SAXSdb — 8gtj

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 4 of Gasdermin-B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Probable E3 ubiquitin-protein ligase ipaH7.8 × 1 （P18014） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Probable E3 ubiquitin-protein ligase ipaH7.8 × 1 （P18014） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GSDMB_HUMAN
Isoform	Q8TAX9-4
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–414； UniProt 1–416 Author chain C； PDBConstruct 8–414； UniProt 1–416

Probable E3 ubiquitin-protein ligase ipaH7.8

Shigella flexneri

UniProt P18014

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Isoform 4 of Gasdermin-B × 1 （Q8TAX9） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Isoform 4 of Gasdermin-B × 1 （Q8TAX9） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPA7_SHIFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–241； UniProt 23–262 Author chain D； PDBConstruct 2–241； UniProt 23–262

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8gtj
Deposition date deposition_date	2022-09-08
Structure title title	Crystal structure of IpaH7.8-LRR and GSDMB isoform-4 complex
Keywords keywords	Complex, Effector, Pyroptosis, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8gtj__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8gtj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8gtj__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.86 Å
Rg (electron density)	28.29 Å
Total Rg	28.98 Å
Atom count	4960
Residues	615
Excluded volume	88638 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8gtj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8gtj__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Isoform 4 of Gasdermin-B
Molecular weight formula_weight	47128.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	9607

GPGSGRPMFSVFEEITRIVVKEMDAGGDMIAVRSLVDADRFRCFHLVGEKRTFFGCRHYTTGLTLMDILDTDGDKWLDELDSGLQGQKAEFQILDNVDSTGELIVRLPKEITISGSFQGFHHQKIKISENRISQQYLATLENRKLKRELPFSFRSINTRENLYLVTETLETVKEETLKSDRQYKFWSQISQGHLSYKHKGQREVTIPPNRVLSYRVKQLVFPNKETMNIHFRGKTKSFPEGKSLGSEDSRNMKEKLEDMESVLKDLTEEKRKDVLNSLAKCLGKEDIRQDLEQRVSEVLISGELHMEDPDKPLLSSLFNAAGVLVEARAKAILDFLDALLELSEEQQFVAEALEKGTLPLLKDQVKSVMEQNWDELASSPPDMDYDPEARILCALYVVVSILLELAEGPTSVSS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Probable E3 ubiquitin-protein ligase ipaH7.8
Molecular weight formula_weight	27840.5 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MSNEHYLRILTEWEKNSSPGEERGIAFNRLSQCFQNQEAVLNLSDLNLTSLPELPKHISALIVENNKLTSLPKLPAFLKELNADNNRLSVIPELPESLTTLSVRSNQLENLPVLPNHLTSLFVENNRLYNLPALPEKLKFLHVYYNRLTTLPDLPDKLEILCAQRNNLVTFPQFSDRNNIRQKEYYFHFNQITTLPESFSQLDSSYRINISGNPLSTRVLQSLQRLTSSPDYHGPQIYFSM

Source Source

Source organism organism	Shigella flexneri
NCBI taxonomy ID ncbi_taxonomy_id	623
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	152

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Unit-cell length a length_a	88.338 Å
Unit-cell length b length_b	88.338 Å
Unit-cell length c length_c	335.624 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	trigonal

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	45.150 Å
R factor r_factor	0.2423
R_work r_work	0.2407
R_free r_free	0.2760

Crystal structure of IpaH7.8-LRR and GSDMB isoform-4 complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 4 of Gasdermin-B

State in the Current Structure

Other States of the Same Protein in the Database

Probable E3 ubiquitin-protein ligase ipaH7.8

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8gtj__assembly_1__model_1

8gtj__assembly_1__model_1 | I(q)

8gtj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of IpaH7.8-LRR and GSDMB isoform-4 complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 4 of Gasdermin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Probable E3 ubiquitin-protein ligase ipaH7.8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8gtj__assembly_1__model_1

8gtj__assembly_1__model_1 | I(q)

8gtj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)