9s4k

Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 4 left tail

Method: ELECTRON MICROSCOPY Dmax: 115.8 Å Quality: GOOD

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

Hemoglobin subunit alpha

OrganismNot specified

UniProt P69905

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 3–142 Not recorded Hemoglobin subunit beta × 1 (P68871) Iron-regulated surface determinant protein H × 2 (Q8NW39) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE;blot time 3 s Resolution 4.00 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.

348 other PDB entries and 412 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–140; UniProt 3–142

Hemoglobin subunit beta

OrganismNot specified

UniProt P68871

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 B; UniProt 3–147 Not recorded Hemoglobin subunit alpha × 1 (P69905) Iron-regulated surface determinant protein H × 2 (Q8NW39) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE;blot time 3 s Resolution 4.00 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.

343 other PDB entries and 399 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBB_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–145; UniProt 3–147

Iron-regulated surface determinant protein H

Staphylococcus aureus

UniProt Q8NW39

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 326–665 Chain D; UniProt 326–665 Not recorded Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE;blot time 3 s Resolution 4.00 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.

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

View Construct and Data Evidence
UniProt name ISDH_STAAW
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 2–341; UniProt 326–665 Author chain D; PDBConstruct 2–341; UniProt 326–665

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 9s4k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9s4k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9s4k
Deposition date deposition_date2025-07-28
Structure title titleHuman carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 4 left tail
Keywords keywordsIron acquisition, Hemophore, Hemoglobin, NEAT domain, METAL TRANSPORT; METAL TRANSPORT
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier35.38
Radius of gyration Rg (electron density) rg_electron34.94
Forward intensity I(0) i0127233000.00
Molecular weight molecular_weight92668.0 kDa
Excluded volume excluded_volume116850 ų
Envelope volume envelope_volume158940 ų
Hydration-shell volume shell_volume39319 ų
Envelope diameter envelope_diameter118.0
Shell Rg shell_rg39.71
Envelope Rg envelope_rg34.98
Shape Rg shape_rg34.92
Total Rg total_rg35.37
Total atoms total_atoms6554
Residues n_residues806
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax115.8
Rg (real space) rg_real35.44
Rg uncertainty (real space) rg_real_error0.96
I(0) (real space) i0_real1.2720e+08
I(0) uncertainty (real space) i0_real_error2.1950e+06
Rg (reciprocal space) rg_reciprocal35.41
I(0) (reciprocal space) i0_reciprocal127200000.0000
Solution quality estimate total_estimate0.8260
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.6
Skewness Skewness skewness0.326
Kurtosis Kurtosis kurtosis-0.542
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22740000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)