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4r9u

Structure of vitamin B12 transporter BtuCD in a nucleotide-bound outward facing state

Method: X-RAY DIFFRACTION Dmax: 109.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vitamin B12 import system permease protein BtuC

Escherichia coli

UniProt P06609

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 1–326 Chain B； UniProt 1–326 Mutation：C18S, C32S, C120S, C156S, C205S, C206S, C267S Vitamin B12 import ATP-binding protein BtuD × 2 （P06611） LDA LAURYL DIMETHYLAMINE-N-OXIDE × 4 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.9；283 K；PEG2000MME (14-18%), NaCl (1.2 M), ADA (100 mM, pH 6.9), VAPOR DIFFUSION, SITTING DROP, temperature 283K Resolution 2.79 Å R-free 0.246

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 4R9U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1L7V Bacterial ABC Transporter Involved in B12 Uptake Deposited 2002-03-18 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–326（326 aa）
Chain B 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) V4O CYCLO-TETRAMETAVANADATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；278 K；PEG 2000, LDAO, Tris, magnesium nitrate, MPD, D2O, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Resolution 3.20 Å R-free 0.286
2QI9 ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF Deposited 2007-07-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–326（326 aa）
Chain B 1–326（326 aa）
Mutation：C18S, C32S, C120S, C156S, C205S, C206S, C267S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C18S, C32S, C120S, C156S, C205S, C206S, C267S Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6 1PE PENTAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；30-38% (w/v) polyethylene glycol 400, 50mM either of Tris‑HCl pH 8.4 or Glycine-NaOH pH 9.4 and 400mM (NH4)2SO4., VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.280
4DBL Crystal structure of E159Q mutant of BtuCDF Deposited 2012-01-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–326（326 aa）
Chain B 1–326（326 aa）
Mutation：C18S, C32S, C120S, C156S, C205S, C206S, C267S Mutation：C18S, C32S, C120S, C156S, C205S, C206S, C267S PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；0.1M sodium citrate, pH 5.4, 0.3-0.4M ammonium sulphate, 30-35% PEG-400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.49 Å R-free 0.251
4DBL Crystal structure of E159Q mutant of BtuCDF Deposited 2012-01-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–326（326 aa）
Chain G 1–326（326 aa）
Mutation：C18S, C32S, C120S, C156S, C205S, C206S, C267S Mutation：C18S, C32S, C120S, C156S, C205S, C206S, C267S PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；0.1M sodium citrate, pH 5.4, 0.3-0.4M ammonium sulphate, 30-35% PEG-400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.49 Å R-free 0.251
4FI3 Structure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state Deposited 2012-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–326（326 aa）
Chain B 1–326（326 aa）
Mutation：C18S, C32S, C120S, C156S, C205S, C206S, C267S Mutation：C18S, C32S, C120S, C156S, C205S, C206S, C267S ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；20-30% PEG400, 100 mM ADA pH6.8, 100 mM Na/K-citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.47 Å R-free 0.274

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BTUC_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–333； UniProt 1–326 Author chain B； PDBConstruct 8–333； UniProt 1–326

Vitamin B12 import ATP-binding protein BtuD

Escherichia coli

UniProt P06611

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 C； UniProt 1–249 Chain D； UniProt 1–249 Mutation：C180S, E159Q, N162C Vitamin B12 import system permease protein BtuC × 2 （P06609） LDA LAURYL DIMETHYLAMINE-N-OXIDE × 4 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.9；283 K；PEG2000MME (14-18%), NaCl (1.2 M), ADA (100 mM, pH 6.9), VAPOR DIFFUSION, SITTING DROP, temperature 283K Resolution 2.79 Å R-free 0.246

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 4R9U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1L7V Bacterial ABC Transporter Involved in B12 Uptake Deposited 2002-03-18 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–249（249 aa）
Chain D 1–249（249 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) V4O CYCLO-TETRAMETAVANADATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；278 K；PEG 2000, LDAO, Tris, magnesium nitrate, MPD, D2O, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Resolution 3.20 Å R-free 0.286
2QI9 ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF Deposited 2007-07-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–249（249 aa）
Chain D 1–249（249 aa）
Mutation：C180S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C180S Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6 1PE PENTAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；30-38% (w/v) polyethylene glycol 400, 50mM either of Tris‑HCl pH 8.4 or Glycine-NaOH pH 9.4 and 400mM (NH4)2SO4., VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.280
4DBL Crystal structure of E159Q mutant of BtuCDF Deposited 2012-01-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–249（249 aa）
Chain D 1–249（249 aa）
Mutation：C180S Mutation：C180S PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；0.1M sodium citrate, pH 5.4, 0.3-0.4M ammonium sulphate, 30-35% PEG-400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.49 Å R-free 0.251
4DBL Crystal structure of E159Q mutant of BtuCDF Deposited 2012-01-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–249（249 aa）
Chain I 1–249（249 aa）
Mutation：C180S Mutation：C180S PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；0.1M sodium citrate, pH 5.4, 0.3-0.4M ammonium sulphate, 30-35% PEG-400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.49 Å R-free 0.251
4FI3 Structure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state Deposited 2012-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–249（249 aa）
Chain D 1–249（249 aa）
Mutation：C180S, E159Q, N162C Mutation：C180S, E159Q, N162C ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；20-30% PEG400, 100 mM ADA pH6.8, 100 mM Na/K-citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.47 Å R-free 0.274

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BTUD_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–249； UniProt 1–249 Author chain D； PDBConstruct 1–249； UniProt 1–249

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 4r9u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4r9u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4r9u
Deposition date deposition_date2014-09-08
Structure title titleStructure of vitamin B12 transporter BtuCD in a nucleotide-bound outward facing state
Keywords keywordsnucleotide, AMPPNP, ATP binding cassette, membrane protein, ABC transporter, BtuF, inner membrane, HYDROLASE; HYDROLASE
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_guinier33.75 Å
Radius of gyration Rg (electron density) rg_electron33.25 Å
Forward intensity I(0) i0220031000.00
Molecular weight molecular_weight125060.0 kDa
Excluded volume excluded_volume159490 ų
Envelope volume envelope_volume202940 ų
Hydration-shell volume shell_volume50203 ų
Envelope diameter envelope_diameter112.0 Å
Shell Rg shell_rg40.77 Å
Envelope Rg envelope_rg33.03 Å
Shape Rg shape_rg33.27 Å
Total Rg total_rg33.76 Å
Total atoms total_atoms8792
Residues n_residues1144
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 dmax109.7 Å
Rg (real space) rg_real33.71 Å
Rg uncertainty (real space) rg_real_error0.94 Å
I(0) (real space) i0_real2.2000e+08
I(0) uncertainty (real space) i0_real_error3.9090e+06
Rg (reciprocal space) rg_reciprocal33.74 Å
I(0) (reciprocal space) i0_reciprocal220000000.0000
Solution quality estimate total_estimate0.8210
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.7 Å
Skewness Skewness skewness0.315
Kurtosis Kurtosis kurtosis-0.415
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha49720000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4r9ua_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.22 — ABC transporter involved in vitamin B12 uptake, BtuC
Superfamily Superfamily superfamilyf.22.1 — ABC transporter involved in vitamin B12 uptake, BtuC
Family Family familyf.22.1.1 — ABC transporter involved in vitamin B12 uptake, BtuC
Domain ID domain_idd4r9ub_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.22 — ABC transporter involved in vitamin B12 uptake, BtuC
Superfamily Superfamily superfamilyf.22.1 — ABC transporter involved in vitamin B12 uptake, BtuC
Family Family familyf.22.1.1 — ABC transporter involved in vitamin B12 uptake, BtuC
Domain ID domain_idd4r9uc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like
Domain ID domain_idd4r9ud_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like

CATH v4.4 (4 domains)

Domain ID domain_id4r9uA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3470 — ABC transporter involved in vitamin B12 uptake, BtuC
Homologous superfamily homologous superfamily10 — ABC transporter involved in vitamin B12 uptake, BtuC
Domain ID domain_id4r9uB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3470 — ABC transporter involved in vitamin B12 uptake, BtuC
Homologous superfamily homologous superfamily10 — ABC transporter involved in vitamin B12 uptake, BtuC
Domain ID domain_id4r9uC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4r9uD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)