[English] 日本語
Yorodumi
- PDB-7kp7: asymmetric mTNF-alpha hTNFR1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kp7
Titleasymmetric mTNF-alpha hTNFR1 complex
Components
  • Tumor necrosis factor
  • Tumor necrosis factor receptor superfamily member 1A
KeywordsCYTOKINE / Tumour necrosis factor alpha / TNF / Receptor / TNFR1 / asymmetric / protein-protein inhibitor
Function / homology
Function and homology information


negative regulation of alkaline phosphatase activity / TNF signaling / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of L-glutamate import across plasma membrane / cellular extravasation ...negative regulation of alkaline phosphatase activity / TNF signaling / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of L-glutamate import across plasma membrane / cellular extravasation / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / Regulation of TNFR1 signaling / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / aortic valve development / tumor necrosis factor receptor activity / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of lipid metabolic process / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / negative regulation of extracellular matrix constituent secretion / response to macrophage colony-stimulating factor / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / positive regulation of apoptotic process involved in morphogenesis / TNFR2 non-canonical NF-kB pathway / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / response to 3,3',5-triiodo-L-thyronine / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / negative regulation of myelination / negative regulation of bicellular tight junction assembly / TNFs bind their physiological receptors / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / tumor necrosis factor binding / negative regulation of amyloid-beta clearance / response to isolation stress / positive regulation of action potential / inflammatory response to wounding / positive regulation of interleukin-18 production / death receptor agonist activity / positive regulation of protein transport / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / negative regulation of cardiac muscle hypertrophy / regulation of osteoclast differentiation / toll-like receptor 3 signaling pathway / embryonic digestive tract development / vascular endothelial growth factor production / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / response to fructose / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / leukocyte tethering or rolling / positive regulation of fever generation / negative regulation of myoblast differentiation / cellular response to toxic substance / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of D-glucose import / negative regulation of oxidative phosphorylation / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of protein-containing complex disassembly / negative regulation of systemic arterial blood pressure / positive regulation of heterotypic cell-cell adhesion / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage derived foam cell differentiation / regulation of immunoglobulin production / TNFR1-mediated ceramide production / positive regulation of hepatocyte proliferation / 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 / positive regulation of podosome assembly / TNFR1-induced proapoptotic signaling / regulation of metabolic process / regulation of reactive oxygen species metabolic process / prostaglandin metabolic process / negative regulation of heart rate / positive regulation of amyloid-beta formation / leukocyte migration / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / response to L-glutamate / regulation of protein secretion / negative regulation of fat cell differentiation
Similarity search - Function
Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / 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 receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / 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 / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor-like domain superfamily / 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 / Tumor necrosis factor receptor superfamily member 1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsArakaki, T.L. / Fox III, D. / Edwards, T.E. / Foley, A. / Ceska, T.
CitationJournal: Nat Commun / Year: 2021
Title: Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF.
Authors: McMillan, D. / Martinez-Fleites, C. / Porter, J. / Fox 3rd, D. / Davis, R. / Mori, P. / Ceska, T. / Carrington, B. / Lawson, A. / Bourne, T. / O'Connell, J.
History
DepositionNov 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Tumor necrosis factor
A: Tumor necrosis factor
C: Tumor necrosis factor
E: Tumor necrosis factor receptor superfamily member 1A
D: Tumor necrosis factor receptor superfamily member 1A
F: Tumor necrosis factor receptor superfamily member 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,81141
Polymers97,8236
Non-polymers3,98835
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19710 Å2
ΔGint-385 kcal/mol
Surface area39610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.220, 139.220, 138.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

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


Mass: 16411.596 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnf, Tnfa, Tnfsf2 / Plasmid: pEMB54 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P06804
#2: Protein Tumor necrosis factor receptor superfamily member 1A / Tumor necrosis factor receptor 1 / TNF-R1 / Tumor necrosis factor receptor type I / TNFR-I / p55 / p60


Mass: 16196.158 Da / Num. of mol.: 3 / Mutation: N25D, C153S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF1A, TNFAR, TNFR1 / Plasmid: pEMB50 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19438
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.0M Ammonium sulfate, 0.1M BisTris pH5.5, and cryo-protected with paraffin oil; Vapor diffusion, sitting drop, temperature 289K.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2014
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 43935 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.98
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 3238 / % possible all: 99.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.16 Å49.07 Å
Translation8.16 Å49.07 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished structure

Resolution: 2.65→49.07 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.446 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2045 4.7 %RANDOM
Rwork0.193 41890 --
obs0.195 43935 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.464 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å2-0 Å2
2--0.45 Å2-0 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6486 0 225 225 6936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196875
X-RAY DIFFRACTIONr_bond_other_d0.0050.026016
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9799397
X-RAY DIFFRACTIONr_angle_other_deg0.941313847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22524.832298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.237151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8521524
X-RAY DIFFRACTIONr_chiral_restr0.070.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217803
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021572
X-RAY DIFFRACTIONr_mcbond_it3.24.8083426
X-RAY DIFFRACTIONr_mcbond_other3.24.8073425
X-RAY DIFFRACTIONr_mcangle_it4.967.1974273
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 134 -
Rwork0.33 3086 -
all-3220 -
obs--99.44 %

+
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