5TJ2 | pdb_00005tj2

Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Ser306 fused to maltose binding protein

• PDB DOI: https://doi.org/10.2210/pdb5TJ2/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-10-03 Released: 2017-02-01 
• Deposition Author(s): Chao, L.K., Herzberg, O.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.252 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Human Gasdermin-B and disease: Sulfatide Binding, Caspase cleavage, and Structural impact of Asthma- and IBS-Associated Polymorphism

Chao, L.K., Kulakova, L., Herzberg, O.

(2017) Proc Natl Acad Sci U S A 

• DOI: https://doi.org/10.1073/pnas.1616783114

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 243.22 kDa 
• Atom Count: 15,875 
• Modeled Residue Count: 2,127 
• Deposited Residue Count: 2,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein	A, B, C, D	553	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 1  Gene Names: malE, OO96_18925, GSDMB, GSDML, PP4052, PRO2521
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAX9 (Homo sapiens) Explore Q8TAX9  Go to UniProtKB:  Q8TAX9
PHAROS:  Q8TAX9 GTEx:  ENSG00000073605

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	E, F, G, H	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.252 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.039	α = 90
b = 152.75	β = 90
c = 255.77	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Chao, L.K., Herzberg, O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM102810

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary