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2gsk

Structure of the BtuB:TonB Complex

Method: X-RAY DIFFRACTION Dmax: 83.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vitamin B12 transporter btuB

Escherichia coli

UniProt P06129

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 25–614 Not recorded protein TONB × 1 （P94739） CA CALCIUM ION × 2 CNC CYANOCOBALAMIN × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 4 OCT N-OCTANE × 3 HEX HEXANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.1；288 K；30% (v/v) PEG 300, 0.1M sodium acetate , pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 288K, pH 5.10 Resolution 2.10 Å R-free 0.251

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 2GSK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NQE OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI Deposited 2003-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–614（594 aa）
Not recorded MG MAGNESIUM ION × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG 3350, magnesium acetate, bis-tris, n-octyl tetraoxyethylene , pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.232
1NQF OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, METHIONINE SUBSTIUTION CONSTRUCT FOR SE-MET SAD PHASING Deposited 2003-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–614（594 aa）
Mutation：W317M, K319M, T321M, W516M, I518M, Y520M Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHELYENE, tris-(2-carboxyethyl)phosphine hydrochloride , pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.288
1NQG OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM Deposited 2003-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–614（594 aa）
Not recorded CA CALCIUM ION × 4 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG 3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHYLENE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.31 Å R-free 0.259
1NQH OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM AND CYANOCOBALAMIN (VITAMIN B12) SUBSTRATE Deposited 2003-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–614（594 aa）
Not recorded CA CALCIUM ION × 4 CNC CYANOCOBALAMIN × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG 3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHYLENE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.10 Å R-free 0.265
1UJW Structure of the complex between BtuB and Colicin E3 Receptor binding domain Deposited 2003-08-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–614（594 aa）
Not recorded GP1 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose × 2 LIM 3-OXO-PENTADECANOIC ACID × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 7 AAE ACETOACETIC ACID × 1 GOL GLYCEROL × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.75 Å R-free 0.293
2GUF In meso crystal structure of the cobalamin transporter, BtuB Deposited 2006-04-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–614（594 aa）
Not recorded MPG [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate × 11 FMT FORMIC ACID × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å R-free 0.225
2YSU Structure of the complex between BtuB and Colicin E2 receptor binding domain Deposited 2007-04-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–614（594 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å R-free 0.315
3M8B Crystal structure of spin-labeled BtuB V10R1 in the apo state Deposited 2010-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–614（594 aa）
Mutation：V10R1A C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 7 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；290 K；2.5% PEG3350,20 mM Bis Tris, 150 mM Magnesium acetate, 10 mM C8E4, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.44 Å R-free 0.248
3M8D Crystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin Deposited 2010-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–614（594 aa）
Mutation：V10R1A CNC CYANOCOBALAMIN × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；290 K；2.5% PEG3350, 150 mM calcium chloride, 20 mM Bis tris, 10 mM C8E4, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.44 Å R-free 0.275
3RGM Crystal structure of spin-labeled BtuB T156R1 Deposited 2011-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–614（594 aa）
Mutation：T156R1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 MG MAGNESIUM ION × 9 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；290 K；3.0% PEG3350, 200 mM magnesium acetate, 10mM C8E4, 20 mM Bis Tris pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.60 Å R-free 0.254
3RGN Crystal structure of spin-labeled BtuB W371R1 Deposited 2011-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–614（594 aa）
Mutation：W371R1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 7 MG MAGNESIUM ION × 3 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；290 K；3.0% PEG3350, 200 mM magnesium acetate, 10 mM C8E4, 20 mM Bis Tris pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.30 Å R-free 0.250
7NSU ColicinE9 intact translocation complex Deposited 2021-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 21–614（594 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane
Resolution 4.70 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BTUB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–590； UniProt 25–614

protein TONB

Escherichia coli

UniProt P94739

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 153–233 Fragment：C-TERMINAL DOMAIN Vitamin B12 transporter btuB × 1 （P06129） CA CALCIUM ION × 2 CNC CYANOCOBALAMIN × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 4 OCT N-OCTANE × 3 HEX HEXANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.1；288 K；30% (v/v) PEG 300, 0.1M sodium acetate , pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 288K, pH 5.10 Resolution 2.10 Å R-free 0.251

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 2GSK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2GRX Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for ferrichrome Deposited 2006-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 33–239（207 aa）
Not recorded PO4 PHOSPHATE ION × 1 FTT 3-HYDROXY-TETRADECANOIC ACID × 4 DPO DIPHOSPHATE × 1 DAO LAURIC ACID × 1 EAP 2-AMINO-VINYL-PHOSPHATE × 1 FCI FERRICROCIN-IRON × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；8% polyethylene glycol 4000, 50 mM MES (pH 6.0), 75 mM NaCl, 5% glycerol, 0.7% C8E4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.329
2GRX Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for ferrichrome Deposited 2006-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 33–239（207 aa）
Not recorded PO4 PHOSPHATE ION × 1 FTT 3-HYDROXY-TETRADECANOIC ACID × 4 DPO DIPHOSPHATE × 1 DAO LAURIC ACID × 1 EAP 2-AMINO-VINYL-PHOSPHATE × 1 FCI FERRICROCIN-IRON × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；8% polyethylene glycol 4000, 50 mM MES (pH 6.0), 75 mM NaCl, 5% glycerol, 0.7% C8E4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.329

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TONB_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–81； UniProt 153–233

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 2gsk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2gsk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2gsk
Deposition date deposition_date2006-04-26
Structure title titleStructure of the BtuB:TonB Complex
Keywords keywordsOUTER-MEMBRANE ACTIVE TRANSPORT, BETA-BARREL, TONB, MEMBRANE PROTEIN, SIGNALING PROTEIN-MEMBRANE PROTEIN COMPLEX; SIGNALING PROTEIN/MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.76 Å
Radius of gyration Rg (electron density) rg_electron25.11 Å
Forward intensity I(0) i092329100.00
Molecular weight molecular_weight76019.0 kDa
Excluded volume excluded_volume95211 ų
Envelope volume envelope_volume116240 ų
Hydration-shell volume shell_volume37069 ų
Envelope diameter envelope_diameter84.6 Å
Shell Rg shell_rg33.90 Å
Envelope Rg envelope_rg25.07 Å
Shape Rg shape_rg25.13 Å
Total Rg total_rg25.95 Å
Total atoms total_atoms5384
Residues n_residues671
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 dmax83.1 Å
Rg (real space) rg_real25.62 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real9.2330e+07
I(0) uncertainty (real space) i0_real_error1.1850e+06
Rg (reciprocal space) rg_reciprocal25.66 Å
I(0) (reciprocal space) i0_reciprocal92330000.0000
Solution quality estimate total_estimate0.8802
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5 Å
Skewness Skewness skewness0.213
Kurtosis Kurtosis kurtosis-0.276
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27730000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.981
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2gska_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamilyf.4.3 — Porins
Family Family familyf.4.3.3 — Ligand-gated protein channel
Domain ID domain_idd2gskb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.212 — TolA/TonB C-terminal domain
Superfamily Superfamily superfamilyd.212.1 — TolA/TonB C-terminal domain
Family Family familyd.212.1.2 — TonB

CATH v4.4 (3 domains)

Domain ID domain_id2gskA01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily10 — TonB-dependent receptor, plug domain
Domain ID domain_id2gskA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily20 — TonB-dependent receptor, beta-barrel domain
Domain ID domain_id2gskB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2420 — TolA/TonB C-terminal domain
Homologous superfamily homologous superfamily10 — TonB
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8. Citations (2)

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9. Files and Curves (10)