[English] 日本語
Yorodumi
- PDB-5l19: Crystal Structure of a human FasL mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l19
TitleCrystal Structure of a human FasL mutant
ComponentsTumor necrosis factor ligand superfamily member 6
KeywordsAPOPTOSIS / FasL / CD95L / TNF ligand
Function / homology
Function and homology information


positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / release of sequestered calcium ion into cytosol by endoplasmic reticulum / cytoplasmic vesicle lumen / FasL/ CD95L signaling / intracellular chloride ion homeostasis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / endosomal lumen acidification ...positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / release of sequestered calcium ion into cytosol by endoplasmic reticulum / cytoplasmic vesicle lumen / FasL/ CD95L signaling / intracellular chloride ion homeostasis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / endosomal lumen acidification / Caspase activation via Death Receptors in the presence of ligand / T cell apoptotic process / response to growth factor / necroptotic signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / RIPK1-mediated regulated necrosis / necroptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / FOXO-mediated transcription of cell death genes / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of endothelial cell apoptotic process / extrinsic apoptotic signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / lysosomal lumen / negative regulation of angiogenesis / cytokine activity / apoptotic signaling pathway / cellular response to type II interferon / caveola / positive regulation of neuron apoptotic process / cell-cell signaling / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / signaling receptor binding / apoptotic process / positive regulation of cell population proliferation / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / DNA-templated transcription / : / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 6 / 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 / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily ...Tumor necrosis factor ligand superfamily member 6 / 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 / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, W. / Bonanno, J.B. / Almo, S.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094665 United States
Albert Einstein Cancer CenterP30CA013330 United States
CitationJournal: Structure / Year: 2016
Title: Crystal Structure of the Complex of Human FasL and Its Decoy Receptor DcR3.
Authors: Liu, W. / Ramagopal, U. / Cheng, H. / Bonanno, J.B. / Toro, R. / Bhosle, R. / Zhan, C. / Almo, S.C.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 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 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6113
Polymers17,4491
Non-polymers1612
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.690, 52.690, 87.385
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

21A-461-

HOH

-
Components

#1: Protein Tumor necrosis factor ligand superfamily member 6 / Apoptosis antigen ligand / APTL / CD95 ligand / CD95-L / Fas antigen ligand / FasL


Mass: 17449.154 Da / Num. of mol.: 1 / Fragment: UNP residues 130-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FASLG, APT1LG1, CD95L, FASL, TNFSF6
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1_S (others)
References: UniProt: P48023
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris:HCl, pH6.5, 20% (W/V) PEG3350, 0.01M Zinc Chloride

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9993 / % possible obs: 99.4 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.834 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLMdata reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MSV

4msv


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.424 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21602 521 5.2 %RANDOM
Rwork0.16512 ---
obs0.16775 9414 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.48 Å20 Å2
2---0.95 Å2-0 Å2
3---3.1 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 6 61 1243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191211
X-RAY DIFFRACTIONr_bond_other_d0.0060.021125
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9621636
X-RAY DIFFRACTIONr_angle_other_deg1.11132587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3415149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00223.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19815205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.23155
X-RAY DIFFRACTIONr_chiral_restr0.1280.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6852.448599
X-RAY DIFFRACTIONr_mcbond_other2.6782.447598
X-RAY DIFFRACTIONr_mcangle_it4.2783.654747
X-RAY DIFFRACTIONr_mcangle_other4.2763.654748
X-RAY DIFFRACTIONr_scbond_it3.9532.647611
X-RAY DIFFRACTIONr_scbond_other3.9212.628608
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2913.814884
X-RAY DIFFRACTIONr_long_range_B_refined8.1918.6411303
X-RAY DIFFRACTIONr_long_range_B_other8.11318.5911292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 44 -
Rwork0.221 675 -
obs--96.64 %

+
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