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- EMDB-54567: Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54567
TitleHuman carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 4 left tail
Map datarefined map with cryoSPARC
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


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / 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 space / extracellular exosome / extracellular region / metal ion binding / membrane / 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: 4.0 Å
AuthorsBuoli Comani V / De Bei O / Gragera M / 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: J Struct Biol X / Year: 2025
Title: Hemoglobin receptor redundancy in : molecular flexibility as a determinant of divergent hemophore activity.
Authors: Valeria Buoli Comani / Omar De Bei / Francesca Pancrazi / Marcos Gragera / Giulia Paris / Marialaura Marchetti / Barbara Campanini / Luca Ronda / Ben F Luisi / Serena Faggiano / Anna Rita ...Authors: Valeria Buoli Comani / Omar De Bei / Francesca Pancrazi / Marcos Gragera / Giulia Paris / Marialaura Marchetti / Barbara Campanini / Luca Ronda / Ben F Luisi / Serena Faggiano / Anna Rita Bizzarri / Stefano Bettati /
Abstract: To overcome iron limitation in the host, exploits sophisticated mechanisms to acquire this essential nutrient, particularly from hemoglobin (Hb). The bacterial hemophores IsdH and IsdB play key ...To overcome iron limitation in the host, exploits sophisticated mechanisms to acquire this essential nutrient, particularly from hemoglobin (Hb). The bacterial hemophores IsdH and IsdB play key roles in binding Hb and extracting heme, but the structural and mechanistic differences underlying their individual contributions remain poorly defined. In this study, we dissected the molecular mechanisms by which IsdH engages Hb and mediates heme extraction, using cryo-electron microscopy, biochemical assays, and single-molecule force spectroscopy. Our structural analyses revealed pronounced conformational heterogeneity within IsdH:Hb complexes, highlighting marked flexibility in the heme-binding domain of IsdH, likely underlying its distinct functional behavior. This plasticity contrasts with the more rigid architecture of IsdB. The flexibility observed in IsdH correlates with our biochemical and biophysical findings, supporting its functional relevance. Unlike IsdB, IsdH does not display selectivity for α- or β-Hb chains and shows reduced involvement of the heme-binding domain in Hb recognition. It also follows a distinct kinetic mechanism for heme capture, which begins upon binding but proceeds more slowly than in IsdB. Finally, IsdH does not exhibit the catch bond-like behavior characteristic of IsdB, suggesting it may act in different physiological niches or conditions. Collectively, these findings highlight a distinct mode of Hb engagement by IsdH, shaped by its dynamic and flexible architecture, and provide mechanistic insight into the diversity of iron acquisition strategies employed by .
History
DepositionJul 28, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54567.png

Downloads & links

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Map

FileDownload / File: emd_54567.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined map with cryoSPARC
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 260 pix.
= 258. Å		0.99 Å/pix.
x 260 pix.
= 258. Å		0.99 Å/pix.
x 260 pix.
= 258. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99231 Å
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Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.24113941 - 0.60349053
Average (Standard dev.)0.00024954652 (±0.019336566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 258.0001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54567_msk_1.map
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Additional map: postprocessed map with deepEMhancer

Fileemd_54567_additional_1.map
Annotationpostprocessed map with deepEMhancer
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Additional map: 3DVA intermediate volume 2

Fileemd_54567_additional_2.map
Annotation3DVA intermediate volume 2
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Additional map: 3DVA intermediate volume 4

Fileemd_54567_additional_3.map
Annotation3DVA intermediate volume 4
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Additional map: 3DVA intermediate volume 1

Fileemd_54567_additional_4.map
Annotation3DVA intermediate volume 1
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Additional map: 3DVA intermediate volume 0 - LEFT TAIL used...

Fileemd_54567_additional_5.map
Annotation3DVA intermediate volume 0 - LEFT TAIL used for the refinement of principal EM map
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Additional map: 3DVA intermediate volume 3

Fileemd_54567_additional_6.map
Annotation3DVA intermediate volume 3
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Half map: half map 2

Fileemd_54567_half_map_1.map
Annotationhalf map 2
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Half map: half map 1

Fileemd_54567_half_map_2.map
Annotationhalf map 1
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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 41.500141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADESLQDAI KNPAIIDKEH TADNWRPIDF QMKNDKGERQ FYHYASTVEP ATVIFTKTGP IIELGLKTAS TWKKFEVYEG DKKLPVELV SYDSDKDYAY IRFPVSNGTR EVKIVSSIEY GENIHEDYDY TLMVFAQPIT NNPDDYVDEE TYNLQKLLAP Y HKAKTLER ...String:
MADESLQDAI KNPAIIDKEH TADNWRPIDF QMKNDKGERQ FYHYASTVEP ATVIFTKTGP IIELGLKTAS TWKKFEVYEG DKKLPVELV SYDSDKDYAY IRFPVSNGTR EVKIVSSIEY GENIHEDYDY TLMVFAQPIT NNPDDYVDEE TYNLQKLLAP Y HKAKTLER QVYELEKLQE KLPEKYKAEY KKKLDQTRVE LADQVKSAVT EFENVTPTND QLTDVQEAHF VVFESEENSE SV MDGFVEH PFYTATLNGQ KYVVMKTKDD SYWKDLIVEG KRVTTVSKDP KNNSRTLIFP YIPDKAVYNA IVKVVVANIG YEG QYHVRI INQDINTKDD DTSQNENLYF QSAWSHPQFE K

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

Concentration6 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: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
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: 2993888
CTF correctionType: NONE
Startup modelType of model: OTHER
Details: ab initio model generated by stochastic gradient descent
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 8528
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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-9s4k:
Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 4 left tail

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