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- EMDB-46483: A widespread heme dechelatase in healthy and pathogenic human mic... -

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Basic information

Entry
Database: EMDB / ID: EMD-46483
TitleA widespread heme dechelatase in healthy and pathogenic human microbiomes.
Map data
Sample
  • Complex: HmuS in complex with heme
    • Protein or peptide: HmuS heme dechelatase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsIron / Microbiome / Heme / METAL TRANSPORT
Function / homologycobaltochelatase activity / CobN/magnesium chelatase / CobN/Magnesium Chelatase / biosynthetic process / membrane / Cobaltochelatase subunit CobN
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria) / Bacteroides (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGauvin CC / Nath AK / Rodrigues da Silva R / Akpoto E / Dubois JL / Lawrence CM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Science Foundation (NSF, United States)DBI-1828765 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM140963 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 8, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46483.png

Downloads & links

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Map

FileDownload / File: emd_46483.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 320 pix.
= 289.92 Å		0.91 Å/pix.
x 320 pix.
= 289.92 Å		0.91 Å/pix.
x 320 pix.
= 289.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.906 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.10028691 - 0.2614512
Average (Standard dev.)0.00007762657 (±0.005725037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 289.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46483_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46483_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_46483_half_map_2.map
Projections & Slices
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Sample components

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Entire : HmuS in complex with heme

EntireName: HmuS in complex with heme
Components
  • Complex: HmuS in complex with heme
    • Protein or peptide: HmuS heme dechelatase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: HmuS in complex with heme

SupramoleculeName: HmuS in complex with heme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 153.058 KDa

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Macromolecule #1: HmuS heme dechelatase

MacromoleculeName: HmuS heme dechelatase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: cobaltochelatase
Source (natural)Organism: Bacteroides (bacteria) / Strain: VPI-5482
Molecular weightTheoretical: 162.423281 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKKKSKIILG GCIVVAALIG LSVWNTWFSA TKIAFVNFQT IQQGSISKAN DNSFIKLSEV SLDNLDRLTS YDMVFINGMG LRIVEEQRQ QIQQAADKGI PVYTSMATNP ANNICNLDSI QQNLIRGYLS NGGKTNYRNM LNYIRKAIDG KASAVPEVED P IERPSDML ...String:
MKKKSKIILG GCIVVAALIG LSVWNTWFSA TKIAFVNFQT IQQGSISKAN DNSFIKLSEV SLDNLDRLTS YDMVFINGMG LRIVEEQRQ QIQQAADKGI PVYTSMATNP ANNICNLDSI QQNLIRGYLS NGGKTNYRNM LNYIRKAIDG KASAVPEVED P IERPSDML YHAGISNPDD EQEFLTVADY EKFMQENNLY KEGARKIMIT GQMADATDLI KALENAGYNV YPVQSMTRFM SF IEEVQPD AVINMAHGRM GDKMVDYLKA RNILLFAPLT INSLVDEWEN DPMGMSGGFM SQSIVTPEID GAIRPFALFA QYE DKEGLR HSYAVPERLK TFVSTIDNYL NLKTKPNFEK KVAIYYYKGP GQNALTAAGM EVVPSLYNLL LRMKQEGYNI SGLP ANAQE LGKMIQAQGA VFNAYAEGAF NDFMQNGHPE LITKEQYESW VKESLRPEKY QEVVDAFGEF PGNYMVTPDG KLGIA RLQF GNVVLLPQNA AGSGDNSFQV VHGTDMAPPH TYIASYLWMQ HGFKADALIH FGTHGSLEFT PRKQVALCSN DWPDRL VGA VPHYYLYSIG NVGEGMMAKR RSYATLQSYL TPPFLESSVR GIYRELMEKI KIYNNSQKAN KDQESLAVKT LTVKMGI HR DLGLDSMANK PYTEDEIARV ENFAEELATE KITGQLYTMG VPYEPERITS SVYAMATEPI AYSLFALDKQ RGKATESA E KHRSVFTQQY LMPARLLVER LMANPSLATD ELICHTAGIT PQELAKARQI EAERNAPKGM MAMMMAAAAK KDQADNEPS GNGHPASAKM EKGPHGKMPA GMKEAMKKMG ANMDPEKAME MAKSMGASPE ALKKMEASMK ANKDTSTDAS GKPAMAGKTE KPQGMSAMM AAMGKAPKEY SKEEVEFALA VAEVERTIKN VGNYKNALLT SPEEELSSLM NALKGGYTAP TPGGDPIANP N TLPTGRNM YAINAEATPT ESAWEKGIAL AKQTIDRYKQ RHNDSIPRKV SYTLWSSEFI ETGGATIAQV LYMLGVEPVR DA FGRVSDL KLIPSTELGR PRIDVVVQTS GQLRDLAASR LFLINRAVEM AAAAKDDKYE NQVASSVIEA ERVLTEKGLS PKD AREIST FRVFGGANGM YGTGIQEMVE SGDRWENESE IADTYLNNMG AYYGSEKNWE VFQKFAFEAA LTRTDVVVQP RQSN TWGAL SLDHVYEFMG GMNLAVRNVT GKDPDAYLSD YRNRNHMKMQ ELKEAVGVES RTTILNPTYI KEKMKGGASS ASEFA EVIT NTYGWNVMKP AAIDKELWDN IYNVYVKDEL NLGVKQYFEQ QNPAALEEMT AVMLESARKG LWQASEEQVA ELSKLH TEI VNTYRPSCSG FVCDNAKLRD FIASKADAQT ATQYKENISK IREAKASGSN KGVVMKKEEM NQTAENQTNT LSNVAVG IA VIIVILALIL FVRKRRKSSQ M

UniProtKB: Cobaltochelatase subunit CobN

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 95 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1.5 mg/mL
BufferpH: 7.1
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3ClTris-Cl
250.0 mMNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 100.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12602 / Average exposure time: 3.06 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 55187 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 18955798 / Details: Blob picked, then particles washed to give
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 2133842
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0)
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-9d26:
A widespread heme dechelatase in healthy and pathogenic human microbiomes.

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