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- EMDB-37340: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme P... -

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Basic information

Entry
Database: EMDB / ID: EMD-37340
TitleCryo-EM structure of ClassIII Lanthipeptide modification enzyme PneKC mutant H522A.
Map data
Sample
  • Complex: Dimeric structure of Class III lanthipeptide modification enzyme PneKC H522A in complex with substrate PneA
    • Protein or peptide: Protein kinase domain-containing protein
    • Protein or peptide: PneA
  • Protein or peptide: Protein kinase domain-containing protein
  • Protein or peptide: PneA
  • Ligand: PHOSPHATE ION
KeywordsLanthibiotic / RiPPs / LanKC / CryoEM / Antimicrobial peptides / Antiviral peptides. / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


peptide modification / protein kinase activity / ATP binding
Similarity search - Function
RamC, N-terminal domain / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / : / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Protein kinase domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsLi Y / Luo M / Shao K / Li J / Li Z
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Structure of PneA bound PneKC at 3.75 Angstroms resolution.
Authors: Li Y / Luo M / Shao K / Li J / Li Z
History
DepositionAug 30, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37340.png

Downloads & links

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Map

FileDownload / File: emd_37340.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.148
Minimum - Maximum-0.5132829 - 0.9406301
Average (Standard dev.)-0.000054420838 (±0.030922165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37340_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_37340_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 : Dimeric structure of Class III lanthipeptide modification enzyme ...

EntireName: Dimeric structure of Class III lanthipeptide modification enzyme PneKC H522A in complex with substrate PneA
Components
  • Complex: Dimeric structure of Class III lanthipeptide modification enzyme PneKC H522A in complex with substrate PneA
    • Protein or peptide: Protein kinase domain-containing protein
    • Protein or peptide: PneA
  • Protein or peptide: Protein kinase domain-containing protein
  • Protein or peptide: PneA
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Dimeric structure of Class III lanthipeptide modification enzyme ...

SupramoleculeName: Dimeric structure of Class III lanthipeptide modification enzyme PneKC H522A in complex with substrate PneA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: Protein kinase domain-containing protein

MacromoleculeName: Protein kinase domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 100.10468 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NFNLEHPFFF TNNDYSTDTS IKYQASLPFN WHEVMNNDEW VYQYPIGKFV ERQGWKIHIS SEYNSSHELL QDVAKICHEM RIPFKHLST EDKFIMRNGK LVSRGFSGKF ITCYPNQNEL ESVLQRLESA LKQYNGPYIL SDKRWDEAPI YLRYGVFRPS R DDEKKVAI ...String:
NFNLEHPFFF TNNDYSTDTS IKYQASLPFN WHEVMNNDEW VYQYPIGKFV ERQGWKIHIS SEYNSSHELL QDVAKICHEM RIPFKHLST EDKFIMRNGK LVSRGFSGKF ITCYPNQNEL ESVLQRLESA LKQYNGPYIL SDKRWDEAPI YLRYGVFRPS R DDEKKVAI DELIVGDEVV KDERLPVFKI PKGIVPPDFL NKWLDKKDKK QGDFPFIIDN AIRFSNSGGI YNARLKEDGK KI ILKEARP YTGLGFDGTY SSEKLASECK ALKILNEWSE APKIYWHGKI WEHTFLGIEH MKGVPLNRWV TNNFPLYEVV DKT KDYLLR VSKIVEKLID LTNKFHSENV YHQDLHLGNI LVKDEDEISI IDWEQAVFSN DEKVVHKVAA PGFRAWRETL PSEI DWYGI RQIAHYLYMP LVTTSDLTYN YVSQTRIEGK KLFESLGYTR EHIDYVESLL SYLDSKCPQI ENISRKKVLK PMHEI RTIE SEQDIQDFII KLLRGFTLTY GQWRKEFQSR FFPVAYYGLN FNQGIAFSDL AILWSYQQLA KKVKNFKFDD YYEIRT QVI NEAVNNFKKS SLSGLFDGKI GTIWLIYEFG EIDRAVELFT THFIEIFENS QNKNLYSGQA GILLVGLYFL SKGEIDN KL GEEILIRLRE YTLNYIENPE TFCKVGASDV QSNDPYENFG GLLYGHAGVA WLFGEAYKLT GESIYKNGLE LAVDKELV A YKVDSNNSLQ YSQGHRLLPY LATGSAGLLL LINRNKEILS SKYLKYLTSL ERATDVVFCV LPGLFNGFCG LEVANNIYS DIDDNFSGQK KLIEQLYRYL CVIEEGFVIA GDNGLKITTD IASGFAGVAI GLVSIMDNKL TILPQI

UniProtKB: Protein kinase domain-containing protein

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Macromolecule #2: Protein kinase domain-containing protein

MacromoleculeName: Protein kinase domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 99.976547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FNLEHPFFFT NNDYSTDTSI KYQASLPFNW HEVMNNDEWV YQYPIGKFVE RQGWKIHISS EYNSSHELLQ DVAKICHEMR IPFKHLSTE DKFIMRNGKV VSRGFSGKFI TCYPNQNELE SVLQRLESAL KQYNGPYILS DKRWDEAPIY LRYGVFRPSR D DEKKVAID ...String:
FNLEHPFFFT NNDYSTDTSI KYQASLPFNW HEVMNNDEWV YQYPIGKFVE RQGWKIHISS EYNSSHELLQ DVAKICHEMR IPFKHLSTE DKFIMRNGKV VSRGFSGKFI TCYPNQNELE SVLQRLESAL KQYNGPYILS DKRWDEAPIY LRYGVFRPSR D DEKKVAID ELIVGDEVVK DERLPVFKIP KGIVPPDFLN KWLDKKDKKQ GDFPFIIDNA IRFSNSGGIY NARLKEDGKK II LKEARPY TGLGFDGTYS SEKLASECKA LKILNEWSEA PKIYWHGKIW EHTFLGIEHM KGVPLNRWVT NNFPLYEVVD KTK DYLLRV SKIVEKLIDL TNKFHSENVY HQDLHLGNIL VKDEDEISII DWEQAVFSND EKVVHKVAAP GFRAWRETLP SEID WYGIR QIAHYLYMPL VTTSDLTYNY VSQTRIEGKK LFESLGYTRE HIDYVESLLS YLDSKCPQIE NISRKKVLKP MHEIR TIES EQDIQDFIIK LLRGFTLTYG QWRKEFQSRF FPVAYYGLNF NQGIAFSDLA ILWSYQQLAK KVKNFKFDDY YEIRTQ VIN EAVNNFKKSS LSGLFDGKIG TIWLIYEFGE IDRAVELFTT HFIEIFENSQ NKNLYSGQAG ILLVGLYFLS KGEIDNK LG EEILIRLREY TLNYIENPET FCKVGASDVQ SNDPYENFGG LLYGHAGVAW LFGEAYKLTG ESIYKNGLEL AVDKELVA Y KVDSNNSLQY SQGHRLLPYL ATGSAGLLLL INRNKEILSS KYLKYLTSLE RATDVVFCVL PGLFNGFCGL EVANNIYSD IDDNFSGQKK LIEQLYRYLC VIEEGFVIAG DNGLKITTDI ASGFAGVAIG LVSIMDNKLT ILPQI

UniProtKB: Protein kinase domain-containing protein

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Macromolecule #3: PneA

MacromoleculeName: PneA / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 1.97222 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QGMAEEVLNL QLVSVQVD

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Macromolecule #4: PneA

MacromoleculeName: PneA / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 1.85816 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VSMAEEVLNL QLVSVQV

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Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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: 7.4
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
25.0 mM(HOCH2)3CNH2Tris

Details: 25mM Tris, 200mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26420
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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