[English] 日本語
Yorodumi
- EMDB-55478: Human carboxyhemoglobin bound to full-length Staphylococcus aureu... -

+
Open data


ID or keywords:

Loading...

-
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: 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
DepositionOct 24, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55478.png

Downloads & links

-
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)

Slices (1/2)

Slices (2/3)

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 °

-
Supplemental data

-
Mask #1

Fileemd_55478_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: deepEMhancer postprocessed map

Fileemd_55478_additional_1.map
AnnotationdeepEMhancer postprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION postprocessed map

Fileemd_55478_additional_2.map
AnnotationRELION postprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_55478_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_55478_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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)

-
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)

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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.

-
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

+
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)

-
Atomic model buiding 1

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more