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- EMDB-60549: Cryo-EM structure of TNFa-TNFR1ecto-nanobody complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60549
TitleCryo-EM structure of TNFa-TNFR1ecto-nanobody complex
Map dataThis consensus map was generated using three maps
Sample
  • Complex: TNF-TNFR1ectodomain-nanobody 3:3:3 complex
    • Protein or peptide: Chains: A,B,C
    • Protein or peptide: Chains: D,E,F
    • Protein or peptide: Chains : G,H,I
KeywordsTNF receptor / Receptor / Receptor cluster / IMMUNE SYSTEM / antibody
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 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 15, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60549.png

Downloads & links

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Map

FileDownload / File: emd_60549.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis consensus map was generated using three maps
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-24.738907000000001 - 39.819262999999999
Average (Standard dev.)0.0056938305 (±0.9887159)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map3 used for consensus map generation

Fileemd_60549_additional_1.map
AnnotationMap3 used for consensus map generation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map2 used for consensus map generation

Fileemd_60549_additional_2.map
AnnotationMap2 used for consensus map generation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map1 used for consensus map generation

Fileemd_60549_additional_3.map
AnnotationMap1 used for consensus map generation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map data of Map1

Fileemd_60549_half_map_1.map
AnnotationHalf map data of Map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map data of Map1

Fileemd_60549_half_map_2.map
AnnotationHalf map data of Map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TNF-TNFR1ectodomain-nanobody 3:3:3 complex

EntireName: TNF-TNFR1ectodomain-nanobody 3:3:3 complex
Components
  • Complex: TNF-TNFR1ectodomain-nanobody 3:3:3 complex
    • Protein or peptide: Chains: A,B,C
    • Protein or peptide: Chains: D,E,F
    • Protein or peptide: Chains : G,H,I

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Supramolecule #1: TNF-TNFR1ectodomain-nanobody 3:3:3 complex

SupramoleculeName: TNF-TNFR1ectodomain-nanobody 3:3:3 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

MacromoleculeName: Chains: A,B,C / 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

MacromoleculeName: Chains: D,E,F / 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 KEMGQVEISS CTVDRDTVCG CRKNQYRHYW SENLFQCFNC SLCLNGTVHL SCQEKQNTVC TCHAGFFLRE NECVSCSNCK KSLECTKLCL ...String:
ADPLVPHLGD REKRDSVCPQ GKYIHPQNNS ICCTKCHKGT YLYNDCPGPG QDTDCRECES GSFTASENHL RHCLSCSKCR KEMGQVEISS CTVDRDTVCG CRKNQYRHYW SENLFQCFNC SLCLNGTVHL SCQEKQNTVC TCHAGFFLRE NECVSCSNCK KSLECTKLCL PQIENVKGTE DSGTTGGGGS HHHHHHHH

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Macromolecule #3: Chains : G,H,I

MacromoleculeName: Chains : G,H,I / type: protein_or_peptide / ID: 3 / Details: TNFR1 antagonist nanobody / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
ADPEVQLLES GGGLVQPGGS LRLSCAASGF TFDKYSMGWV RQAPGKGLEW VSQISDTADR TYYAHAVKGR FTISRDNSKN TLYLQMNSLR AEDTAVYYCA IYTGRWVPFE YWGQGTLVTV SSSGLVPR

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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

Concentration1.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloride
0.00021 % (w/w)C56H92O25glyco-diosgenin (GDN)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 989850
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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