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전자현미경 데이터
TNFa-TNFR1 굽은 모양 cluster의 CryoEM 구조
  • Accession
    KIX10061484
  • Submission date
    2026-09-10
Project Detail
Dataset detail - Accession, 프로젝트의 영문 제목, 프로젝트의 국문 제목, 프로젝트의 영문 설명, 프로젝트의 국문 설명
Accession
 KAP242521
프로젝트의 영문 제목
Structural Elucidation of Ligand-Induced Higher-Order TNFα-TNFR1 Clustering and Signaling Assemblies on Membranes
프로젝트의 국문 제목
막 환경에서 리간드 유도성 TNFα-TNFR1 고차 클러스터링 및 신호전달 복합체 구조 규명
프로젝트의 영문 설명
This project elucidates the two-dimensional, regular higher-order clustering architecture and self-assembly mechanism of TNFR1 induced by ligand (TNFα) binding within a membrane environment. Beyond the conventional 1:3 ligand-receptor stoichiometry, it unveils the molecular principles by which inter-receptor lattice arrays on the cell membrane trigger the downstream signaling complex (Complex I) formation. Furthermore, by uncovering the cluster disassembly mechanism mediated by antagonists, this work provides a crucial structural framework for developing allosteric inhibitors that overcome the limitations of competitive antagonists, paving the way for next-generation therapeutics against autoimmune diseases.
프로젝트의 국문 설명
본 프로젝트는 막 환경에서 리간드(TNFα) 결합에 의해 유도되는 TNFR1의 2차원 규칙적 고차 클러스터링(Higher-order clustering) 구조와 자가조립 메커니즘을 규명합니다. 단순한 1:3 리간드-수용체 결합을 넘어 세포막 상에서 수용체 간 격자(Lattice) 배열이 하위 신호전달 복합체(Complex I) 형성을 촉발하는 분자적 원리를 제시합니다. 나아가 길항제(Antagonist)에 의한 클러스터 해체 기전을 규명하여, 기존 경쟁적 억제제의 한계를 극복하는 알로스테릭 저해제 및 자가면역질환 표적 차세대 신약 개발의 핵심 구조적 기반을 제공합니다.
메타데이터 정보
메타데이터 입력
장비 유형
TEM
Name
김지원
Email address
mokona5@postech.ac.kr
Role assignment
Researcher
Role notation
Sample preparation, Raw data collection, Image analysis, Computational image processing
Contributor
Contributor name
이지오
Contributor email
jieoh@postech.ac.kr
Contributor role assignment
Principal investgator
Contributor role notation
typeOfInstrument
TEM
Representative image data file
Title - English
CryoEM structure of TNFa-TNFR1 bent cluster
Title - Korean
TNFa-TNFR1 굽은 모양 cluster의 CryoEM 구조
Experimental method
Single particle analysis
Raw Data
Data upload
Pixel size
Pixel size
Pixel units
Accelerating Voltage
Working distance
Emission current
Signal type
Stage temperature
Map data
Map data
Select raw data
Annotated data upload
Light micrograph for CLEM
Light micrograph data upload
Light micrograph - Manufacturer and model
Light source type
Objective Magnification
Optical section (Z)
Optical section (Z) thickness
Timelapse (T)
Timelapse (T) fps
Information for channels and target molecules
Data type
Process information
Image format
Image analysis program
Description of the light micrograph for CLEM
Raw Data
Data upload
Pixel size For Data upload
Pixel size
Pixel units
Stage Tilt
Tilt angle (alpha axis)
Tilt angle (beta axis)
EMPIAR ID
Description of the raw data
Map data
Annotated data
Select raw data
Annotated data upload
Description of the annotated data
Light micrograph for CLEM
Light micrograph data upload
Light micrograph - Manufacturer and model
Light source type
Objective Magnification
Optical section (Z)
Optical section (Z) thickness
Timelapse (T)
Timelapse (T) fps
Information for channels and target molecules
Data type
Process information
Image format
Image analysis program
Description of the light micrograph for CLEM
Raw Data
Data upload
Data upload
Pixel size
Pixel size
0.823
Pixel units
Å
Select the raw data type of SPA
Raw multiframe(raw movies)
Stage Tilt
Tilt angle (alpha axis)
Tilt angle (beta axis)
EMPIAR ID
Web database deposition ID
Enter EMDB ID
60489
Enter PDB ID
Description of input data
Map data
Yes
Map data
Upload map data
Pixel size
Pixel size
0.82
Pixel units
Å
Select the map data type
Unsharpened map
Recommended contour level
Resolution at 0.143 FSC
Applied symmetry
Software for reconstruction
Other database id
Enter EMDB ID
Enter PDB ID
Description of map data
Raw Data
Other types of raw data
Data upload
Pixel size
Pixel size
Pixel units
Select the raw data type of SPA
Stage Tilt
Tilt angle (alpha axis)
Tilt angle (beta axis)
EMPIAR ID
Web database deposition ID
Enter EMDB ID
Enter PDB ID
Description of input data
Map data
Map data
Upload map data
Pixel size
Pixel size
Pixel units
Select the map data type
Recommended contour level
Resolution at 0.143 FSC
Helical parameter
Rise value of helical parameter
Twist value of helical parameter
Software for refinement
Other database id
Enter EMDB ID
Enter PDB ID
Description of map data
Raw Data
Upload raw tilt series / serial sectioning data
Annotated data
Select raw data
Pixel size
Pixel size
Pixel units
Tilt series
Minimum angle
Maximum angle
Angle imcrement
Excluded views
Or write manually
Tilt axis (image rotation)
Add fiducial markers
Description of tilt series/ serial sectioning data
EMPIAR ID
Web database deposition ID
Enter EMDB ID
Enter PDB ID
Upload tomogram
Pixel size
Pixel size
Pixel units
Software for reconstruction
Description of tomogram data
Upload labeled data
Pixel size
Pixel size
Pixel units
Software for segmentation
Description of labeled data
Light micrograph for CLEM
Light micrograph data upload
Light micrograph - Manufacturer and model
Light source type
Objective Magnification
Optical section (Z)
Optical section (Z) thickness
Timelapse (T)
Timelapse (T) fps
Information for channels and target molecules
Data type
Process information
Image format
Image analysis program
Description of the light micrograph for CLEM
Raw Data
Upload averaged 3D map data
Pixel size
Pixel size
Pixel units
Recommended contour level
Resolution at 0.143 FSC
Applied symmetry
Software for refinement
Upload raw tilt series
Pixel size
Pixel size
Pixel units
EMPIAR ID
Web database deposition ID
Enter EMDB ID
Enter PDB ID
Description of input data
Annotated data
Select raw data
Tilt series
Minimum angle
Maximum angle
Angle imcrement
Excluded views
Or write manually
Tilt axis (image rotation)
Add fiducial markers
Description of tilt series
Upload tomogram
Pixel size
Pixel size
Pixel units
Software for reconstruction
Description of tomogram data
Upload subtomograms
Pixel size
Pixel size
Pixel units
Upload labeled data
Pixel size
Pixel size
Pixel units
Software for segmentation
Description of labeled data
Light micrograph for CLEM
Light micrograph data upload
Light micrograph - Manufacturer and model
Light source type
Objective Magnification
Optical section (Z)
Optical section (Z) thickness
Timelapse (T)
Timelapse (T) fps
Information for channels and target molecules
Data type
Process information
Image format
Image analysis program
Description of the light micrograph for CLEM
typeOfInstrument
TEM
Category
Sample name
Scientific name
Natural source- Taxonomy ID (NCBI)
Sample Description
Category
Select raw data
Sample type
Sample name
Scientific name
Natural source- Taxonomy ID (NCBI)
Strain
Sample Description
Category
Select raw data
FoilHole_21565443_Data_21550188_21550190_20230721_215756_fractions.tiff
Sample type
Protein etc.
Protein
1 Protein name
TNFa
Number of copies
9
Recombinant protein sequence
Recombinant protein sequence
MVSAIVLYVL LAAAAHSAFA ADPVRSSSRT PSDKPVAHVV ANPQAEGQLQ WLNRRANALL ANGVELRDNQ LVVPSEGLYL IYSQVLFKGQGCPSTHVLLT HTISRIAVSY QTKVNLLSAI KSPCQRETPE GAEAKPWYEP IYLGGVFQLE KGDRLSAEIN RPDYLDFAES GQVYFGIIALEFRSGRLVPR GS
Description of recombinant protein sequence
MVSAIVLYVLLAAAAHSAFAADPVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIALEFRSGRLVPRGS
Total molecular weight of all identical protomers
21 kDa
Natural source
Scientific name
Homo sapiens
Natural source- Taxonomy ID (NCBI)
Strain
Homo sapiens
Expression source
Natural source와 다름
Protein
Organism used for expression
Trichoplusia ni
NCBI Taxonomy ID of expression source
7111
Cell strain of expression source
2 Protein name
TNFR1
Number of copies
9
Recombinant protein sequence
Recombinant protein sequence
MVSAIVLYVL LAAAAHSAFA ADPLVPHLGD REKRDSVCPQ GKYIHPQNNS ICCTKCHKGT YLYNDCPGPG QDTDCRECES GSFTASENHLRHCLSCSKCR KEMGQVEISS CTVDRDTVCG CRKNQYRHYW SENLFQCFNC SLCLNGTVHL SCQEKQNTVC TCHAGFFLRE NECVSCSNCKKSLECTKLCL PQIENVKGTE DSGTTGGGGS HHHHHHHH
Description of recombinant protein sequence
MVSAIVLYVLLAAAAHSAFAADPLVPHLGDREKRDSVCPQGKYIHPQNNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCRKEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLSCQEKQNTVCTCHAGFFLRENECVSCSNCKKSLECTKLCLPQIENVKGTEDSGTTGGGGSHHHHHHHH
Total molecular weight of all identical protomers
24 kDa
Natural source
Scientific name
Homo sapiens
Natural source- Taxonomy ID (NCBI)
Strain
Homo sapiens
Expression source
Natural source와 다름
Protein
Organism used for expression
Trichoplusia ni
NCBI Taxonomy ID of expression source
7111
Cell strain of expression source
Ligand
Name of ligand
Description of ligand
Nucleic acid
Nucleic acid sequence
Description of nucleic acid
Natural source- Sample Description
Name
Scientific Name
Natural source- Taxonomy ID (NCBI)
Sample Description
Type of sample preparation method
Vitrification(for cryo-EM)
Sample preparation method information
Type of fixation
Fixation Infomation
Fixation description
Pre-staining solution formulation
Description of pre-staining procedure
Embedding resin
Resin mixture formulation
Ultra-thin section type
Thickness of section
Depth of serial section
Post-staining solution formulation
Description of post-staining method
Immuno-labeling
Immuno labeling object for fixation
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Fixation Infomation
Vitrification method
Equipment model name for Plunge freezing
Description of Plunge freezing
Equipment model name for high pressure freezing
Cryoprotectant for high pressure freezing
Description of high pressure freezing
Ultramicrotome Type
Equipment name for freeze substitution
Description of freeze substitution
Embedding resin
Resin mixture formulation
Ultra-thin section type
Thickness of section
Depth of serial section
Post-staining solution formulation
Description of post-staining method
Immuno-labeling
Immuno labeling
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Sample preparation method information
Concentration of sample used
Sample concentration
Unit
Applied sample volume
Staining solution
Description of staining
Grid Manufacturer
Grid type
Glow discharge applied
Surface polarity
Surface charge
Atmosphere
Immuno-labeling
Immuno labeling object for fixation
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Sample preparation method information
Vitrification method
Plunge freezing
Vitrification information
Concentration of sample used
Sample concentration
0.1
Unit
mg/mL
Applied sample volume
Plunge freezer manufacturer
Plunge freezer model
Grid Manufacturer
Grid type
Glow discharge applied
No
Surface polarity
Surface charge
Atmosphere
Description of vitrification
lipid monolayer
Immuno-labeling
No
Immuno labeling object for vitrification
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Vitrification information
Method name
Concentration of sample used
Sample concentration
Unit
Applied sample volume
Plunge freezer manufacturer
Plunge freezer model
Grid Manufacturer
Grid type
Glow discharge applied
Surface polarity
Surface charge
Atmosphere
Description of vitrification
Immuno-labeling
Immuno labeling object for vitrification
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Sample preparation method information
Method name
Description of method
Immuno Labeling
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Sputtering
Coat target
Discharge current
Deposition time
Description of sputtering
typeOfInstrument
TEM
typeOfInstrument
TEM
Site
Site of data collection
IMP, POSTECH
Site Address
Imaging Instrument - Manufacturer
Thermo Fisher Scientific(FEI)
Imaging Instrument - Model
Krios G4
Beam Source - Accelerating Voltage
300 kV
Imaging mode
Bright field
Defocus range
Min
Max
Gun type
Gun type
Thermonic emission type
Filed emission type
Related data
KBI
  • 전자현미경 데이터
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