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- EMDB-60488: Cluster structure of BAFF-BAFFR-TRAF3(His) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60488
TitleCluster structure of BAFF-BAFFR-TRAF3(His) complex
Map data
Sample
  • Complex: Cluster structure of the BAFF-BAFFR-TRAF3(His) complex
    • Protein or peptide: Chains: A,B,C,G,H,I,M,N,O,S,T,U,Y,Z,a,e,f,g,k,l,m
    • Protein or peptide: Chains: D,E,F,J,K,L,P,Q,R,V,W,X,b,c,d,h,i,j,n,o,p
KeywordsReceptor cluster / Signal complex / membrane receptor / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 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_60488.png

Downloads & links

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Map

FileDownload / File: emd_60488.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.)
1.09 Å/pix.
x 400 pix.
= 435.2 Å		1.09 Å/pix.
x 400 pix.
= 435.2 Å		1.09 Å/pix.
x 400 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.4271677 - 3.6074162
Average (Standard dev.)0.0011312871 (±0.06861189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60488_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60488_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 : Cluster structure of the BAFF-BAFFR-TRAF3(His) complex

EntireName: Cluster structure of the BAFF-BAFFR-TRAF3(His) complex
Components
  • Complex: Cluster structure of the BAFF-BAFFR-TRAF3(His) complex
    • Protein or peptide: Chains: A,B,C,G,H,I,M,N,O,S,T,U,Y,Z,a,e,f,g,k,l,m
    • Protein or peptide: Chains: D,E,F,J,K,L,P,Q,R,V,W,X,b,c,d,h,i,j,n,o,p

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Supramolecule #1: Cluster structure of the BAFF-BAFFR-TRAF3(His) complex

SupramoleculeName: Cluster structure of the BAFF-BAFFR-TRAF3(His) complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Chains: A,B,C,G,H,I,M,N,O,S,T,U,Y,Z,a,e,f,g,k,l,m

MacromoleculeName: Chains: A,B,C,G,H,I,M,N,O,S,T,U,Y,Z,a,e,f,g,k,l,m / type: protein_or_peptide / ID: 1 / Details: TRAF3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHG GGGSKNDGSG GGGSNTGLLE SQLSRHDQML SVHDIRLADM DLRFQVLETA SYNGVLIWKI RDYKRRKQEA VMGKTLSLYS QPFYTGYFGY KMCARVYLNG DGMGKGTHLS LFFVIMRGEY DALLPWPFKQ KVTLMLMDQG SSRRHLGDAF KPDPNSSSFK ...String:
MHHHHHHHHG GGGSKNDGSG GGGSNTGLLE SQLSRHDQML SVHDIRLADM DLRFQVLETA SYNGVLIWKI RDYKRRKQEA VMGKTLSLYS QPFYTGYFGY KMCARVYLNG DGMGKGTHLS LFFVIMRGEY DALLPWPFKQ KVTLMLMDQG SSRRHLGDAF KPDPNSSSFK KPTGEMNIAS GCPVFVAQTV LENGTYIKDD TIFIKVIVDT SDLPDPGGSL VPR

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Macromolecule #2: Chains: D,E,F,J,K,L,P,Q,R,V,W,X,b,c,d,h,i,j,n,o,p

MacromoleculeName: Chains: D,E,F,J,K,L,P,Q,R,V,W,X,b,c,d,h,i,j,n,o,p / type: protein_or_peptide / ID: 2 / Details: BAFFR / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ ESVGAGAGEA ALPLPGLLFG APALLGLAL VLALVLVGLV SWRRRQRRLR GASSAEAPDG DKDAPEPLDK VIILSPGISD ATAPAWPPPG EDPGTTPPGH S VPVPATEL ...String:
MRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ ESVGAGAGEA ALPLPGLLFG APALLGLAL VLALVLVGLV SWRRRQRRLR GASSAEAPDG DKDAPEPLDK VIILSPGISD ATAPAWPPPG EDPGTTPPGH S VPVPATEL GSTELVTTKT AGPEQQSNSL EVLFQ

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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

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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 493981
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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