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9yjw

Transferrin Binding Protein A

Method: ELECTRON MICROSCOPY Dmax: 122.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transferrin-binding protein A

Neisseria meningitidis serogroup B

UniProt Q9JPJ0

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 25–915 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.20 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 9YJW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3V89 The crystal structure of transferrin binding protein A (TbpA) from Neisseria meningitidis serogroup B in complex with the C-lobe of human transferrin Deposited 2011-12-22 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–915（891 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；21% PEG 1000, 100mM sodium acetate buffer (pH 4.8), 200mM NaCl, 0.1% LDAO and 3% heptane-1,2,3-triol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.287
9CLT Transferrin Binding Protein A in complex with transferrin binding protein B and transferrin (iron bound to N lobe only) Deposited 2024-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–915（891 aa）
Not recorded BCT BICARBONATE ION × 1 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9CMG Transferrin Binding Protein A in complex with transferrin binding protein B and transferrin (iron bound in both lobes of Tf) Deposited 2024-07-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–915（891 aa）
Not recorded BCT BICARBONATE ION × 2 FE FE (III) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
9DC4 Transferrin Binding Protein A in complex with transferrin binding protein B, transferrin and globular domain of TonB Deposited 2024-08-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 25–915（891 aa）
Not recorded BCT BICARBONATE ION × 1 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9NHQ The cryo-EM structure of NmTbpA and NmTbpB in a complex Deposited 2025-02-25 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–915（891 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å

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

View Construct and Data Evidence
UniProt name Q9JPJ0_NEIME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 25–915； UniProt 25–915

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 9yjw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9yjw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9yjw
Deposition date deposition_date2025-10-05
Structure title titleTransferrin Binding Protein A
Keywords keywordsMembrane protein, metal transporter, iron import, ton B-dependent transporter, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.48 Å
Radius of gyration Rg (electron density) rg_electron32.75 Å
Forward intensity I(0) i0148760000.00
Molecular weight molecular_weight93522.0 kDa
Excluded volume excluded_volume115510 ų
Envelope volume envelope_volume154510 ų
Hydration-shell volume shell_volume41351 ų
Envelope diameter envelope_diameter134.7 Å
Shell Rg shell_rg37.55 Å
Envelope Rg envelope_rg33.25 Å
Shape Rg shape_rg32.75 Å
Total Rg total_rg33.13 Å
Total atoms total_atoms6609
Residues n_residues842
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 dmax122.6 Å
Rg (real space) rg_real32.80 Å
Rg uncertainty (real space) rg_real_error1.27 Å
I(0) (real space) i0_real1.4880e+08
I(0) uncertainty (real space) i0_real_error2.5560e+06
Rg (reciprocal space) rg_reciprocal32.66 Å
I(0) (reciprocal space) i0_reciprocal148700000.0000
Solution quality estimate total_estimate0.7901
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.5 Å
Skewness Skewness skewness0.709
Kurtosis Kurtosis kurtosis0.422
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20320000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.491; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.864; Smooth: 0.930
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)