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- EMDB-60485: Pentagonal cluster of BAFF-BAFFR ectodomain complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60485
TitlePentagonal cluster of BAFF-BAFFR ectodomain complex
Map data
Sample
  • Complex: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 13C
    • Protein or peptide: Tumor necrosis factor ligand superfamily member 13b, soluble form
KeywordsBAFF receptor / Receptor / Receptor cluster / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsLim CS / Lee JO
Funding support Korea, Republic Of, 1 items
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 CS / Lee JO
History
DepositionJun 9, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60485.png

Downloads & links

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Map

FileDownload / File: emd_60485.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-2.3462617 - 3.429065
Average (Standard dev.)-0.0002033979 (±0.062247124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60485_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60485_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex

EntireName: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
Components
  • Complex: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 13C
    • Protein or peptide: Tumor necrosis factor ligand superfamily member 13b, soluble form

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Supramolecule #1: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex

SupramoleculeName: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Tumor necrosis factor receptor superfamily member 13C

MacromoleculeName: Tumor necrosis factor receptor superfamily member 13C / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.585881 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
ADPDYKDDDD KRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ ESVGAGAGEA ALPLPGLLG GGGSHHHHHH HH

UniProtKB: Tumor necrosis factor receptor superfamily member 13C

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Macromolecule #2: Tumor necrosis factor ligand superfamily member 13b, soluble form

MacromoleculeName: Tumor necrosis factor ligand superfamily member 13b, soluble form
type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.401756 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GSGGSAVQGP EETVTQDCLQ LIADSETPTI QKGSYTFVPW LLSFKRGSAL EEKENKILVK ETGYFFIYGQ VLYTDKTYAM GHLIQRKKV HVFGDELSLV TLFRCIQNMP ETLPNNSCYS AGIAKLEEGD ELQLAIPREN AQISLDGDVT FFGALKLL

UniProtKB: Tumor necrosis factor ligand superfamily member 13B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 100500
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 220800
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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Atomic model buiding 1

Initial modelPDB ID:

4v46


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

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

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