6swh

Crystal structure of the ternary complex between the type 1 pilus proteins FimC, FimI and FimA from E. coli

Method: X-RAY DIFFRACTION Dmax: 132.0 Å Quality: REASONABLE

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

Chaperone protein FimC

Escherichia coli (strain K12)

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 37–241 Not recorded Fimbrin-like protein FimI × 1 (P39264) Type-1 fimbrial protein, A chain × 1 (P04128) PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;0.8 M sodium formate, 100 mM Tris/acetic acid pH 8.5, 16% PEG 4000 (w/v) Resolution 2.80 Å R-free 0.207
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 37–241 Not recorded Fimbrin-like protein FimI × 1 (P39264) Type-1 fimbrial protein, A chain × 1 (P04128) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;0.8 M sodium formate, 100 mM Tris/acetic acid pH 8.5, 16% PEG 4000 (w/v) Resolution 2.80 Å R-free 0.207

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 55 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 A; PDBConstruct 1–205; UniProt 37–241 Author chain D; PDBConstruct 1–205; UniProt 37–241

Fimbrin-like protein FimI

Escherichia coli (strain K12)

UniProt P39264

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 20–179 Not recorded Chaperone protein FimC × 1 (P31697) Type-1 fimbrial protein, A chain × 1 (P04128) PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;0.8 M sodium formate, 100 mM Tris/acetic acid pH 8.5, 16% PEG 4000 (w/v) Resolution 2.80 Å R-free 0.207
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 20–179 Not recorded Chaperone protein FimC × 1 (P31697) Type-1 fimbrial protein, A chain × 1 (P04128) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;0.8 M sodium formate, 100 mM Tris/acetic acid pH 8.5, 16% PEG 4000 (w/v) Resolution 2.80 Å R-free 0.207

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.

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIMI_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–160; UniProt 20–179 Author chain E; PDBConstruct 1–160; UniProt 20–179

Type-1 fimbrial protein, A chain

Escherichia coli (strain K12)

UniProt P04128

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 37–182 Not recorded Chaperone protein FimC × 1 (P31697) Fimbrin-like protein FimI × 1 (P39264) PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;0.8 M sodium formate, 100 mM Tris/acetic acid pH 8.5, 16% PEG 4000 (w/v) Resolution 2.80 Å R-free 0.207
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 37–182 Not recorded Chaperone protein FimC × 1 (P31697) Fimbrin-like protein FimI × 1 (P39264) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;0.8 M sodium formate, 100 mM Tris/acetic acid pH 8.5, 16% PEG 4000 (w/v) Resolution 2.80 Å R-free 0.207

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.

20 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIMA1_ECOLI
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 8–153; UniProt 37–182 Author chain F; PDBConstruct 8–153; UniProt 37–182

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 6swh

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6swh
Deposition date deposition_date2019-09-20
Structure title titleCrystal structure of the ternary complex between the type 1 pilus proteins FimC, FimI and FimA from E. coli
Keywords keywordsstructural protein, structural protein complex, pilus assembly inhibition; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.00
Radius of gyration Rg (electron density) rg_electron39.07
Forward intensity I(0) i0166091000.00
Molecular weight molecular_weight102580.0 kDa
Excluded volume excluded_volume127950 ų
Envelope volume envelope_volume175170 ų
Hydration-shell volume shell_volume40646 ų
Envelope diameter envelope_diameter135.1
Shell Rg shell_rg40.53
Envelope Rg envelope_rg39.02
Shape Rg shape_rg39.06
Total Rg total_rg39.20
Total atoms total_atoms7217
Residues n_residues961
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 dmax132.0
Rg (real space) rg_real39.40
Rg uncertainty (real space) rg_real_error1.25
I(0) (real space) i0_real1.6610e+08
I(0) uncertainty (real space) i0_real_error2.9500e+06
Rg (reciprocal space) rg_reciprocal39.16
I(0) (reciprocal space) i0_reciprocal166000000.0000
Solution quality estimate total_estimate0.6391
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.4
Skewness Skewness skewness0.475
Kurtosis Kurtosis kurtosis-0.531
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15970000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 0.816; Smooth: 0.728

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6swha1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.11 — PapD-like
Family Family familyb.1.11.1 — Pilus chaperone
Domain ID domain_idd6swha2
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.2 — Periplasmic chaperone C-domain
Family Family familyb.7.2.1 — Periplasmic chaperone C-domain
Domain ID domain_idd6swhb_
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.3 — Bacterial adhesins
Family Family familyb.2.3.0 — automated matches
Domain ID domain_idd6swhc_
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.3 — Bacterial adhesins
Family Family familyb.2.3.0 — automated matches
Domain ID domain_idd6swhd1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.11 — PapD-like
Family Family familyb.1.11.1 — Pilus chaperone
Domain ID domain_idd6swhd2
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.2 — Periplasmic chaperone C-domain
Family Family familyb.7.2.1 — Periplasmic chaperone C-domain
Domain ID domain_idd6swhe_
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.3 — Bacterial adhesins
Family Family familyb.2.3.0 — automated matches
Domain ID domain_idd6swhf_
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.3 — Bacterial adhesins
Family Family familyb.2.3.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id6swhB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1090 — Fimbrial-type adhesion domain
Domain ID domain_id6swhE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1090 — Fimbrial-type adhesion domain
Domain ID domain_id6swhF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1090 — Fimbrial-type adhesion domain

8. Citations (1)

9. Files and Curves (10)