[English] 日本語
Yorodumi
- PDB-9jec: Cryo-EM structure of canine TNF-alpha complexed with nanobody TNF30K -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jec
TitleCryo-EM structure of canine TNF-alpha complexed with nanobody TNF30K
Components
  • Tumor necrosis factor
  • nanobody TNF30K
KeywordsCYTOKINE / canine / TNF / nanobody / lymphokine
Function / homology
Function and homology information


TNFR1-induced proapoptotic signaling / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / TNFR1-mediated ceramide production / TNFR2 non-canonical NF-kB pathway / TNF signaling / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus ...TNFR1-induced proapoptotic signaling / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / TNFR1-mediated ceramide production / TNFR2 non-canonical NF-kB pathway / TNF signaling / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of protein transport / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / negative regulation of vascular wound healing / negative regulation of cytokine production involved in immune response / negative regulation of amyloid-beta clearance / inflammatory response to wounding / death receptor agonist activity / epithelial cell proliferation involved in salivary gland morphogenesis / embryonic digestive tract development / negative regulation of D-glucose import / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / necroptotic signaling pathway / leukocyte tethering or rolling / negative regulation of myoblast differentiation / positive regulation of protein-containing complex disassembly / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / regulation of immunoglobulin production / negative regulation of mitotic cell cycle / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of bicellular tight junction assembly / regulation of reactive oxygen species metabolic process / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / regulation of synapse organization / negative regulation of endothelial cell proliferation / positive regulation of JUN kinase activity / positive regulation of MAP kinase activity / negative regulation of interleukin-6 production / humoral immune response / negative regulation of blood vessel endothelial cell migration / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of osteoblast differentiation / positive regulation of synaptic transmission / phagocytic cup / negative regulation of lipid catabolic process / positive regulation of vascular associated smooth muscle cell proliferation / JNK cascade / extracellular matrix organization / antiviral innate immune response / regulation of insulin secretion / response to glucocorticoid / osteoclast differentiation / positive regulation of interleukin-1 beta production / cytokine activity / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / positive regulation of interleukin-8 production / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / positive regulation of JNK cascade / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / recycling endosome / cellular response to type II interferon / cellular response to nicotine / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / positive regulation of type II interferon production / positive regulation of protein phosphorylation / glucose metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process
Similarity search - Function
Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWeng, J. / Li, Z. / Xu, J. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000032 China
Other governmentSKLBEE2022007
CitationJournal: To Be Published
Title: Cryo-EM structure of canine TNF-alpha complexed with nanobody TNF30K
Authors: Weng, J. / Li, Z. / Xu, J. / Wei, Z.
History
DepositionSep 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor necrosis factor
B: Tumor necrosis factor
C: Tumor necrosis factor
D: nanobody TNF30K
E: nanobody TNF30K
F: nanobody TNF30K


Theoretical massNumber of molelcules
Total (without water)100,7616
Polymers100,7616
Non-polymers00
Water00
1


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

-
Components

#1: Protein Tumor necrosis factor / Cachectin / TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a


Mass: 19123.730 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: TNF, TNFA, TNFSF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P51742
#2: Antibody nanobody TNF30K


Mass: 14463.364 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Hexamer complex of canine TNF-alpha and nanobody TNF30K
Type: COMPLEX
Details: a hexamer complex consist of one canine TNF-alpha trimer with three nanobody TNF30K molecules
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.01 MDa / Experimental value: NO
Source (natural)Organism: Canis lupus familiaris (dog)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.4
Details: 10 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 2.7 mM KCl, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mmol/LDisodium hydrogen phosphateNa2HPO41
21.8 mmol/LPotassium dihydrogen phosphateKH2PO41
3137 mmol/Lsodium chlorideNaCl1
42.7 mmol/Lpotassium chlorideKCl1
SpecimenConc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was FPLC purified and monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 543326 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 104.38 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00556120
ELECTRON MICROSCOPYf_angle_d0.63658313
ELECTRON MICROSCOPYf_chiral_restr0.0468921
ELECTRON MICROSCOPYf_plane_restr0.00431068
ELECTRON MICROSCOPYf_dihedral_angle_d4.4566837

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more