← Back to search
8qsr

Cryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in the inward-facing conformation

Method: ELECTRON MICROSCOPY Dmax: 104.0 Å Quality: GOOD
▼

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

PTS system glucose-specific EIICB component

Escherichia coli

UniProt P69786

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–477 Chain B； UniProt 1–477 Not recorded BGC beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.56 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 8QSR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IBA GLUCOSE PERMEASE (DOMAIN IIB), NMR, 11 STRUCTURES Deposited 1996-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 391–476（86 aa） Fragment：DOMAIN IIB
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1O2F COMPLEX OF ENZYME IIAGLC AND IIBGLC PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE Deposited 2003-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 387–476（90 aa）
Not recorded PO3 PHOSPHITE ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 10 mM SODIUM PHOSPHATE
Resolution not provided
3BP3 Crystal structure of EIIB Deposited 2007-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 396–477（82 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.65 Å R-free 0.241
3BP3 Crystal structure of EIIB Deposited 2007-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 396–477（82 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.65 Å R-free 0.241
3BP8 Crystal structure of Mlc/EIIB complex Deposited 2007-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 401–475（75 aa） Fragment：UNP residues 401-475
Chain D 401–475（75 aa） Fragment：UNP residues 401-475
Not recorded ACT ACETATE ION × 3 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；6% PEG 6K, 0.1M MgCl2, 0.1M sodium acetate, pH5.5
Resolution 2.85 Å R-free 0.301
3BP8 Crystal structure of Mlc/EIIB complex Deposited 2007-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 401–475（75 aa） Fragment：UNP residues 401-475
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；6% PEG 6K, 0.1M MgCl2, 0.1M sodium acetate, pH5.5
Resolution 2.85 Å R-free 0.301
3BP8 Crystal structure of Mlc/EIIB complex Deposited 2007-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 401–475（75 aa） Fragment：UNP residues 401-475
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；6% PEG 6K, 0.1M MgCl2, 0.1M sodium acetate, pH5.5
Resolution 2.85 Å R-free 0.301
8QST Cryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in the inward- and outward-facing conformation Deposited 2023-10-11 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–477（477 aa）
Chain B 1–477（477 aa）
Not recorded BGC beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
9HNP Cryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in an intermediate state Deposited 2024-12-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–477（477 aa）
Chain B 1–477（477 aa）
Not recorded LMT DODECYL-BETA-D-MALTOSIDE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTGCB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–477； UniProt 1–477 Author chain B； PDBConstruct 1–477； UniProt 1–477

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 8qsr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8qsr
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8qsr
Deposition date deposition_date2023-10-11
Structure title titleCryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in the inward-facing conformation
Keywords keywordsglucose transport protein, membrane protein, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier30.32 Å
Radius of gyration Rg (electron density) rg_electron30.46 Å
Forward intensity I(0) i086213300.00
Molecular weight molecular_weight82096.0 kDa
Excluded volume excluded_volume106290 ų
Envelope volume envelope_volume124870 ų
Hydration-shell volume shell_volume35692 ų
Envelope diameter envelope_diameter108.0 Å
Shell Rg shell_rg35.85 Å
Envelope Rg envelope_rg30.44 Å
Shape Rg shape_rg30.46 Å
Total Rg total_rg30.97 Å
Total atoms total_atoms11746
Residues n_residues766
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax104.0 Å
Rg (real space) rg_real30.50 Å
Rg uncertainty (real space) rg_real_error0.75 Å
I(0) (real space) i0_real8.6210e+07
I(0) uncertainty (real space) i0_real_error1.3660e+06
Rg (reciprocal space) rg_reciprocal30.42 Å
I(0) (reciprocal space) i0_reciprocal86210000.0000
Solution quality estimate total_estimate0.8502
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary32.0 Å
Skewness Skewness skewness0.536
Kurtosis Kurtosis kurtosis-0.159
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9612000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.906; Smooth: 0.829
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

9. Files and Curves (10)