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- PDB-9v9c: Cryo-EM structure of human TNFR1 DD filament -

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Basic information

Entry
Database: PDB / ID: 9v9c
TitleCryo-EM structure of human TNFR1 DD filament
ComponentsTumor necrosis factor receptor superfamily member 1A, membrane form
KeywordsPROTEIN FIBRIL / Death doamin
Function / homology
Function and homology information


: / pulmonary valve development / tumor necrosis factor receptor superfamily complex / aortic valve development / : / negative regulation of extracellular matrix constituent secretion / tumor necrosis factor receptor activity / positive regulation of apoptotic process involved in morphogenesis / TNFs bind their physiological receptors / tumor necrosis factor binding ...: / pulmonary valve development / tumor necrosis factor receptor superfamily complex / aortic valve development / : / negative regulation of extracellular matrix constituent secretion / tumor necrosis factor receptor activity / positive regulation of apoptotic process involved in morphogenesis / TNFs bind their physiological receptors / tumor necrosis factor binding / negative regulation of cardiac muscle hypertrophy / TNF signaling / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-induced proapoptotic signaling / TNFR1-mediated ceramide production / prostaglandin metabolic process / positive regulation of lipid metabolic process / Interleukin-10 signaling / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / cell surface receptor signaling pathway via JAK-STAT / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / negative regulation of canonical NF-kappaB signal transduction / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / negative regulation of inflammatory response / intrinsic apoptotic signaling pathway in response to DNA damage / cytokine-mediated signaling pathway / protein polyubiquitination / positive regulation of inflammatory response / signaling receptor activity / transcription by RNA polymerase II / positive regulation of canonical NF-kappaB signal transduction / signaling receptor complex / defense response to bacterium / membrane raft / inflammatory response / Golgi membrane / cell surface / positive regulation of transcription by RNA polymerase II / : / extracellular region / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. ...Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsZhao, K. / Liu, J.P. / Liu, C. / Yuan, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2026
Title: Electric dipole moment drives the dynamics of the TNFR1 complex I signalosome
Authors: Zhao, K. / Liu, J.P. / Liu, C. / Yuan, J.Y.
History
DepositionMay 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 1A, membrane form
B: Tumor necrosis factor receptor superfamily member 1A, membrane form
C: Tumor necrosis factor receptor superfamily member 1A, membrane form
D: Tumor necrosis factor receptor superfamily member 1A, membrane form
E: Tumor necrosis factor receptor superfamily member 1A, membrane form
F: Tumor necrosis factor receptor superfamily member 1A, membrane form
I: Tumor necrosis factor receptor superfamily member 1A, membrane form
L: Tumor necrosis factor receptor superfamily member 1A, membrane form
O: Tumor necrosis factor receptor superfamily member 1A, membrane form
R: Tumor necrosis factor receptor superfamily member 1A, membrane form
G: Tumor necrosis factor receptor superfamily member 1A, membrane form
J: Tumor necrosis factor receptor superfamily member 1A, membrane form
M: Tumor necrosis factor receptor superfamily member 1A, membrane form
P: Tumor necrosis factor receptor superfamily member 1A, membrane form
S: Tumor necrosis factor receptor superfamily member 1A, membrane form
H: Tumor necrosis factor receptor superfamily member 1A, membrane form
K: Tumor necrosis factor receptor superfamily member 1A, membrane form
N: Tumor necrosis factor receptor superfamily member 1A, membrane form
Q: Tumor necrosis factor receptor superfamily member 1A, membrane form
T: Tumor necrosis factor receptor superfamily member 1A, membrane form


Theoretical massNumber of molelcules
Total (without water)260,71820
Polymers260,71820
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Tumor necrosis factor receptor superfamily member 1A, membrane form


Mass: 13035.875 Da / Num. of mol.: 20 / Fragment: TNFR1 death domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF1A, TNFAR, TNFR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19438
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: TNFR1 DD filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.15.2_3472 / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 138.364 ° / Axial rise/subunit: 5.30557 Å / Axial symmetry: C1
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 512379 / Symmetry type: HELICAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00814580
ELECTRON MICROSCOPYf_angle_d0.72219700
ELECTRON MICROSCOPYf_dihedral_angle_d16.6679080
ELECTRON MICROSCOPYf_chiral_restr0.0512200
ELECTRON MICROSCOPYf_plane_restr0.0052580

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