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- EMDB-54546: Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54546
TitleHuman carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 3IsdH(alpha2beta):Hbtet complex
Map dataRELION postprocessed map
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 / 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 / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / 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: 3.1 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 Staphylococcus aureus: molecular flexibility as a determinant of divergent hemophore activity
Authors: Comani VB / Bei OD / Pancrazi F / Gragera M / Paris G / Marchetti M / Campanini B / Ronda L / Luisi BF / Faggiano S / Bizzarri AR / Bettati S
History
DepositionJul 24, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54546.png

Downloads & links

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Map

FileDownload / File: emd_54546.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99231 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0007
Minimum - Maximum-0.002186856 - 0.004861267
Average (Standard dev.)0.000006418035 (±0.00010140511)
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_54546_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: deepEMhancer map

Fileemd_54546_additional_1.map
AnnotationdeepEMhancer map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_54546_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_54546_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: 2 / 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: 2 / 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: 3 / 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: 4 / 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 137997
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-9s3p:
Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 3IsdH(alpha2beta):Hbtet complex

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