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- EMDB-55478: Human carboxyhemoglobin bound to full-length Staphylococcus aureu... -

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Basic information

Entry
Database: EMDB / ID: EMD-55478
TitleHuman carboxyhemoglobin bound to full-length Staphylococcus aureus IsdH - 1IsdH:2Hbdim complex
Map data
Sample
  • Complex: Complex between human carboxyhemoglobin and Staphylococcus aureus hemophore IsdH
    • Complex: Human hemoglobin subunit alpha
    • Complex: Human hemoglobin subunit beta
    • Complex: Iron-regulated surface determinant protein H
KeywordsIron acquisition / Hemophore / Hemoglobin / NEAT domain / METAL TRANSPORT
Biological speciesHomo sapiens (human) / Staphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.29 Å
AuthorsBuoli Comani V / De Bei O / Luisi BF / Bettati S
Funding support Italy, United Kingdom, 2 items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca2020AE3LTA Italy
Wellcome Trust200873/Z/16/Z United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Refining the mechanism of heme acquisition from free hemoglobin by IsdH.
Authors: Valeria Buoli Comani / Omar De Bei / Giulia Paris / Marialaura Marchetti / Francesca Pancrazi / Barbara Campanini / Luca Ronda / Ben F Luisi / Serena Faggiano / Anna Rita Bizzarri / Stefano Bettati /
Abstract: is a human pathogen whose virulence depends on iron acquisition. The bacterium expresses the hemophores IsdB and IsdH that enable heme capture from host hemoglobin (Hb). Unlike IsdB, IsdH can bind ... is a human pathogen whose virulence depends on iron acquisition. The bacterium expresses the hemophores IsdB and IsdH that enable heme capture from host hemoglobin (Hb). Unlike IsdB, IsdH can bind both free Hb and Hb:haptoglobin (Hb:Hp) complexes. Here, we present a comprehensive structural analysis of full-length IsdH in complex with free Hb, overcoming the limitations of previous studies based on truncated IsdH constructs. Cryo-EM revealed a previously unobserved oligomeric state and a unique binding pose of the N-terminal Hb-binding domain, likely representing the initial step of Hb engagement. Time-resolved and single-molecule force spectroscopy experiments delineated the sequential steps and mechanical aspects of Hb binding and heme extraction. Together, these findings provide an integrated structural and functional view of the IsdH-Hb interaction in the absence of Hp, as may occur during hemolysis, and offer insights into heme scavenging and potential avenues for therapeutic inhibition.
History
DepositionOct 24, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55478.png

Downloads & links

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Map

FileDownload / File: emd_55478.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.46 Å/pix.
x 210 pix.
= 306.18 Å		1.46 Å/pix.
x 210 pix.
= 306.18 Å		1.46 Å/pix.
x 210 pix.
= 306.18 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.458 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.021257253 - 0.08016093
Average (Standard dev.)0.000148679 (±0.0027856557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 306.18 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55478_msk_1.map
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Additional map: deepEMhancer postprocessed map

Fileemd_55478_additional_1.map
AnnotationdeepEMhancer postprocessed map
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Additional map: RELION postprocessed map

Fileemd_55478_additional_2.map
AnnotationRELION postprocessed map
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Half map: #1

Fileemd_55478_half_map_1.map
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Half map: #2

Fileemd_55478_half_map_2.map
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Sample components

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Entire : Complex between human carboxyhemoglobin and Staphylococcus aureus...

EntireName: Complex between human carboxyhemoglobin and Staphylococcus aureus hemophore IsdH
Components
  • Complex: Complex between human carboxyhemoglobin and Staphylococcus aureus hemophore IsdH
    • Complex: Human hemoglobin subunit alpha
    • Complex: Human hemoglobin subunit beta
    • Complex: Iron-regulated surface determinant protein H

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Supramolecule #1: Complex between human carboxyhemoglobin and Staphylococcus aureus...

SupramoleculeName: Complex between human carboxyhemoglobin and Staphylococcus aureus hemophore IsdH
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Human hemoglobin subunit alpha

SupramoleculeName: Human hemoglobin subunit alpha / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Human hemoglobin subunit beta

SupramoleculeName: Human hemoglobin subunit beta / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Iron-regulated surface determinant protein H

SupramoleculeName: Iron-regulated surface determinant protein H / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
1.0 mMC10H16N2O8EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 15 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 38.5 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 3 s.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 4752 / Average exposure time: 4.39 sec. / Average electron dose: 53.78 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 654333
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold3 prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 4842
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 5.0) / Details: stochastic gradient descent
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationSoftware - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL

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