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- PDB-5tj4: Gasdermin-B C-terminal domain containing the polymorphism residue... -

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Basic information

Entry
Database: PDB / ID: 5tj4
TitleGasdermin-B C-terminal domain containing the polymorphism residues Gly299:Pro306 fused to maltose binding protein
ComponentsSugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
KeywordsLIGAND BINDING PROTEIN / alpha helices / fusion protein / C-terminal domain / 1 SNP
Function / homology
Function and homology information


cytotoxic T cell pyroptotic cell death / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / defense response to Gram-negative bacterium ...cytotoxic T cell pyroptotic cell death / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to bacterium / plasma membrane / cytoplasm
Similarity search - Function
Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain
Similarity search - Domain/homology
alpha-maltose / : / Gasdermin-B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsChao, L.K. / Herzberg, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM102810 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Gene polymorphism linked to increased asthma and IBD risk alters gasdermin-B structure, a sulfatide and phosphoinositide binding protein.
Authors: Chao, K.L. / Kulakova, L. / Herzberg, O.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
B: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
C: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
D: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
E: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
F: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
G: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
H: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
I: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
J: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)617,17422
Polymers613,70510
Non-polymers3,46912
Water00
1
A: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7132
Polymers61,3711
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7363
Polymers61,3711
Non-polymers3652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7132
Polymers61,3711
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7132
Polymers61,3711
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7363
Polymers61,3711
Non-polymers3652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7132
Polymers61,3711
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7132
Polymers61,3711
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7132
Polymers61,3711
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7132
Polymers61,3711
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7132
Polymers61,3711
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.599, 274.569, 174.019
Angle α, β, γ (deg.)90.000, 96.090, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA1 - 14051 - 556
21GLYGLYBB1 - 14051 - 556
12GLYGLYAA1 - 14051 - 556
22GLYGLYCC1 - 14051 - 556
13ALAALAAA1 - 14031 - 554
23ALAALADD1 - 14031 - 554
14GLYGLYAA1 - 14051 - 556
24GLYGLYEE1 - 14051 - 556
15GLYGLYAA1 - 14051 - 556
25GLYGLYFF1 - 14051 - 556
16GLYGLYAA1 - 14051 - 556
26GLYGLYGG1 - 14051 - 556
17GLYGLYAA1 - 14051 - 556
27GLYGLYHH1 - 14051 - 556
18ALAALAAA1 - 14031 - 554
28ALAALAII1 - 14031 - 554
19GLYGLYAA1 - 14051 - 556
29GLYGLYJJ1 - 14051 - 556
110THRTHRBB1 - 14071 - 558
210THRTHRCC1 - 14071 - 558
111ALAALABB1 - 14031 - 554
211ALAALADD1 - 14031 - 554
112VALVALBB1 - 14091 - 560
212VALVALEE1 - 14091 - 560
113GLYGLYBB1 - 14051 - 556
213GLYGLYFF1 - 14051 - 556
114THRTHRBB1 - 14071 - 558
214THRTHRGG1 - 14071 - 558
115VALVALBB1 - 14091 - 560
215VALVALHH1 - 14091 - 560
116ALAALABB1 - 14031 - 554
216ALAALAII1 - 14031 - 554
117SERSERBB1 - 14081 - 559
217SERSERJJ1 - 14081 - 559
118ALAALACC1 - 14031 - 554
218ALAALADD1 - 14031 - 554
119THRTHRCC1 - 14071 - 558
219THRTHREE1 - 14071 - 558
120GLYGLYCC1 - 14051 - 556
220GLYGLYFF1 - 14051 - 556
121THRTHRCC1 - 14071 - 558
221THRTHRGG1 - 14071 - 558
122THRTHRCC1 - 14071 - 558
222THRTHRHH1 - 14071 - 558
123ALAALACC1 - 14031 - 554
223ALAALAII1 - 14031 - 554
124THRTHRCC1 - 14071 - 558
224THRTHRJJ1 - 14071 - 558
125ALAALADD1 - 14031 - 554
225ALAALAEE1 - 14031 - 554
126ALAALADD1 - 14031 - 554
226ALAALAFF1 - 14031 - 554
127LEULEUDD1 - 14021 - 553
227LEULEUGG1 - 14021 - 553
128ALAALADD1 - 14031 - 554
228ALAALAHH1 - 14031 - 554
129ALAALADD1 - 14031 - 554
229ALAALAII1 - 14031 - 554
130ALAALADD1 - 14031 - 554
230ALAALAJJ1 - 14031 - 554
131GLYGLYEE1 - 14051 - 556
231GLYGLYFF1 - 14051 - 556
132THRTHREE1 - 14071 - 558
232THRTHRGG1 - 14071 - 558
133VALVALEE1 - 14091 - 560
233VALVALHH1 - 14091 - 560
134ALAALAEE1 - 14031 - 554
234ALAALAII1 - 14031 - 554
135SERSEREE1 - 14081 - 559
235SERSERJJ1 - 14081 - 559
136GLYGLYFF1 - 14051 - 556
236GLYGLYGG1 - 14051 - 556
137GLYGLYFF1 - 14051 - 556
237GLYGLYHH1 - 14051 - 556
138ALAALAFF1 - 14031 - 554
238ALAALAII1 - 14031 - 554
139GLYGLYFF1 - 14051 - 556
239GLYGLYJJ1 - 14051 - 556
140THRTHRGG1 - 14071 - 558
240THRTHRHH1 - 14071 - 558
141ALAALAGG1 - 14031 - 554
241ALAALAII1 - 14031 - 554
142THRTHRGG1 - 14071 - 558
242THRTHRJJ1 - 14071 - 558
143ALAALAHH1 - 14031 - 554
243ALAALAII1 - 14031 - 554
144SERSERHH1 - 14081 - 559
244SERSERJJ1 - 14081 - 559
145ALAALAII1 - 14031 - 554
245ALAALAJJ1 - 14031 - 554

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

#1: Protein
Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein / Gasdermin-like protein


Mass: 61370.527 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli, Homo sapiens / Gene: malE, OO96_18925, GSDMB, GSDML, PP4052, PRO2521 / Plasmid: pMALX(E) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178SBV6, UniProt: Q8TAX9
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
Sequence detailsThe sequence of this entry corresponds to a common polymorphism present in half of the population.

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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: 3.47 Å3/Da / Density % sol: 64.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6 / Details: 2.1 M sodium malonate / Temp details: room temperature

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.5→173.04 Å / Num. obs: 99563 / % possible obs: 99.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIB
Resolution: 3.5→173.04 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.893 / SU B: 33.775 / SU ML: 0.504 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.56
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 5198 5 %RANDOM
Rwork0.213 ---
obs0.2148 99563 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 229.18 Å2 / Biso mean: 89.428 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å22.94 Å2
2--1.25 Å2-0 Å2
3----3.8 Å2
Refinement stepCycle: final / Resolution: 3.5→173.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39606 0 232 0 39838
Biso mean--65.07 --
Num. residues----5462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01940675
X-RAY DIFFRACTIONr_bond_other_d0.010.0237264
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.9755644
X-RAY DIFFRACTIONr_angle_other_deg1.988385230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82355431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58725.511548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56155708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.91315100
X-RAY DIFFRACTIONr_chiral_restr0.0970.26559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02147165
X-RAY DIFFRACTIONr_gen_planes_other0.0060.028657
X-RAY DIFFRACTIONr_mcbond_it6.0129.34321817
X-RAY DIFFRACTIONr_mcbond_other6.0129.34221816
X-RAY DIFFRACTIONr_mcangle_it9.73214.00727217
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A580320.09
12B580320.09
21A585040.1
22C585040.1
31A576240.1
32D576240.1
41A581600.1
42E581600.1
51A567840.1
52F567840.1
61A555240.1
62G555240.1
71A543780.1
72H543780.1
81A530180.1
82I530180.1
91A542520.1
92J542520.1
101B568240.1
102C568240.1
111B580680.09
112D580680.09
121B592980.09
122E592980.09
131B574960.09
132F574960.09
141B567620.09
142G567620.09
151B553420.09
152H553420.09
161B536320.09
162I536320.09
171B555520.09
172J555520.09
181C572920.09
182D572920.09
191C578440.1
192E578440.1
201C569760.1
202F569760.1
211C550480.1
212G550480.1
221C538300.1
222H538300.1
231C527680.1
232I527680.1
241C542520.1
242J542520.1
251D580180.08
252E580180.08
261D575060.09
262F575060.09
271D560880.08
272G560880.08
281D544060.09
282H544060.09
291D537540.1
292I537540.1
301D544500.08
302J544500.08
311E573820.09
312F573820.09
321E565260.09
322G565260.09
331E549400.09
332H549400.09
341E534760.1
342I534760.1
351E558880.09
352J558880.09
361F556480.09
362G556480.09
371F541820.09
372H541820.09
381F531560.1
382I531560.1
391F537540.09
392J537540.09
401G538820.09
402H538820.09
411G525740.1
412I525740.1
421G542920.08
422J542920.08
431H520020.1
432I520020.1
441H527100.1
442J527100.1
451I513800.09
452J513800.09
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 415 -
Rwork0.299 7384 -
all-7799 -
obs--99.97 %

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