4j3o

Crystal structure of the FimD usher traversed by the pilus tip complex assembly composed of FimC:FimF:FimG:FimH

Method: X-RAY DIFFRACTION Dmax: 127.6 Å Quality: REASONABLE

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

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 Fragment:UNP residues 24-167 Protein FimH × 1 (P08191) Chaperone protein FimC × 1 (P31697) Protein FimF × 1 (P08189) Outer membrane usher protein FimD × 1 (P30130) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;1.6-2.0M sodium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.80 Å R-free 0.299

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 1
Chains and sequence ranges Author chain G; PDBConstruct 1–144; UniProt 24–167

Protein FimH

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 Fragment:UNP residues 22-300 Protein FimG × 1 (P08190) Chaperone protein FimC × 1 (P31697) Protein FimF × 1 (P08189) Outer membrane usher protein FimD × 1 (P30130) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;1.6-2.0M sodium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.80 Å R-free 0.299

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 2
Chains and sequence ranges Author chain H; PDBConstruct 1–279; UniProt 22–300

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 Fragment:UNP residues 37-241 Protein FimG × 1 (P08190) Protein FimH × 1 (P08191) Protein FimF × 1 (P08189) Outer membrane usher protein FimD × 1 (P30130) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;1.6-2.0M sodium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.80 Å R-free 0.299

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 3
Chains and sequence ranges Author chain C; PDBConstruct 1–205; UniProt 37–241

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 Fragment:UNP residues 21-176 Protein FimG × 1 (P08190) Protein FimH × 1 (P08191) Chaperone protein FimC × 1 (P31697) Outer membrane usher protein FimD × 1 (P30130) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;1.6-2.0M sodium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.80 Å R-free 0.299

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 4
Chains and sequence ranges Author chain F; PDBConstruct 1–154; UniProt 23–176

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 Fragment:UNP residues 46-878 Protein FimG × 1 (P08190) Protein FimH × 1 (P08191) Chaperone protein FimC × 1 (P31697) Protein FimF × 1 (P08189) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;1.6-2.0M sodium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.80 Å R-free 0.299

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 5
Chains and sequence ranges Author chain D; PDBConstruct 1–833; UniProt 46–878

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 4j3o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4j3o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4j3o
Deposition date deposition_date2013-02-06
Structure title titleCrystal structure of the FimD usher traversed by the pilus tip complex assembly composed of FimC:FimF:FimG:FimH
Keywords keywords;beta barrel, immunglobuline-like fold, type 1 pilus assembly, pilus subunit translocation, adhesion, D-Mannose-binding, bacterial outer membrane, CELL ADHESION-CHAPERONE-MEMBRANE PROTEIN complex ;; CELL ADHESION/CHAPERONE/MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier45.23
Radius of gyration Rg (electron density) rg_electron46.48
Forward intensity I(0) i0433963000.00
Molecular weight molecular_weight166450.0 kDa
Excluded volume excluded_volume206710 ų
Envelope volume envelope_volume299180 ų
Hydration-shell volume shell_volume60507 ų
Envelope diameter envelope_diameter185.5
Shell Rg shell_rg44.52
Envelope Rg envelope_rg46.94
Shape Rg shape_rg46.47
Total Rg total_rg46.42
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 dmax127.6
Rg (real space) rg_real41.35
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real4.1400e+08
I(0) uncertainty (real space) i0_real_error6.1500e+06
Rg (reciprocal space) rg_reciprocal45.24
I(0) (reciprocal space) i0_reciprocal433500000.0000
Solution quality estimate total_estimate0.7190
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.8
Skewness Skewness skewness0.520
Kurtosis Kurtosis kurtosis-0.139
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.2050
Highest regularization parameter α highest_alpha39020000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 0.970; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.797

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id4j3oC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4j3oC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4j3oD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily410 — PapC, N-terminal domain
Domain ID domain_id4j3oD03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily3110 — Outer membrane usher protein
Domain ID domain_id4j3oD04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily2610 — Outer membrane usher protein FimD, plug domain
Domain ID domain_id4j3oD05
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily2070 — PapC, C-terminal domain
Domain ID domain_id4j3oF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1090 — Fimbrial-type adhesion domain
Domain ID domain_id4j3oG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1090 — Fimbrial-type adhesion domain
Domain ID domain_id4j3oH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1090 — Fimbrial-type adhesion domain
Domain ID domain_id4j3oH02
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)