9fy9

Cryo-EM structure of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1

Method: ELECTRON MICROSCOPY Dmax: 125.1 Å Quality: REASONABLE

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

Chaperone protein FimC

Escherichia coli

UniProt P31697

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 37–241 Not recorded Outer membrane usher protein FimD × 1 (P30130) Protein FimF × 1 (P08189) Protein FimG × 1 (P08190) Type 1 fimbrin D-mannose specific adhesin × 1 (P08191) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.30 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.

22 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIMC_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain C; PDBConstruct 2–206; UniProt 37–241

Outer membrane usher protein FimD

Escherichia coli

UniProt P30130

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 46–878 Not recorded Chaperone protein FimC × 1 (P31697) Protein FimF × 1 (P08189) Protein FimG × 1 (P08190) Type 1 fimbrin D-mannose specific adhesin × 1 (P08191) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.30 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.

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIMD_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–833; UniProt 46–878

Protein FimF

Escherichia coli

UniProt P08189

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 23–176 Not recorded Chaperone protein FimC × 1 (P31697) Outer membrane usher protein FimD × 1 (P30130) Protein FimG × 1 (P08190) Type 1 fimbrin D-mannose specific adhesin × 1 (P08191) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.30 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.

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIMF_ECOLI
Isoform
PDB entities 3
Chains and sequence ranges Author chain F; PDBConstruct 1–154; UniProt 23–176

Protein FimG

Escherichia coli

UniProt P08190

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 24–167 Not recorded Chaperone protein FimC × 1 (P31697) Outer membrane usher protein FimD × 1 (P30130) Protein FimF × 1 (P08189) Type 1 fimbrin D-mannose specific adhesin × 1 (P08191) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.30 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.

15 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIMG_ECOLI
Isoform
PDB entities 4
Chains and sequence ranges Author chain G; PDBConstruct 1–144; UniProt 24–167

Type 1 fimbrin D-mannose specific adhesin

Escherichia coli

UniProt P08191

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 22–300 Not recorded Chaperone protein FimC × 1 (P31697) Outer membrane usher protein FimD × 1 (P30130) Protein FimF × 1 (P08189) Protein FimG × 1 (P08190) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.30 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.

57 other PDB entries and 138 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIMH_ECOLI
Isoform
PDB entities 5
Chains and sequence ranges Author chain H; PDBConstruct 1–279; UniProt 22–300

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 9fy9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9fy9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9fy9
Deposition date deposition_date2024-07-03
Structure title titleCryo-EM structure of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1
Keywords keywordschaperone, usher, pilus, tip, CELL ADHESION; CELL ADHESION
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier44.64
Radius of gyration Rg (electron density) rg_electron46.03
Forward intensity I(0) i0378147000.00
Molecular weight molecular_weight155580.0 kDa
Excluded volume excluded_volume193470 ų
Envelope volume envelope_volume275600 ų
Hydration-shell volume shell_volume57317 ų
Envelope diameter envelope_diameter186.3
Shell Rg shell_rg43.31
Envelope Rg envelope_rg46.38
Shape Rg shape_rg46.01
Total Rg total_rg45.94
Total atoms total_atoms10974
Residues n_residues1446
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax125.1
Rg (real space) rg_real40.73
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real3.6110e+08
I(0) uncertainty (real space) i0_real_error5.7600e+06
Rg (reciprocal space) rg_reciprocal44.65
I(0) (reciprocal space) i0_reciprocal377700000.0000
Solution quality estimate total_estimate0.7208
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.9
Skewness Skewness skewness0.524
Kurtosis Kurtosis kurtosis-0.206
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.1481
Highest regularization parameter α highest_alpha37480000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.885; Stabil: 0.971; Sysdev: 0.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.818

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)