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- PDB-8zuj: Pentagonal cluster of BAFF-BAFFR ectodomain complex -

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Basic information

Entry
Database: PDB / ID: 8zuj
TitlePentagonal cluster of BAFF-BAFFR ectodomain complex
Components
  • Tumor necrosis factor ligand superfamily member 13b, soluble form
  • Tumor necrosis factor receptor superfamily member 13C
KeywordsIMMUNE SYSTEM / BAFF receptor / Receptor / Receptor cluster
Function / homology
Function and homology information


B cell costimulation / positive regulation of germinal center formation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / tumor necrosis factor receptor binding / germinal center formation / skin development / B cell homeostasis / B cell proliferation ...B cell costimulation / positive regulation of germinal center formation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / tumor necrosis factor receptor binding / germinal center formation / skin development / B cell homeostasis / B cell proliferation / positive regulation of T cell proliferation / T cell proliferation / tumor necrosis factor-mediated signaling pathway / positive regulation of B cell proliferation / T cell costimulation / cytokine activity / TNFR2 non-canonical NF-kB pathway / signaling receptor activity / adaptive immune response / receptor ligand activity / external side of plasma membrane / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / Tumor necrosis factor receptor 13C/17 / : / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 13C / Tumor necrosis factor ligand superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsLim, C.S. / Lee, J.O.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: To Be Published
Title: Ordered clustering of TNF and BAFF ligand-receptor-adaptor complexes attached to an artificial lipid membrane
Authors: Lim, C.S. / Lee, J.O.
History
DepositionJun 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 13C
B: Tumor necrosis factor receptor superfamily member 13C
C: Tumor necrosis factor receptor superfamily member 13C
D: Tumor necrosis factor ligand superfamily member 13b, soluble form
E: Tumor necrosis factor ligand superfamily member 13b, soluble form
F: Tumor necrosis factor ligand superfamily member 13b, soluble form
G: Tumor necrosis factor receptor superfamily member 13C
H: Tumor necrosis factor receptor superfamily member 13C
I: Tumor necrosis factor receptor superfamily member 13C
J: Tumor necrosis factor ligand superfamily member 13b, soluble form
K: Tumor necrosis factor ligand superfamily member 13b, soluble form
L: Tumor necrosis factor ligand superfamily member 13b, soluble form
M: Tumor necrosis factor receptor superfamily member 13C
N: Tumor necrosis factor receptor superfamily member 13C
O: Tumor necrosis factor receptor superfamily member 13C
P: Tumor necrosis factor ligand superfamily member 13b, soluble form
Q: Tumor necrosis factor ligand superfamily member 13b, soluble form
R: Tumor necrosis factor ligand superfamily member 13b, soluble form
S: Tumor necrosis factor receptor superfamily member 13C
T: Tumor necrosis factor receptor superfamily member 13C
U: Tumor necrosis factor receptor superfamily member 13C
V: Tumor necrosis factor ligand superfamily member 13b, soluble form
W: Tumor necrosis factor ligand superfamily member 13b, soluble form
X: Tumor necrosis factor ligand superfamily member 13b, soluble form
Y: Tumor necrosis factor receptor superfamily member 13C
Z: Tumor necrosis factor receptor superfamily member 13C
a: Tumor necrosis factor receptor superfamily member 13C
b: Tumor necrosis factor ligand superfamily member 13b, soluble form
c: Tumor necrosis factor ligand superfamily member 13b, soluble form
d: Tumor necrosis factor ligand superfamily member 13b, soluble form


Theoretical massNumber of molelcules
Total (without water)419,81530
Polymers419,81530
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Tumor necrosis factor receptor superfamily member 13C / B-cell-activating factor receptor / BAFF receptor / BAFF-R / BLyS receptor 3


Mass: 10585.881 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF13C, BAFFR, BR3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96RJ3
#2: Protein
Tumor necrosis factor ligand superfamily member 13b, soluble form


Mass: 17401.756 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TNFSF13B, BAFF, BLYS, TALL1, TNFSF20, ZTNF4, UNQ401/PRO738
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y275
Has protein modificationY

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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: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2150 mMSodium chlorideNaCl1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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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 / Nominal magnification: 100500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220800 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 4V46

4v46


Accession code: 4V46 / Source name: PDB / Type: experimental model

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