[English] 日本語
Yorodumi
- PDB-5wqt: Structure of a protein involved in pyroptosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wqt
TitleStructure of a protein involved in pyroptosis
ComponentsGasdermin-D
KeywordsSIGNALING PROTEIN / pyrtosis
Function / homology
Function and homology information


pore complex assembly / : / Release of apoptotic factors from the mitochondria / wide pore channel activity / NLRP3 inflammasome complex / cardiolipin binding / Regulation of TLR by endogenous ligand / phosphatidic acid binding / Interleukin-1 processing / phosphatidylinositol-4-phosphate binding ...pore complex assembly / : / Release of apoptotic factors from the mitochondria / wide pore channel activity / NLRP3 inflammasome complex / cardiolipin binding / Regulation of TLR by endogenous ligand / phosphatidic acid binding / Interleukin-1 processing / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / protein secretion / Pyroptosis / Purinergic signaling in leishmaniasis infection / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-1 beta production / mitochondrial membrane / protein homooligomerization / positive regulation of inflammatory response / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain
Similarity search - Domain/homology
CITRIC ACID / Gasdermin-D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsKuang, S. / Li, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis.
Authors: Kuang, S. / Zheng, J. / Yang, H. / Li, S. / Duan, S. / Shen, Y. / Ji, C. / Gan, J. / Xu, X.W. / Li, J.
History
DepositionNov 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Nov 8, 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gasdermin-D
B: Gasdermin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6857
Polymers45,0242
Non-polymers6615
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.886, 86.165, 112.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 22511.994 Da / Num. of mol.: 2 / Fragment: C-terminal (UNP RESIDUES 276-484)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMD, DFNA5L, GSDMDC1, FKSG10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P57764
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7
Details: 20mM Sodium bromide, 0.1M Hepes sodium pH7.0, 1.5M Sodium citrate tribasic dihydrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.64→68.33 Å / Num. obs: 13984 / % possible obs: 98 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.194 / Rsym value: 0.194 / Net I/σ(I): 13.25
Reflection shellResolution: 2.64→2.7 Å / Redundancy: 6 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 2.22 / CC1/2: 0.911 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B5R

5b5r


Resolution: 2.64→68.33 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.791 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R: 0.912 / ESU R Free: 0.364 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 708 5.1 %RANDOM
Rwork0.23544 ---
obs0.238 13276 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.198 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å20 Å2-0 Å2
2--2.77 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.64→68.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 44 38 2959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192961
X-RAY DIFFRACTIONr_bond_other_d0.0020.022871
X-RAY DIFFRACTIONr_angle_refined_deg1.4172.0314034
X-RAY DIFFRACTIONr_angle_other_deg0.96136632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18326.381105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13715444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3191510
X-RAY DIFFRACTIONr_chiral_restr0.0680.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213324
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02542
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_it2.5425.0631579
X-RAY DIFFRACTIONr_mcbond_other2.5275.0611578
X-RAY DIFFRACTIONr_mcangle_it4.1937.5751965
X-RAY DIFFRACTIONr_mcangle_other4.1937.5781966
X-RAY DIFFRACTIONr_scbond_it2.5915.3341382
X-RAY DIFFRACTIONr_scbond_other2.5855.3281380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3417.8952069
X-RAY DIFFRACTIONr_long_range_B_refined7.05139.1373140
X-RAY DIFFRACTIONr_long_range_B_other7.05139.1553141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.64→2.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 50 -
Rwork0.299 932 -
obs--95.71 %

+
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