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- EMDB-51885: Haemophilus influenzae serotype b capsule polymerase bcs3 in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-51885
TitleHaemophilus influenzae serotype b capsule polymerase bcs3 in complex with acceptor polymer
Map data
Sample
  • Complex: Physiological dimeric assembly of Bcs3
    • Protein or peptide: Bcs3
  • Ligand: MAGNESIUM ION
  • Ligand: beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate
  • Ligand: water
KeywordsCapsule polymerase / Haemophilus influenzae serotype b / Pathogens / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / metal ion binding / plasma membrane
Similarity search - Function
Domain of unknown function DUF5776 / Domain of unknown function (DUF5776) / CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / : / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsDi Domenico V / Mast T / Cifuente JO / Schulze J / Litschko C / Alcaide A / Villegas JC / Fiebig T / Guerin ME
Funding support Spain, United States, Germany, 3 items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO) Spain
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Haemophilus influenzae serotype b capsule polymerase bcs3 in complex with acceptor polymer
Authors: Di Domenico V / Mast T / Cifuente JO / Schulze J / Litschko C / Alcaide A / Villegas JC / Fiebig T / Guerin ME
History
DepositionOct 22, 2024-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51885.png

Downloads & links

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Map

FileDownload / File: emd_51885.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 360 pix.
= 235.08 Å		0.65 Å/pix.
x 360 pix.
= 235.08 Å		0.65 Å/pix.
x 360 pix.
= 235.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.653 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.11190754 - 0.30199856
Average (Standard dev.)0.00097024394 (±0.011461934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 235.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_51885_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51885_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51885_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Physiological dimeric assembly of Bcs3

EntireName: Physiological dimeric assembly of Bcs3
Components
  • Complex: Physiological dimeric assembly of Bcs3
    • Protein or peptide: Bcs3
  • Ligand: MAGNESIUM ION
  • Ligand: beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate
  • Ligand: water

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Supramolecule #1: Physiological dimeric assembly of Bcs3

SupramoleculeName: Physiological dimeric assembly of Bcs3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Haemophilus influenzae (bacteria)

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Macromolecule #1: Bcs3

MacromoleculeName: Bcs3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Haemophilus influenzae (bacteria)
Molecular weightTheoretical: 137.381172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VDKTWLFGSY AWQGNPKALF LYMLVNCKET HECWWVADNE ESMKSIKKST GLKNITFTDS EKAKELFPHA DVYVTENFRE SYPVYMNEN IKVFNTWHGV GLKHIELALG MNSVLAESIV RKYVRNYDIY KNNVLFLTTS QAMEDHFLED MAISKELIIR G KYPRNAVY ...String:
VDKTWLFGSY AWQGNPKALF LYMLVNCKET HECWWVADNE ESMKSIKKST GLKNITFTDS EKAKELFPHA DVYVTENFRE SYPVYMNEN IKVFNTWHGV GLKHIELALG MNSVLAESIV RKYVRNYDIY KNNVLFLTTS QAMEDHFLED MAISKELIIR G KYPRNAVY GPNGIHTYDI NTLLPKNKSQ YSQTILFCPT YRIGAIQGVL NSLLPDFAKL EEVCRHKNQL FIVKVHPFMK KD NYFAEMS EKYKDSEYIL FWNDDYDIYE AFNSIDLAII DYSSIFYDLL DAGVEKFIRY VPDLDEYQND LELIGDYADL TEG RIVKSF QQLLNCLDNA NIKIISTKRK QYLMDYFFGF KKENKSMESL IADVDNCQLQ PKSLKELHTF DIFDTLIRRS TLRP FSIFD YVRDKAKASG IKFPLALTEN WINVRNRAEH DVRDIMRKTT FERQSDKIEI TLDDIYTRLQ KNLLLTDEQT DFLKQ AEIE AEIAHVEPIQ KRINYLFSLK AKGHDVAMAS DMYLPEDVIY KMLDRADTRL REIPLYLSST IGYQKSTGKL YQHIFF DLD YQYSRWTHYG DNKHADGSVP RRLGIQTAVH DIDDFIPFEN AMVNAMDNYN RYPAYQLATK MHRYRTQLVQ ENGFGNT LF ETKYYNYAYV GASFVPYINW AIKDAIKRGY ETIYFISRDG HFLKQIADKI IEIRGYNVKT KYIYGSRKAW RLPSFITK V DDETFWQFGN FVGMDSFEDL VKASYLSESE LLSLFPEFES LRHAKHLRGE IAENIRKIFK NSPAYHEKVL AIAAEKRKM VRQYIQQEIN PKEKFAFVEF WGRGYTQDTF GRLLNDAFGK EVKNPFYYVR SFTDDMGTSV RHNFILAPQN FSFFEPIFAQ TPYDSIPDY YEEKGRIEPI INHRDRSVSD LISEGLLKFT EDYLALNTQD EDYFDAALSQ FNYQYQLNTP NDQFICNVFS E LKDNISSF GVEKPYAPAL TLKQLESITS KQELDKLTQS IPISLSKSDV KVIDYYNKIQ KNYNLPAYNS TPMRKAYAVN PL EQYVWST QVPFRVLSLK QNSFYLDVSF AETTKRKDIF LKELNEIDVI AVDWLKGGVP RLLTEHGYIT AHKDWVKKSF NDD KTNNIE EPKVKNKEKS KVLEVNTTVT NNNKQAIGKL DNNIDKSLEH HHHHH

UniProtKB: Bcs3

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate

MacromoleculeName: beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate / type: ligand / ID: 3 / Number of copies: 12 / Formula: KOF
Molecular weightTheoretical: 364.24 Da
Chemical component information

ChemComp-KOF:
beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 72 / 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

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTrisTris
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 27103 / Average electron dose: 51.85 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1578386
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8a0m

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 388941
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8a0m


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: OTHER
Output model

PDB-9h5i:
Haemophilus influenzae serotype b capsule polymerase bcs3 in complex with acceptor polymer

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