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1zdv

Solution Structure of the type 1 pilus assembly platform FimD(25-139)

Method: SOLUTION NMR Dmax: 43.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 70–184 Fragment：N-TERMINAL DOMAIN Residues 70-184 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；293 K；Pressure ambient NMR sample composition：Uniform labeling with 13C, 15N; 90 % H2O, 10% D2O | 90% H2O/10% D2O Resolution not provided

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 1ZDV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ZDX Solution Structure of the type 1 pilus assembly platform FimD(25-125) Deposited 2005-04-15 Different construct Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 70–170（101 aa） Fragment：N-TERMINAL DOMAIN Residues 70-170
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；293 K；Pressure ambient
NMR sample composition Uniform labeling with 13C, 15N; 90 % H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
1ZE3 Crystal Structure of the Ternary Complex of FIMD (N-Terminal Domain) with FIMC and the Pilin Domain of FIMH Deposited 2005-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 46–170（125 aa） Fragment：FimD N-terminal domain
Not recorded EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 6000, MES buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.84 Å R-free 0.217
3BWU Crystal structure of the ternary complex of FimD (N-Terminal Domain, FimDN) with FimC and the N-terminally truncated pilus subunit FimF (FimFt) Deposited 2008-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 46–170（125 aa） Fragment：N-terminal domain, Residues 1-125
Not recorded EDO 1,2-ETHANEDIOL × 13 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20 mM Tris/HCl pH 8.0, 20% PEG 8000, 50 mM succinic acid pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.76 Å R-free 0.212
4J3O Crystal structure of the FimD usher traversed by the pilus tip complex assembly composed of FimC:FimF:FimG:FimH Deposited 2013-02-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 46–878（833 aa） Fragment：UNP residues 46-878
Not recorded No recorded non-water small molecule 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
7B0X Crystal structure of the ternary complex of the E. coli type 1 pilus proteins FimC, FimI and the N-terminal domain of FimD Deposited 2020-11-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 46–170（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Hepes pH 8.4, 15 % PEG 4000
Resolution 1.70 Å R-free 0.252
9BOG Structural basis for adhesin secretion by the outer-membrane usher in type 1 pili Deposited 2024-05-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 46–878（833 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.99 Å
9FW9 Cryo-EM structure of the type 1 pilus assembly platform as part of the FimA-bound chaperone-usher pilus complex (FimDHGFAnC - body 2) Deposited 2024-06-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 46–878（833 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
9FWB Cryo-EM structure of the type 1 pilus assembly platform as part of the FimA-bound chaperone-usher pilus complex (Local refinement including FimD, FimC, FimAn and FimAn-1) Deposited 2024-06-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 46–878（833 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9FWZ Cryo-EM structure of the type 1 pilus assembly platform as part of the FimA-bound chaperone-usher pilus complex (Local refinement including FimD, FimC, FimAn, FimAn-1 and FimAn-2) Deposited 2024-07-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 46–878（833 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
9FX8 Cryo-EM structure of the FimI-bound type 1 pilus assembly platform complex - Local refinement Deposited 2024-07-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 46–878（833 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
9FXB Cryo-EM structure of the type 1 pilus assembly platform as part of the FimI-bound chaperone-usher pilus complex (FimDHGFAnIC - body 2) Deposited 2024-07-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 46–878（833 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.30 Å
9FXS Cryo-EM structure of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement Deposited 2024-07-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 46–878（833 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
9FY9 Cryo-EM structure of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1 Deposited 2024-07-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 46–878（833 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å

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 1
Chains and sequence ranges Author chain A； PDBConstruct 1–115； UniProt 70–184

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 1zdv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1zdv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1zdv
Deposition date deposition_date2005-04-15
Structure title titleSolution Structure of the type 1 pilus assembly platform FimD(25-139)
Keywords keywordsBETA SHEET, ALPHA HELIX, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.70 Å
Radius of gyration Rg (electron density) rg_electron13.33 Å
Forward intensity I(0) i0918647000.00
Molecular weight molecular_weight247220.0 kDa
Excluded volume excluded_volume305260 ų
Envelope volume envelope_volume23378 ų
Hydration-shell volume shell_volume13512 ų
Envelope diameter envelope_diameter48.9 Å
Shell Rg shell_rg20.53 Å
Envelope Rg envelope_rg14.83 Å
Shape Rg shape_rg13.34 Å
Total Rg total_rg13.38 Å
Total atoms total_atoms34420
Residues n_residues2300
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 dmax43.5 Å
Rg (real space) rg_real13.59 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real9.1860e+08
I(0) uncertainty (real space) i0_real_error1.0210e+07
Rg (reciprocal space) rg_reciprocal13.60 Å
I(0) (reciprocal space) i0_reciprocal918600000.0000
Solution quality estimate total_estimate0.7141
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.0 Å
Skewness Skewness skewness0.022
Kurtosis Kurtosis kurtosis-0.433
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha287500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.991; Smooth: 0.992
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1zdva1
Class classb — All beta proteins
Fold Fold foldb.167 — FimD N-terminal domain-like
Superfamily Superfamily superfamilyb.167.1 — FimD N-terminal domain-like
Family Family familyb.167.1.1 — Usher N-domain

CATH v4.4 (1 domains)

Domain ID domain_id1zdvA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily410 — PapC, N-terminal domain
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8. Citations (1)

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9. Files and Curves (10)