8i8r

Cryo-EM Structure of OmpC3-MlaA Complex in MSP2N2 Nanodiscs

Method: ELECTRON MICROSCOPY Dmax: 122.8 Å Quality: GOOD

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

Outer membrane porin C

Escherichia coli K-12

UniProt P06996

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 22–367 Chain B; UniProt 22–367 Chain C; UniProt 22–367 Not recorded Intermembrane phospholipid transport system lipoprotein MlaA × 1 (P76506) KDL (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;Tris-buffered saline (TBS) buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl) cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.93 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.

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OMPC_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–346; UniProt 22–367 Author chain B; PDBConstruct 1–346; UniProt 22–367 Author chain C; PDBConstruct 1–346; UniProt 22–367

Intermembrane phospholipid transport system lipoprotein MlaA

Escherichia coli K-12

UniProt P76506

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 18–251 Mutation:Q205C Outer membrane porin C × 3 (P06996) KDL (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;Tris-buffered saline (TBS) buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl) cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.93 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 MLAA_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–234; UniProt 18–251

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 8i8r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8i8r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8i8r
Deposition date deposition_date2023-02-05
Structure title titleCryo-EM Structure of OmpC3-MlaA Complex in MSP2N2 Nanodiscs
Keywords keywordsbacteria, outer membrane, phospholipid, lipid asymmetry, membrane protein, protein complex structure, channel, LIPID TRANSPORT; LIPID TRANSPORT
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier35.63
Radius of gyration Rg (electron density) rg_electron35.60
Forward intensity I(0) i0325063000.00
Molecular weight molecular_weight143470.0 kDa
Excluded volume excluded_volume178280 ų
Envelope volume envelope_volume241800 ų
Hydration-shell volume shell_volume56086 ų
Envelope diameter envelope_diameter130.9
Shell Rg shell_rg42.33
Envelope Rg envelope_rg35.70
Shape Rg shape_rg35.60
Total Rg total_rg36.06
Total atoms total_atoms10151
Residues n_residues1232
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 dmax122.8
Rg (real space) rg_real35.66
Rg uncertainty (real space) rg_real_error1.11
I(0) (real space) i0_real3.2510e+08
I(0) uncertainty (real space) i0_real_error5.7980e+06
Rg (reciprocal space) rg_reciprocal35.64
I(0) (reciprocal space) i0_reciprocal325100000.0000
Solution quality estimate total_estimate0.8468
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.9
Skewness Skewness skewness0.464
Kurtosis Kurtosis kurtosis0.110
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41220000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.779

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)