[English] 日本語
Yorodumi
- PDB-3mi8: The structure of TL1A-DCR3 COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mi8
TitleThe structure of TL1A-DCR3 COMPLEX
Components
  • TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
  • Tumor necrosis factor receptor superfamily member 6B
KeywordsIMMUNE SYSTEM / DCR3 / TL1A / TNF / TNFR / DECOY RECEPTOR / IMMUNITY / DISULFIDE BOND / GLYCOPROTEIN / SECRETED / RECEPTOR
Function / homology
Function and homology information


TNFs bind their physiological receptors / activation of NF-kappaB-inducing kinase activity / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / cytokine activity / signaling receptor activity / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / immune response / signaling receptor binding ...TNFs bind their physiological receptors / activation of NF-kappaB-inducing kinase activity / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / cytokine activity / signaling receptor activity / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / immune response / signaling receptor binding / apoptotic process / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Tumor necrosis factor receptor 6B, N-terminal / : / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. ...Tumor necrosis factor receptor 6B, N-terminal / : / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / Jelly Rolls - #40 / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 15 / Tumor necrosis factor receptor superfamily member 6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.951 Å
AuthorsZhan, C. / Patskovsky, Y. / Yan, Q. / Li, Z. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Structure / Year: 2011
Title: Decoy Strategies: The Structure of TL1A:DcR3 Complex.
Authors: Zhan, C. / Patskovsky, Y. / Yan, Q. / Li, Z. / Ramagopal, U. / Cheng, H. / Brenowitz, M. / Hui, X. / Nathenson, S.G. / Almo, S.C.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
D: Tumor necrosis factor receptor superfamily member 6B


Theoretical massNumber of molelcules
Total (without water)40,1822
Polymers40,1822
Non-polymers00
Water724
1
A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
D: Tumor necrosis factor receptor superfamily member 6B

A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
D: Tumor necrosis factor receptor superfamily member 6B

A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
D: Tumor necrosis factor receptor superfamily member 6B


Theoretical massNumber of molelcules
Total (without water)120,5476
Polymers120,5476
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11720 Å2
ΔGint-55 kcal/mol
Surface area35790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.080, 161.080, 161.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

-
Components

#1: Protein TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM / VASCULAR ENDOTHELIAL CELL GROWTH INHIBITOR / TNF LIGAND-RELATED MOLECULE 1 / TUMOR NECROSIS FACTOR ...VASCULAR ENDOTHELIAL CELL GROWTH INHIBITOR / TNF LIGAND-RELATED MOLECULE 1 / TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15 / MEMBRANE FORM / TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15 / SECRETED FORM


Mass: 20893.684 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-251 / Mutation: C135S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TL1, TNFSF15, VEGI / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: O95150
#2: Protein Tumor necrosis factor receptor superfamily member 6B / Decoy receptor for Fas ligand / Decoy receptor 3 / DcR3 / M68


Mass: 19288.488 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DcR3, TNFRSF6B / Plasmid: PMT/BIP/V5-HIS / Cell line (production host): S2 / Production host: DROSOPHILA (fruit flies) / References: UniProt: O95407
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.33 Å3/Da / Density % sol: 71.62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.4M K/Na tartrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 15595 / Num. obs: 15595 / Redundancy: 20.9 % / Biso Wilson estimate: 91.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 36.6
Reflection shellResolution: 2.95→3 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 3.9 / Num. unique all: 767

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3K51

3k51


Resolution: 2.951→25.16 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.413 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26096 764 5 %RANDOM
Rwork0.23225 ---
obs0.23367 14621 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 84.694 Å2
Refinement stepCycle: LAST / Resolution: 2.951→25.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 0 4 1964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222020
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9412753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68923.07791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96615299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0781514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211565
X-RAY DIFFRACTIONr_mcbond_it2.72121265
X-RAY DIFFRACTIONr_mcangle_it4.89832033
X-RAY DIFFRACTIONr_scbond_it6.094755
X-RAY DIFFRACTIONr_scangle_it9.4916720
LS refinement shellResolution: 2.951→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 66 -
Rwork0.321 1048 -
obs--99.73 %

+
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