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- EMDB-60497: Trigonal pyramid cluster of TNF-TNFR1 ectodomain complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60497
TitleTrigonal pyramid cluster of TNF-TNFR1 ectodomain complex
Map data
Sample
  • Complex: Trigonal pyramid cluster of TNF-TNFR1 ectodomain 3:3 complex
    • Protein or peptide: Chains: A,B,C,G,H,I,M,N,O,S,T,U
    • Protein or peptide: Chains: D,E,F,J,K,L,P,Q,R,V,W,X
KeywordsTNF receptor / Receptor / Receptor cluster / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.17 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 10, 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_60497.png

Downloads & links

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Map

FileDownload / File: emd_60497.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 417.792 Å		1.09 Å/pix.
x 384 pix.
= 417.792 Å		1.09 Å/pix.
x 384 pix.
= 417.792 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: 0.115
Minimum - Maximum-0.0017593238 - 2.2760746
Average (Standard dev.)0.00063952606 (±0.017374262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 417.79202 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60497_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_60497_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 : Trigonal pyramid cluster of TNF-TNFR1 ectodomain 3:3 complex

EntireName: Trigonal pyramid cluster of TNF-TNFR1 ectodomain 3:3 complex
Components
  • Complex: Trigonal pyramid cluster of TNF-TNFR1 ectodomain 3:3 complex
    • Protein or peptide: Chains: A,B,C,G,H,I,M,N,O,S,T,U
    • Protein or peptide: Chains: D,E,F,J,K,L,P,Q,R,V,W,X

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Supramolecule #1: Trigonal pyramid cluster of TNF-TNFR1 ectodomain 3:3 complex

SupramoleculeName: Trigonal pyramid cluster of TNF-TNFR1 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: Chains: A,B,C,G,H,I,M,N,O,S,T,U

MacromoleculeName: Chains: A,B,C,G,H,I,M,N,O,S,T,U / type: protein_or_peptide / ID: 1 / Details: TNF ligand / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
ADPVRSSSRT PSDKPVAHVV ANPQAEGQLQ WLNRRANALL ANGVELRDNQ LVVPSEGLYL IYSQVLFKGQ GCPSTHVLLT HTISRIAVS YQTKVNLLSA IKSPCQRETP EGAEAKPWYE PIYLGGVFQL EKGDRLSAEI NRPDYLDFAE SGQVYFGIIA L EFRSGRLV PR

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Macromolecule #2: Chains: D,E,F,J,K,L,P,Q,R,V,W,X

MacromoleculeName: Chains: D,E,F,J,K,L,P,Q,R,V,W,X / type: protein_or_peptide / ID: 2 / Details: TNFR1 ectodomain / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ADPLVPHLGD REKRDSVCPQ GKYIHPQNNS ICCTKCHKGT YLYNDCPGPG QDTDCRECES GSFTASENHL RHCLSCSKCR KEMGQVEIS SCTVDRDTVC GCRKNQYRHY WSENLFQCFN CSLCLNGTVH LSCQEKQNTV CTCHAGFFLR ENECVSCSNC K KSLECTKL ...String:
ADPLVPHLGD REKRDSVCPQ GKYIHPQNNS ICCTKCHKGT YLYNDCPGPG QDTDCRECES GSFTASENHL RHCLSCSKCR KEMGQVEIS SCTVDRDTVC GCRKNQYRHY WSENLFQCFN CSLCLNGTVH LSCQEKQNTV CTCHAGFFLR ENECVSCSNC K KSLECTKL CLPQIENVKG TEDSGTTGGG GSHHHHHHHH

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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: 5.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31211
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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