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- PDB-5b5r: Crystal structure of GSDMA3 -

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Basic information

Entry
Database: PDB / ID: 5b5r
TitleCrystal structure of GSDMA3
ComponentsGasdermin-A3
KeywordsTRANSPORT PROTEIN / pyroptosis excutioner
Function / homology
Function and homology information


sebaceous gland cell differentiation / avascular cornea development in camera-type eye / negative regulation of timing of anagen / hair cycle / wide pore channel activity / mammary gland development / phosphatidylinositol-4-phosphate binding / positive regulation of extrinsic apoptotic signaling pathway / skin development / hair follicle morphogenesis ...sebaceous gland cell differentiation / avascular cornea development in camera-type eye / negative regulation of timing of anagen / hair cycle / wide pore channel activity / mammary gland development / phosphatidylinositol-4-phosphate binding / positive regulation of extrinsic apoptotic signaling pathway / skin development / hair follicle morphogenesis / phosphatidylserine binding / pyroptosis / somatic stem cell population maintenance / hair follicle development / extrinsic apoptotic signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-1 beta production / mitochondrial membrane / negative regulation of canonical Wnt signaling pathway / defense response to bacterium / positive regulation of apoptotic process / perinuclear region of cytoplasm / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Gasdermin, pore forming domain / Gasdermin pore forming domain / Gasdermin, PUB domain / Gasdermin PUB domain
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.902 Å
AuthorsDing, J. / Shao, F.
CitationJournal: Nature / Year: 2016
Title: Pore-forming activity and structural autoinhibition of the gasdermin family.
Authors: Ding, J. / Wang, K. / Liu, W. / She, Y. / Sun, Q. / Shi, J. / Sun, H. / Wang, D.C. / Shao, F.
History
DepositionMay 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gasdermin-A3


Theoretical massNumber of molelcules
Total (without water)52,8541
Polymers52,8541
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.453, 103.414, 49.625
Angle α, β, γ (deg.)90.00, 110.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gasdermin-A3 / Gasdermin-3


Mass: 52854.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdma3, Gsdm3 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5Y4Y6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.16 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-Tris (pH 6.5), 19% polyethylene glycol 3550, 10 mM TCEP

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 44110 / % possible obs: 97.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.4 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.902→37.914 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.31
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.232 2210 5.01 %
Rwork0.1871 --
obs0.1893 44110 69.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.902→37.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 0 218 3474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053313
X-RAY DIFFRACTIONf_angle_d0.8484476
X-RAY DIFFRACTIONf_dihedral_angle_d16.0081273
X-RAY DIFFRACTIONf_chiral_restr0.029533
X-RAY DIFFRACTIONf_plane_restr0.003562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9019-1.94320.3344510.2626976X-RAY DIFFRACTION26
1.9432-1.98840.3126640.25961240X-RAY DIFFRACTION32
1.9884-2.03810.2619740.251391X-RAY DIFFRACTION37
2.0381-2.09320.2568820.24421585X-RAY DIFFRACTION43
2.0932-2.15480.2785980.23531841X-RAY DIFFRACTION48
2.1548-2.22440.25361040.21951951X-RAY DIFFRACTION52
2.2244-2.30390.28221230.22222377X-RAY DIFFRACTION63
2.3039-2.39610.2481420.20622695X-RAY DIFFRACTION71
2.3961-2.50510.20361600.20492927X-RAY DIFFRACTION79
2.5051-2.63720.27651740.19423308X-RAY DIFFRACTION87
2.6372-2.80230.26041810.20393375X-RAY DIFFRACTION89
2.8023-3.01860.24661910.20043566X-RAY DIFFRACTION95
3.0186-3.32220.23082000.19393768X-RAY DIFFRACTION98
3.3222-3.80260.22541900.16423648X-RAY DIFFRACTION97
3.8026-4.78940.21171870.14843591X-RAY DIFFRACTION95
4.7894-37.92150.18351890.16713661X-RAY DIFFRACTION97

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