[English] 日本語
Yorodumi
- EMDB-60486: Cluster structure of the BAFF-BAFFR-TRAF3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60486
TitleCluster structure of the BAFF-BAFFR-TRAF3 complex
Map data
Sample
  • Complex: Cluster structure of the BAFF-BAFFR-TRAF3 complex
    • Protein or peptide: TNF receptor-associated factor 3
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 13C
KeywordsReceptor cluster / Signal complex / membrane receptor / IMMUNE SYSTEM
Function / homology
Function and homology information


B cell costimulation / regulation of interferon-beta production / TRAF3 deficiency - HSE / 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 ...B cell costimulation / regulation of interferon-beta production / TRAF3 deficiency - HSE / 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 / regulation of canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / toll-like receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / regulation of proteolysis / positive regulation of type I interferon production / ubiquitin ligase complex / positive regulation of T cell proliferation / tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / positive regulation of B cell proliferation / T cell costimulation / 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 / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / signaling receptor activity / TRAF3-dependent IRF activation pathway / protein phosphatase binding / regulation of apoptotic process / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / endosome / endosome membrane / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / mitochondrion / zinc ion binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / Tumor necrosis factor receptor 13C/17 / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa ...Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / Tumor necrosis factor receptor 13C/17 / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / 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
Similarity search - Domain/homology
TNF receptor-associated factor 3 / Tumor necrosis factor receptor superfamily member 13C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsLim CS / Lee JO
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: To Be Published
Title: Ordered clustering of TNF and BAFF ligand-receptor-adaptor complexes attached to an artificial lipid membrane
Authors: Lim CS / Lee JO
History
DepositionJun 9, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60486.png

Downloads & links

-
Map

FileDownload / File: emd_60486.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.222
Minimum - Maximum-0.004323417 - 1.8643266
Average (Standard dev.)0.002063532 (±0.030712537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60486_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60486_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cluster structure of the BAFF-BAFFR-TRAF3 complex

EntireName: Cluster structure of the BAFF-BAFFR-TRAF3 complex
Components
  • Complex: Cluster structure of the BAFF-BAFFR-TRAF3 complex
    • Protein or peptide: TNF receptor-associated factor 3
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 13C

-
Supramolecule #1: Cluster structure of the BAFF-BAFFR-TRAF3 complex

SupramoleculeName: Cluster structure of the BAFF-BAFFR-TRAF3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: TNF receptor-associated factor 3

MacromoleculeName: TNF receptor-associated factor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.444441 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSNSLEKKVS LLQNESVEKN KSIQSLHNQI CSFEIEIERQ KEMLRNNESK ILHLQRVIDS QAEKLKELDK EIRPFRQNWE EADSMKSSV ESLQNRVTEL ESVDKSAGQV ARNTGLLESQ LSRHDQMLSV HDIRLADMDL RFQVLETASY NGVLIWKIRD Y KRRKQEAV ...String:
MSNSLEKKVS LLQNESVEKN KSIQSLHNQI CSFEIEIERQ KEMLRNNESK ILHLQRVIDS QAEKLKELDK EIRPFRQNWE EADSMKSSV ESLQNRVTEL ESVDKSAGQV ARNTGLLESQ LSRHDQMLSV HDIRLADMDL RFQVLETASY NGVLIWKIRD Y KRRKQEAV MGKTLSLYSQ PFYTGYFGYK MCARVYLNGD GMGKGTHLSL FFVIMRGEYD ALLPWPFKQK VTLMLMDQGS SR RHLGDAF KPDPNSSSFK KPTGEMNIAS GCPVFVAQTV LENGTYIKDD TIFIKVIVDT SDLPDPGGSL VPR

UniProtKB: TNF receptor-associated factor 3

-
Macromolecule #2: Tumor necrosis factor receptor superfamily member 13C

MacromoleculeName: Tumor necrosis factor receptor superfamily member 13C / type: protein_or_peptide / ID: 2 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.902789 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ ESVGAGAGEA ALPLPGLLFG APALLGLAL VLALVLVGLV SWRRRQRRLR GASSAEAPDG DKDAPEPLDK VIILSPGISD ATAPAWPPPG EDPGTTPPGH S VPVPATEL ...String:
MRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ ESVGAGAGEA ALPLPGLLFG APALLGLAL VLALVLVGLV SWRRRQRRLR GASSAEAPDG DKDAPEPLDK VIILSPGISD ATAPAWPPPG EDPGTTPPGH S VPVPATEL GSTELVTTKT AGPEQQSNSL EVLFQ

UniProtKB: Tumor necrosis factor receptor superfamily member 13C

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205165
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

8t5p

source_name: PDB, initial_model_type: experimental model

2gkw

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8zuk:
Cluster structure of the BAFF-BAFFR-TRAF3 complex

+
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