6e15

Handover mechanism of the growing pilus by the bacterial outer membrane usher FimD

Method: ELECTRON MICROSCOPY Dmax: 178.6 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 1–241 Not recorded Fimbrial biogenesis outer membrane usher protein × 1 (A0A0F3W955) Protein FimF × 1 (P08189) Protein FimG × 1 (P08190) Type 1 fimbrin D-mannose specific adhesin × 1 (P08191) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 5.10 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 1–241; UniProt 1–241

Fimbrial biogenesis outer membrane usher protein

Escherichia coli

UniProt A0A0F3W955

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 1–878 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 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 5.10 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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A0F3W955_ECOLX
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–878; UniProt 1–878

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 22–176 Not recorded Chaperone protein FimC × 1 (P31697) Fimbrial biogenesis outer membrane usher protein × 1 (A0A0F3W955) Protein FimG × 1 (P08190) Type 1 fimbrin D-mannose specific adhesin × 1 (P08191) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 5.10 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 2–156; UniProt 22–176

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 11–167 Not recorded Chaperone protein FimC × 1 (P31697) Fimbrial biogenesis outer membrane usher protein × 1 (A0A0F3W955) Protein FimF × 1 (P08189) Type 1 fimbrin D-mannose specific adhesin × 1 (P08191) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 5.10 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 2–158; UniProt 11–167

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 1–300 Not recorded Chaperone protein FimC × 1 (P31697) Fimbrial biogenesis outer membrane usher protein × 1 (A0A0F3W955) Protein FimF × 1 (P08189) Protein FimG × 1 (P08190) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 5.10 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 1–300; UniProt 1–300

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 6e15

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6e15
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6e15
Deposition date deposition_date2018-07-09
Structure title titleHandover mechanism of the growing pilus by the bacterial outer membrane usher FimD
Keywords keywordspili, chaperone, usher, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier46.43
Radius of gyration Rg (electron density) rg_electron47.79
Forward intensity I(0) i0435589000.00
Molecular weight molecular_weight166450.0 kDa
Excluded volume excluded_volume206710 ų
Envelope volume envelope_volume310190 ų
Hydration-shell volume shell_volume62161 ų
Envelope diameter envelope_diameter187.3
Shell Rg shell_rg44.74
Envelope Rg envelope_rg46.97
Shape Rg shape_rg47.78
Total Rg total_rg47.68
Total atoms total_atoms11732
Residues n_residues1554
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 dmax178.6
Rg (real space) rg_real49.52
Rg uncertainty (real space) rg_real_error1.23
I(0) (real space) i0_real4.4000e+08
I(0) uncertainty (real space) i0_real_error8.7270e+06
Rg (reciprocal space) rg_reciprocal46.44
I(0) (reciprocal space) i0_reciprocal435100000.0000
Solution quality estimate total_estimate0.5622
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.3
Skewness Skewness skewness0.831
Kurtosis Kurtosis kurtosis0.243
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha1.0290
Highest regularization parameter α highest_alpha48530000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.452; Stabil: 0.862; Sysdev: 0.000; Positv: 1.000; Valcen: 0.821; Smooth: 0.563

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)