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5yud

Flagellin derivative in complex with the NLR protein NAIP5

Method: ELECTRON MICROSCOPY Dmax: 142.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Baculoviral IAP repeat-containing protein 1e

Mus musculus

UniProt Q8CGT2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–1403 Not recorded Phase 2 flagellin,Flagellin × 1 （P52616,P06179） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.28 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q8CGT2_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1403； UniProt 1–1403

Phase 2 flagellin,Flagellin

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

UniProt P06179

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 452–495 Not recorded Baculoviral IAP repeat-containing protein 1e × 1 （Q8CGT2） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.28 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5YUD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IO1 CRYSTAL STRUCTURE OF F41 FRAGMENT OF FLAGELLIN Deposited 2000-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 53–450（398 aa） Fragment：F41 L-TYPE (RESIDUES 54-451)
Mutation：G426A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；289 K；PEG 6000, NaCl, Glycerol, Iso-Propanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.00 Å R-free 0.266
1UCU R-type straight flagellar filament made of full-length flagellin Deposited 2003-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–494（494 aa）
Mutation：A449V No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL；pH 7.8；150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL
Resolution 4.00 Å
3A5X L-type straight flagellar filament made of full-length flagellin Deposited 2009-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–495（494 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL；pH 7.8；150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6CH3 Crystal structure of the cytoplasmic domain of FlhA and FliS-FliC complex Deposited 2018-02-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 455–495（41 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；tascimate
Resolution 2.68 Å R-free 0.258
8FML Cryo-EM structure of NLR family apoptosis inhibitory protein 5 (NAIP5) in complex with a full-length flagellin (FliC) ligand Deposited 2022-12-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–495（495 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9IWQ Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament Deposited 2024-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–495（494 aa）
Mutation：G426A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.08 Å
9M5T Structure of the flagellar filament in short-length at 3.02 angstroms resolution Deposited 2025-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 44 PDB declaration: 44-meric
Chain AA 1–495（495 aa）
Chain AB 1–495（495 aa）
Chain AC 1–495（495 aa）
Chain AD 1–495（495 aa）
Chain AE 1–495（495 aa）
Chain AF 1–495（495 aa）
Chain AG 1–495（495 aa）
Chain AH 1–495（495 aa）
Chain AI 1–495（495 aa）
Chain AJ 1–495（495 aa）
Chain AK 1–495（495 aa）
Chain BA 1–495（495 aa）
Chain BB 1–495（495 aa）
Chain BC 1–495（495 aa）
Chain BD 1–495（495 aa）
Chain BE 1–495（495 aa）
Chain BF 1–495（495 aa）
Chain BG 1–495（495 aa）
Chain BH 1–495（495 aa）
Chain BI 1–495（495 aa）
Chain BJ 1–495（495 aa）
Chain BK 1–495（495 aa）
Chain CA 1–495（495 aa）
Chain CB 1–495（495 aa）
Chain CC 1–495（495 aa）
Chain CD 1–495（495 aa）
Chain CE 1–495（495 aa）
Chain CF 1–495（495 aa）
Chain CG 1–495（495 aa）
Chain CH 1–495（495 aa）
Chain CI 1–495（495 aa）
Chain CJ 1–495（495 aa）
Chain CK 1–495（495 aa）
Chain DA 1–495（495 aa）
Chain DB 1–495（495 aa）
Chain DC 1–495（495 aa）
Chain DD 1–495（495 aa）
Chain DE 1–495（495 aa）
Chain DF 1–495（495 aa）
Chain DG 1–495（495 aa）
Chain DH 1–495（495 aa）
Chain DI 1–495（495 aa）
Chain DJ 1–495（495 aa）
Chain DK 1–495（495 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
9M67 the flagellar filament cap FliD in complex with FliC Deposited 2025-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 1–495（495 aa）
Chain B 1–495（495 aa）
Chain C 1–495（495 aa）
Chain D 1–495（495 aa）
Chain E 1–495（495 aa）
Chain F 1–495（495 aa）
Chain G 1–495（495 aa）
Chain H 1–495（495 aa）
Chain I 1–495（495 aa）
Chain J 1–495（495 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9M6H structure of FliD-FliC at a 10:10 stoichiometry Deposited 2025-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: 20-meric
Chain B 54–454（401 aa）
Chain D 54–454（401 aa）
Chain F 54–454（401 aa）
Chain H 54–454（401 aa）
Chain J 54–454（401 aa）
Chain L 54–454（401 aa）
Chain N 54–454（401 aa）
Chain P 54–454（401 aa）
Chain R 54–454（401 aa）
Chain T 54–454（401 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FLIC_SALTY
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 32–75； UniProt 452–495

Phase 2 flagellin,Flagellin

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

UniProt P52616

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 31–52 Not recorded Baculoviral IAP repeat-containing protein 1e × 1 （Q8CGT2） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.28 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name FLJB_SALTY
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 4–25； UniProt 31–52

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5yud

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5yud
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5yud
Deposition date deposition_date2017-11-21
Structure title titleFlagellin derivative in complex with the NLR protein NAIP5
Keywords keywordsFlagellin, NAIP5, NLRC4, Cryo-EM, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.18 Å
Radius of gyration Rg (electron density) rg_electron41.09 Å
Forward intensity I(0) i0327486000.00
Molecular weight molecular_weight149410.0 kDa
Excluded volume excluded_volume187770 ų
Envelope volume envelope_volume256880 ų
Hydration-shell volume shell_volume53613 ų
Envelope diameter envelope_diameter141.3 Å
Shell Rg shell_rg45.01 Å
Envelope Rg envelope_rg40.52 Å
Shape Rg shape_rg41.06 Å
Total Rg total_rg41.40 Å
Total atoms total_atoms10510
Residues n_residues1313
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax142.6 Å
Rg (real space) rg_real41.37 Å
Rg uncertainty (real space) rg_real_error1.19 Å
I(0) (real space) i0_real3.2750e+08
I(0) uncertainty (real space) i0_real_error5.4640e+06
Rg (reciprocal space) rg_reciprocal41.18 Å
I(0) (reciprocal space) i0_reciprocal327400000.0000
Solution quality estimate total_estimate0.7954
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.3 Å
Skewness Skewness skewness0.474
Kurtosis Kurtosis kurtosis-0.341
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha40480000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)