[English] 日本語
Yorodumi
- PDB-1l0a: DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l0a
TitleDOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3
Components
  • TNF receptor associated factor 3
  • TRAF family member-associated NF-kappa-b activator
KeywordsSIGNALING PROTEIN / CD40 / NF-kB signaling / TANK / TNF receptor / TRAF3
Function / homology
Function and homology information


regulation of interferon-beta production / positive regulation of protein deubiquitination / TRAF3 deficiency - HSE / positive regulation of ubiquitin-specific protease activity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / serine/threonine protein kinase complex ...regulation of interferon-beta production / positive regulation of protein deubiquitination / TRAF3 deficiency - HSE / positive regulation of ubiquitin-specific protease activity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / 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 / deubiquitinase activator activity / regulation of canonical NF-kappaB signal transduction / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / molecular function inhibitor activity / toll-like receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / type I interferon-mediated signaling pathway / regulation of proteolysis / cellular response to interleukin-1 / positive regulation of type I interferon production / ubiquitin ligase complex / negative regulation of tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / 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) / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / cellular response to tumor necrosis factor / ubiquitin protein ligase activity / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / protein phosphatase binding / regulation of apoptotic process / defense response to virus / molecular adaptor activity / cell surface receptor signaling pathway / endosome membrane / endosome / apoptotic process / DNA damage response / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / protein-containing complex / mitochondrion / zinc ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
TRAF family member-associated NF-kappa-B activator / Tbk1/Ikki binding domain / TBD domain / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / TRAF-type zinc finger ...TRAF family member-associated NF-kappa-B activator / Tbk1/Ikki binding domain / TBD domain / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / 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 / 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
TNF receptor-associated factor 3 / TRAF family member-associated NF-kappa-B activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, C. / Ni, C.-Z. / Havert, M.L. / Cabezas, E. / He, J. / Kaiser, D. / Reed, J.C. / Satterthwait, A.C. / Cheng, G. / Ely, K.R.
CitationJournal: Structure / Year: 2002
Title: Downstream regulator TANK binds to the CD40 recognition site on TRAF3.
Authors: Li, C. / Ni, C.Z. / Havert, M.L. / Cabezas, E. / He, J. / Kaiser, D. / Reed, J.C. / Satterthwait, A.C. / Cheng, G. / Ely, K.R.
History
DepositionFeb 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 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 1.5Feb 14, 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
B: TRAF family member-associated NF-kappa-b activator


Theoretical massNumber of molelcules
Total (without water)23,8872
Polymers23,8872
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-10 kcal/mol
Surface area11800 Å2
MethodPISA
2
A: TNF receptor associated factor 3
B: TRAF family member-associated NF-kappa-b activator

A: TNF receptor associated factor 3
B: TRAF family member-associated NF-kappa-b activator

A: TNF receptor associated factor 3
B: TRAF family member-associated NF-kappa-b activator


Theoretical massNumber of molelcules
Total (without water)71,6626
Polymers71,6626
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area13860 Å2
ΔGint-77 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.000, 83.000, 76.700
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 / TRAF3 / CD40 receptor associated factor 1 / CRAF1 / CD40 binding protein / CD40BP


Mass: 21833.135 Da / Num. of mol.: 1 / Fragment: Residues 377-568 / Mutation: T195K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13114
#2: Protein/peptide TRAF family member-associated NF-kappa-b activator / TANK / TRAF-interacting protein / I-TRAF


Mass: 2054.343 Da / Num. of mol.: 1 / Fragment: Residues 178-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q92844
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100mM MES, 15% PEG1000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: unpublished data

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 7076 / Num. obs: 7042 / % possible obs: 99.5 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 5.5 % / % possible all: 100
Reflection
*PLUS
Num. obs: 7263 / Num. measured all: 38649 / Rmerge(I) obs: 0.08

-
Processing

Software
NameVersionClassification
CNSrefinement
MAR345data collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 386 -random
Rwork0.23 ---
all-7076 --
obs-7042 99.5 %-
Displacement parametersBiso mean: 37.3 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 0 28 1703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.42
Refinement
*PLUS
Rfactor obs: 0.23 / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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