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9nhq

The cryo-EM structure of NmTbpA and NmTbpB in a complex

Method: ELECTRON MICROSCOPY Dmax: 180.1 Å Quality: REASONABLE
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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 25–915 Not recorded Transferrin-binding protein B × 1 （Q9JPI9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 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 9NHQ 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 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 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 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 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
9YJW Transferrin Binding Protein A Deposited 2025-10-05 Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–915（891 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
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

Transferrin-binding protein B

Neisseria meningitidis serogroup B

UniProt Q9JPI9

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 22–712 Not recorded Transferrin-binding protein A × 1 （Q9JPJ0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 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 9NHQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3V8U The crystal structure of transferrin binding protein B (TbpB) from Neisseria meningitidis serogroup B Deposited 2011-12-23 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–712（691 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；2.0 M NaCl and 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.308
3V8U The crystal structure of transferrin binding protein B (TbpB) from Neisseria meningitidis serogroup B Deposited 2011-12-23 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–712（691 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；2.0 M NaCl and 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.308
9CLM Transferrin Binding Protein A in complex with transferrin binding protein B and two molecules of transferrin Deposited 2024-07-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–712（712 aa）
Not recorded BCT BICARBONATE ION × 3 FE FE (III) ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
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 construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 20–712（693 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 construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 20–712（693 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 22–712（691 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
9PA8 NmTbpB and Tf protein complex Deposited 2025-06-25 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–712（691 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 3.10 Å
9YZ4 Neisseria gonorrhoeae Transferrin Binding Protein A in complex with Transferrin Binding Protein B and transferrin (iron bound in N lobe only) Deposited 2025-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–712（692 aa）
Not recorded BCT BICARBONATE ION × 1 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.26 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9JPI9_NEIME
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 23–713； UniProt 22–712

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 9nhq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9nhq
Deposition date deposition_date2025-02-25
Structure title titleThe cryo-EM structure of NmTbpA and NmTbpB in a complex
Keywords keywordsNeisseria outer membrane protein, Ton B dependent transporter, lipo protein, iron transport, MEMBRANE PROTEIN; MEMBRANE 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_guinier49.49 Å
Radius of gyration Rg (electron density) rg_electron50.46 Å
Forward intensity I(0) i0365154000.00
Molecular weight molecular_weight151840.0 kDa
Excluded volume excluded_volume187400 ų
Envelope volume envelope_volume282580 ų
Hydration-shell volume shell_volume50261 ų
Envelope diameter envelope_diameter175.5 Å
Shell Rg shell_rg49.19 Å
Envelope Rg envelope_rg49.27 Å
Shape Rg shape_rg50.50 Å
Total Rg total_rg50.27 Å
Total atoms total_atoms10738
Residues n_residues1400
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 dmax180.1 Å
Rg (real space) rg_real50.31 Å
Rg uncertainty (real space) rg_real_error2.57 Å
I(0) (real space) i0_real3.6520e+08
I(0) uncertainty (real space) i0_real_error7.4390e+06
Rg (reciprocal space) rg_reciprocal49.50 Å
I(0) (reciprocal space) i0_reciprocal364800000.0000
Solution quality estimate total_estimate0.6938
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.4 Å
Skewness Skewness skewness0.520
Kurtosis Kurtosis kurtosis-0.525
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28520000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.526; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.437; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)