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5vxx

Cryo-EM reconstruction of Neisseria gonorrhoeae Type IV pilus

Method: ELECTRON MICROSCOPY Dmax: 214.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fimbrial protein

OrganismNot specified

UniProt P02974

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 21 其他Polymer 21 PDB declaration: 21-meric（21） Consistent with protein copy count Chain A； UniProt 8–165 Chain B； UniProt 8–165 Chain C； UniProt 8–165 Chain D； UniProt 8–165 Chain E； UniProt 8–165 Chain F； UniProt 8–165 Chain G； UniProt 8–165 Chain H； UniProt 8–165 Chain I； UniProt 8–165 Chain J； UniProt 8–165 Chain K； UniProt 8–165 Chain L； UniProt 8–165 Chain M； UniProt 8–165 Chain N； UniProt 8–165 Chain O； UniProt 8–165 Chain P； UniProt 8–165 Chain Q； UniProt 8–165 Chain R； UniProt 8–165 Chain S； UniProt 8–165 Chain T； UniProt 8–165 Chain U； UniProt 8–165 Mutation：P69S, S71T alpha-D-galactopyranose-(1-3)-2,4-bisacetamido-2,4,6-trideoxy-beta-D-glucopyranose × 21 OPE PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER × 21 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；PBS buffer 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.

Other PDB Difference from Current Entry 5VXX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AY2 STRUCTURE OF THE FIBER-FORMING PROTEIN PILIN AT 2.6 ANGSTROMS RESOLUTION Deposited 1997-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 8–165（158 aa）
Not recorded PT PLATINUM (II) ION × 2 HTO HEPTANE-1,2,3-TRIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；PROTEIN WAS CRYSTALLIZED FROM 60% PEG400, 50 MM CHESS, PH 8.0, 1% BETA-OCTYL GLUCOSIDE, 0.6% 1,2,3-HEPTANETRIOL.
Resolution 2.60 Å
2HI2 Crystal structure of native Neisseria gonorrhoeae Type IV pilin at 2.3 Angstroms Resolution Deposited 2006-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 8–165（158 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HTO HEPTANE-1,2,3-TRIOL × 1 OPE PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；22% PEG 400 5% HEPTANE TRIOL 50 mM CHES, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 298K
Resolution 2.30 Å R-free 0.282
2HIL Structure of the Neisseria gonorrhoeae Type IV pilus filament from x-ray crystallography and electron cryomicroscopy Deposited 2006-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 8–165（158 aa）
Chain B 8–165（158 aa）
Chain C 8–165（158 aa）
Chain D 8–165（158 aa）
Chain E 8–165（158 aa）
Chain F 8–165（158 aa）
Chain G 8–165（158 aa）
Chain H 8–165（158 aa）
Chain I 8–165（158 aa）
Chain J 8–165（158 aa）
Chain K 8–165（158 aa）
Chain L 8–165（158 aa）
Chain M 8–165（158 aa）
Chain N 8–165（158 aa）
Chain O 8–165（158 aa）
Chain P 8–165（158 aa）
Chain Q 8–165（158 aa）
Chain R 8–165（158 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) OPE PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER × 18 ELECTRON MICROSCOPY
cryo-EM buffer 50 mM CHES；pH 9.5；50 mM CHES
cryo-EM vitrification conditions Cryogen ETHANE；5 ul of sample were applied to grids for 1 minute, blotted for 2.5 seconds then plunge-frozen in liquid ethane using an FEI Vitrobot
Resolution 12.50 Å
2PIL Crystallographic Structure of Phosphorylated Pilin from Neisseria: Phosphoserine Sites Modify Type IV Pilus Surface Chemistry Deposited 1998-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 8–165（158 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PT PLATINUM (II) ION × 1 HTO HEPTANE-1,2,3-TRIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；PROTEIN WAS CRYSTALLIZED FROM 60% PEG400, 50 MM CHESS, PH 8.0, 1% BETA-OCTYL GLUCOSIDE, 0.6% 1,2,3-HEPTANETRIOL.
Resolution 2.60 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FMM1_NEIGO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–158； UniProt 8–165 Author chain B； PDBConstruct 1–158； UniProt 8–165 Author chain C； PDBConstruct 1–158； UniProt 8–165 Author chain D； PDBConstruct 1–158； UniProt 8–165 Author chain E； PDBConstruct 1–158； UniProt 8–165 Author chain F； PDBConstruct 1–158； UniProt 8–165 Author chain G； PDBConstruct 1–158； UniProt 8–165 Author chain H； PDBConstruct 1–158； UniProt 8–165 Author chain I； PDBConstruct 1–158； UniProt 8–165 Author chain J； PDBConstruct 1–158； UniProt 8–165 Author chain K； PDBConstruct 1–158； UniProt 8–165 Author chain L； PDBConstruct 1–158； UniProt 8–165 Author chain M； PDBConstruct 1–158； UniProt 8–165 Author chain N； PDBConstruct 1–158； UniProt 8–165 Author chain O； PDBConstruct 1–158； UniProt 8–165 Author chain P； PDBConstruct 1–158； UniProt 8–165 Author chain Q； PDBConstruct 1–158； UniProt 8–165 Author chain R； PDBConstruct 1–158； UniProt 8–165 Author chain S； PDBConstruct 1–158； UniProt 8–165 Author chain T； PDBConstruct 1–158； UniProt 8–165 Author chain U； PDBConstruct 1–158； UniProt 8–165

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 5vxx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5vxx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5vxx
Deposition date deposition_date2017-05-24
Structure title titleCryo-EM reconstruction of Neisseria gonorrhoeae Type IV pilus
Keywords keywordsMelted helix, type IV pili, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier64.71 Å
Radius of gyration Rg (electron density) rg_electron67.22 Å
Forward intensity I(0) i01933780000.00
Molecular weight molecular_weight366950.0 kDa
Excluded volume excluded_volume458920 ų
Envelope volume envelope_volume585870 ų
Hydration-shell volume shell_volume84157 ų
Envelope diameter envelope_diameter286.7 Å
Shell Rg shell_rg52.38 Å
Envelope Rg envelope_rg69.52 Å
Shape Rg shape_rg67.20 Å
Total Rg total_rg66.94 Å
Total atoms total_atoms25767
Residues n_residues3276
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 dmax214.6 Å
Rg (real space) rg_real65.51 Å
Rg uncertainty (real space) rg_real_error2.02 Å
I(0) (real space) i0_real1.9250e+09
I(0) uncertainty (real space) i0_real_error4.1340e+07
Rg (reciprocal space) rg_reciprocal63.11 Å
I(0) (reciprocal space) i0_reciprocal1922000000.0000
Solution quality estimate total_estimate0.6902
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.7 Å
Skewness Skewness skewness0.685
Kurtosis Kurtosis kurtosis-0.342
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0110
Highest regularization parameter α highest_alpha1255000000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.387; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.583; Smooth: 0.222
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)