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- PDB-8zuk: Cluster structure of the BAFF-BAFFR-TRAF3 complex -

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Basic information

Entry
Database: PDB / ID: 8zuk
TitleCluster structure of the BAFF-BAFFR-TRAF3 complex
Components
  • TNF receptor-associated factor 3
  • Tumor necrosis factor receptor superfamily member 13C
KeywordsIMMUNE SYSTEM / Receptor cluster / Signal complex / membrane receptor
Function / homology
Function and homology information


B cell costimulation / regulation of interferon-beta production / TRAF3 deficiency - HSE / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / serine/threonine protein kinase complex / thioesterase binding ...B cell costimulation / regulation of interferon-beta production / TRAF3 deficiency - HSE / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / serine/threonine protein kinase complex / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / toll-like receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / regulation of proteolysis / positive regulation of type I interferon production / ubiquitin ligase complex / positive regulation of T cell proliferation / tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / positive regulation of B cell proliferation / T cell costimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / regulation of cytokine production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / signaling receptor activity / TRAF3-dependent IRF activation pathway / protein phosphatase binding / regulation of apoptotic process / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / endosome / endosome membrane / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / mitochondrion / zinc ion binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / Tumor necrosis factor receptor 13C/17 / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa ...Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / Tumor necrosis factor receptor 13C/17 / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
TNF receptor-associated factor 3 / Tumor necrosis factor receptor superfamily member 13C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 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: FSC / Data content type: FSC / 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: TNF receptor-associated factor 3
B: TNF receptor-associated factor 3
C: TNF receptor-associated factor 3
D: Tumor necrosis factor receptor superfamily member 13C
E: Tumor necrosis factor receptor superfamily member 13C
F: Tumor necrosis factor receptor superfamily member 13C
G: TNF receptor-associated factor 3
H: TNF receptor-associated factor 3
I: TNF receptor-associated factor 3
J: Tumor necrosis factor receptor superfamily member 13C
K: Tumor necrosis factor receptor superfamily member 13C
L: Tumor necrosis factor receptor superfamily member 13C
M: TNF receptor-associated factor 3
N: TNF receptor-associated factor 3
O: TNF receptor-associated factor 3
P: Tumor necrosis factor receptor superfamily member 13C
Q: Tumor necrosis factor receptor superfamily member 13C
R: Tumor necrosis factor receptor superfamily member 13C
S: TNF receptor-associated factor 3
T: TNF receptor-associated factor 3
U: TNF receptor-associated factor 3
V: Tumor necrosis factor receptor superfamily member 13C
W: Tumor necrosis factor receptor superfamily member 13C
X: Tumor necrosis factor receptor superfamily member 13C
Y: TNF receptor-associated factor 3
Z: TNF receptor-associated factor 3
a: TNF receptor-associated factor 3
b: Tumor necrosis factor receptor superfamily member 13C
c: Tumor necrosis factor receptor superfamily member 13C
d: Tumor necrosis factor receptor superfamily member 13C
e: TNF receptor-associated factor 3
f: TNF receptor-associated factor 3
g: TNF receptor-associated factor 3
h: Tumor necrosis factor receptor superfamily member 13C
i: Tumor necrosis factor receptor superfamily member 13C
j: Tumor necrosis factor receptor superfamily member 13C
k: TNF receptor-associated factor 3
l: TNF receptor-associated factor 3
m: TNF receptor-associated factor 3
n: Tumor necrosis factor receptor superfamily member 13C
o: Tumor necrosis factor receptor superfamily member 13C
p: Tumor necrosis factor receptor superfamily member 13C


Theoretical massNumber of molelcules
Total (without water)1,162,29242
Polymers1,162,29242
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 ...
TNF receptor-associated factor 3 / CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein ...CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein 1 / LAP1 / RING-type E3 ubiquitin transferase TRAF3


Mass: 35444.441 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF3, CAP-1, CRAF1, TRAFAMN / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q13114, RING-type E3 ubiquitin transferase
#2: Protein ...
Tumor necrosis factor receptor superfamily member 13C / B-cell-activating factor receptor / BAFF receptor / BAFF-R / BLyS receptor 3


Mass: 19902.789 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF13C, BAFFR, BR3 / Cell line (production host): HEK293s GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q96RJ3
Has protein modificationN

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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: Cluster structure of the BAFF-BAFFR-TRAF3 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205165 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18T5P

8t5p

18T5P1PDBexperimental model
22GKW

2gkw

12GKW2PDBexperimental model
RefinementCross valid method: NONE

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