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- EMDB-55389: Human carboxyhemoglobin bound to full-length Staphylococcus aureu... -

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Basic information

Entry
Database: EMDB / ID: EMD-55389
TitleHuman carboxyhemoglobin bound to full-length Staphylococcus aureus IsdH - IsdH:Hbdim complex
Map data
Sample
  • Complex: Complex between human carboxyhemoglobin and Staphylococcus aureus hemophore IsdH
    • Complex: Human hemoglobin subunit alpha
      • Protein or peptide: Hemoglobin subunit alpha
    • Complex: Human hemoglobin subunit beta
      • Protein or peptide: Hemoglobin subunit beta
    • Complex: Iron-regulated surface determinant protein H
      • Protein or peptide: Iron-regulated surface determinant protein H
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
KeywordsIron acquisition / Hemophore / Hemoglobin / NEAT domain / METAL TRANSPORT
Function / homology
Function and homology information


cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / erythrocyte development / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / Late endosomal microautophagy / platelet aggregation / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / : / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / YSIRK type signal peptide ...Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
Hemoglobin subunit beta / Hemoglobin subunit alpha / Iron-regulated surface determinant protein H
Similarity search - Component
Biological speciesHomo sapiens (human) / Staphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 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 16, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55389.png

Downloads & links

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Map

FileDownload / File: emd_55389.map.gz / Format: CCP4 / Size: 448.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 490 pix.
= 496.782 Å		1.01 Å/pix.
x 490 pix.
= 496.782 Å		1.01 Å/pix.
x 490 pix.
= 496.782 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01384 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.012089457 - 0.03858508
Average (Standard dev.)-0.000014290289 (±0.0006877597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions490490490
Spacing490490490
CellA=B=C: 496.7821 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55389_msk_1.map
Projections & Slices
AxesZYX

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Additional map: RELION postprocessed map

Fileemd_55389_additional_1.map
AnnotationRELION postprocessed map
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Additional map: DeepEMhancer map

Fileemd_55389_additional_2.map
AnnotationDeepEMhancer map
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Histogram

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Half map: half map 1

Fileemd_55389_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_55389_half_map_2.map
Annotationhalf map 2
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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
      • Protein or peptide: Hemoglobin subunit alpha
    • Complex: Human hemoglobin subunit beta
      • Protein or peptide: Hemoglobin subunit beta
    • Complex: Iron-regulated surface determinant protein H
      • Protein or peptide: Iron-regulated surface determinant protein H
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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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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Macromolecule #1: Hemoglobin subunit alpha

MacromoleculeName: Hemoglobin subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.051222 KDa
SequenceString:
LSPADKTNVK AAWGKVGAHA GEYGAEALER MFLSFPTTKT YFPHFDLSHG SAQVKGHGKK VADALTNAVA HVDDMPNALS ALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R

UniProtKB: Hemoglobin subunit alpha

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Macromolecule #2: Hemoglobin subunit beta

MacromoleculeName: Hemoglobin subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.791067 KDa
SequenceString:
HLTPEEKSAV TALWGKVNVD EVGGEALGRL LVVYPWTQRF FESFGDLSTP DAVMGNPKVK AHGKKVLGAF SDGLAHLDNL KGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH

UniProtKB: Hemoglobin subunit beta

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Macromolecule #3: Iron-regulated surface determinant protein H

MacromoleculeName: Iron-regulated surface determinant protein H / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 70.354781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH ADESLKDAIK DPALENKEHD IGPREQVNFQ LLDKNNETQY YHFFSIKDPA DVYYTKKKAE VELDINTAS TWKKFEVYEN NQKLPVRLVS YSPVPEDHAY IRFPVSDGTQ ELKIVSSTQI DDGEETNYDY TKLVFAKPIY N DPSLVKSD ...String:
MGSSHHHHHH SSGLVPRGSH ADESLKDAIK DPALENKEHD IGPREQVNFQ LLDKNNETQY YHFFSIKDPA DVYYTKKKAE VELDINTAS TWKKFEVYEN NQKLPVRLVS YSPVPEDHAY IRFPVSDGTQ ELKIVSSTQI DDGEETNYDY TKLVFAKPIY N DPSLVKSD TNDAVVTNDQ SSSDASNQTN TNTSNQNTST INNANNQPQA TTNMSQPAQP KSSANADQAS SQPAHETNSN GN TNDKTNE SSNQSDVNQQ YPPADESLQD AIKNPAIIDK EHTADNWRPI DFQMKNDKGE RQFYHYASTV EPATVIFTKT GPI IELGLK TASTWKKFEV YEGDKKLPVE LVSYDSDKDY AYIRFPVSNG TREVKIVSSI EYGENIHEDY DYTLMVFAQP ITNN PDDYV DEETYNLQKL LAPYHKAKTL ERQVYELEKL QEKLPEKYKA EYKKKLDQTR VELADQVKSA VTEFENVTPT NDQLT DVQE AHFVVFESEE NSESVMDGFV EHPFYTATLN GQKYVVMKTK DDSYWKDLIV EGKRVTTVSK DPKNNSRTLI FPYIPD KAV YNAIVKVVVA NIGYEGQYHV RIINQDINTK DDDTSQNENL YFQSAWSHPQ FEK

UniProtKB: Iron-regulated surface determinant protein H

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Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 4 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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 reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 66502
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
Output model

PDB-9szw:
Human carboxyhemoglobin bound to full-length Staphylococcus aureus IsdH - IsdH:Hbdim complex

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