,r,v,w type: protein_or_peptide / ID: 1 / Details: BAFFR ectodomain / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: ADPDYKDDDD KRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ ESVGAGAGEA ALPLPGLLG GGGSHHHHHH HH |
-Macromolecule #2: Chains: 3,4,5,D,E,F,J,K,L,P,Q,R,U,W,X,b,c,d,h,i,j,n,o,p,s,t,u,x,y,z
Macromolecule | Name: Chains: 3,4,5,D,E,F,J,K,L,P,Q,R,U,W,X,b,c,d,h,i,j,n,o,p,s,t,u,x,y,z type: protein_or_peptide / ID: 2 / Details: BAFF ligand / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: GSGGSAVQGP EETVTQDCLQ LIADSETPTI QKGSYTFVPW LLSFKRGSAL EEKENKILVK ETGYFFIYGQ VLYTDKTYAM GHLIQRKKVH VFGDELSLVT LFRCIQNMPE TLPNNSCYSA GIAKLEEGDE LQLAIPRENA QISLDGDVTF FGALKLL |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | |||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |