[English] 日本語
Yorodumi
- PDB-1fll: MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fll
TitleMOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3
Components
  • B-CELL SURFACE ANTIGEN CD40
  • TNF RECEPTOR ASSOCIATED FACTOR 3
KeywordsAPOPTOSIS / TRAF3 WITH CD40 PEPTIDE / TNF SIGNALING
Function / homology
Function and homology information


positive regulation of protein kinase C signaling / cellular response to erythropoietin / regulation of interferon-beta production / varicosity / TRAF3 deficiency - HSE / B cell mediated immunity / positive regulation of interleukin-4-mediated signaling pathway / immune response-regulating cell surface receptor signaling pathway / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway ...positive regulation of protein kinase C signaling / cellular response to erythropoietin / regulation of interferon-beta production / varicosity / TRAF3 deficiency - HSE / B cell mediated immunity / positive regulation of interleukin-4-mediated signaling pathway / immune response-regulating cell surface receptor signaling pathway / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / positive regulation of isotype switching to IgG isotypes / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / serine/threonine protein kinase complex / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / toll-like receptor signaling pathway / defense response to protozoan / response to cobalamin / negative regulation of NF-kappaB transcription factor activity / B cell activation / B cell proliferation / regulation of proteolysis / cellular response to interleukin-1 / response to type II interferon / positive regulation of endothelial cell apoptotic process / cell surface receptor signaling pathway via JAK-STAT / positive regulation of blood vessel endothelial cell migration / positive regulation of type I interferon production / ubiquitin ligase complex / antigen binding / tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / regulation of cytokine production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / RING-type E3 ubiquitin transferase / platelet activation / cytoplasmic side of plasma membrane / intracellular calcium ion homeostasis / cellular response to mechanical stimulus / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / cellular response to tumor necrosis factor / signaling receptor activity / TRAF3-dependent IRF activation pathway / cellular response to lipopolysaccharide / protein-containing complex assembly / protein phosphatase binding / regulation of apoptotic process / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / positive regulation of MAPK cascade / endosome / endosome membrane / inflammatory response / protein domain specific binding / external side of plasma membrane / neuronal cell body / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / zinc ion binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TNF receptor-associated factor 3 / TRAF3, MATH domain / Tumour necrosis factor receptor 5 / Tumour necrosis factor receptor 5, N-terminal / : / : / TNF receptor-associated factor 2/3/5, RING domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : ...TNF receptor-associated factor 3 / TRAF3, MATH domain / Tumour necrosis factor receptor 5 / Tumour necrosis factor receptor 5, N-terminal / : / : / TNF receptor-associated factor 2/3/5, RING domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / 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 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 5 / TNF receptor-associated factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsNi, C.-Z. / Welsh, K. / Leo, E. / Chiou, C.-K. / Wu, H. / Reed, J.C. / Ely, K.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Molecular basis for CD40 signaling mediated by TRAF3.
Authors: Ni, C.Z. / Welsh, K. / Leo, E. / Chiou, C.K. / Wu, H. / Reed, J.C. / Ely, K.R.
History
DepositionAug 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TNF RECEPTOR ASSOCIATED FACTOR 3
X: B-CELL SURFACE ANTIGEN CD40
B: TNF RECEPTOR ASSOCIATED FACTOR 3
Y: B-CELL SURFACE ANTIGEN CD40


Theoretical massNumber of molelcules
Total (without water)56,1624
Polymers56,1624
Non-polymers00
Water00
1
A: TNF RECEPTOR ASSOCIATED FACTOR 3
X: B-CELL SURFACE ANTIGEN CD40


Theoretical massNumber of molelcules
Total (without water)28,0812
Polymers28,0812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TNF RECEPTOR ASSOCIATED FACTOR 3
Y: B-CELL SURFACE ANTIGEN CD40


Theoretical massNumber of molelcules
Total (without water)28,0812
Polymers28,0812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-7 kcal/mol
Surface area14590 Å2
MethodPISA
3
B: TNF RECEPTOR ASSOCIATED FACTOR 3
Y: B-CELL SURFACE ANTIGEN CD40

B: TNF RECEPTOR ASSOCIATED FACTOR 3
Y: B-CELL SURFACE ANTIGEN CD40

B: TNF RECEPTOR ASSOCIATED FACTOR 3
Y: B-CELL SURFACE ANTIGEN CD40


Theoretical massNumber of molelcules
Total (without water)84,2436
Polymers84,2436
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11180 Å2
ΔGint-75 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.760, 83.760, 212.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein TNF RECEPTOR ASSOCIATED FACTOR 3


Mass: 25885.521 Da / Num. of mol.: 2 / Fragment: TRAF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / References: UniProt: Q13114
#2: Protein/peptide B-CELL SURFACE ANTIGEN CD40


Mass: 2195.341 Da / Num. of mol.: 2 / Fragment: CD40 (246-266) PEPTIDE / Mutation: N246K, C258S / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS)
References: UniProt: P25942

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: unknown

-
Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 29115 / % possible obs: 78.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 14
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.26 / % possible all: 74.5
Reflection shell
*PLUS
% possible obs: 74.5 %

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.5→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.312 351 -RANDOM
Rwork0.173 ---
obs0.173 7586 72.6 %-
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 0 0 3558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

+
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