7pch

Human carboxyhemoglobin bound to Staphylococcus aureus hemophore IsdB - 1:2 complex

Method: ELECTRON MICROSCOPY Dmax: 120.6 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–142 Chain C; UniProt 2–142 Not recorded Hemoglobin subunit beta × 2 (P68871) Iron-regulated surface determinant protein B × 2 (Q8NX66) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2;CHAPSO was added immediately before plunge freezing to overcome preferred orientation of the particles in the vitreous ice. cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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 1–141; UniProt 2–142 Author chain C; PDBConstruct 1–141; UniProt 2–142

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–147 Chain D; UniProt 2–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) Iron-regulated surface determinant protein B × 2 (Q8NX66) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2;CHAPSO was added immediately before plunge freezing to overcome preferred orientation of the particles in the vitreous ice. cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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 1–146; UniProt 2–147 Author chain D; PDBConstruct 1–146; UniProt 2–147

Iron-regulated surface determinant protein B

Staphylococcus aureus subsp. aureus MW2

UniProt Q8NX66

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 125–485 Chain F; UniProt 125–485 Not recorded Hemoglobin subunit alpha × 2 (P69905) Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2;CHAPSO was added immediately before plunge freezing to overcome preferred orientation of the particles in the vitreous ice. cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ISDB_STAAW
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 2–362; UniProt 125–485 Author chain F; PDBConstruct 2–362; UniProt 125–485

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 7pch

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7pch
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7pch
Deposition date deposition_date2021-08-03
Structure title titleHuman carboxyhemoglobin bound to Staphylococcus aureus hemophore IsdB - 1:2 complex
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_guinier36.03
Radius of gyration Rg (electron density) rg_electron35.10
Forward intensity I(0) i0302864000.00
Molecular weight molecular_weight143940.0 kDa
Excluded volume excluded_volume181680 ų
Envelope volume envelope_volume238470 ų
Hydration-shell volume shell_volume55254 ų
Envelope diameter envelope_diameter126.3
Shell Rg shell_rg42.52
Envelope Rg envelope_rg34.58
Shape Rg shape_rg35.05
Total Rg total_rg35.81
Total atoms total_atoms10156
Residues n_residues1254
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 dmax120.6
Rg (real space) rg_real35.83
Rg uncertainty (real space) rg_real_error1.00
I(0) (real space) i0_real3.0290e+08
I(0) uncertainty (real space) i0_real_error4.5600e+06
Rg (reciprocal space) rg_reciprocal35.96
I(0) (reciprocal space) i0_reciprocal302900000.0000
Solution quality estimate total_estimate0.8755
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.6
Skewness Skewness skewness0.138
Kurtosis Kurtosis kurtosis-0.367
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha36430000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.960

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id7pchE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850
Domain ID domain_id7pchE02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1270
Domain ID domain_id7pchE03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850
Domain ID domain_id7pchF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850
Domain ID domain_id7pchF02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1270
Domain ID domain_id7pchF03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850

8. Citations (1)

9. Files and Curves (10)