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- EMDB-66127: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme T... -

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Basic information

Entry
Database: EMDB / ID: EMD-66127
TitleCryo-EM structure of ClassIII Lanthipeptide modification enzyme TherKC with chain A bounded to substrate TherA and ATPrS.
Map data
Sample
  • Complex: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme TherKC mutant R685A.
    • Protein or peptide: Lantibiotic
    • Protein or peptide: Protein kinase domain-containing protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsLanthipeptide modification enzyme / PEPTIDE BINDING PROTEIN
Function / homology: / :
Function and homology information
Biological speciesThermoactinomyces sp. DSM 45892 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsZhang H / Luo M
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Structural Basis for the lanthipeptide biosynthesis mechanism of a dimeric Class III lanthipeptide synthetase
Authors: Zhang H / Luo M
History
DepositionSep 7, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66127.png

Downloads & links

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Map

FileDownload / File: emd_66127.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.)
0.98 Å/pix.
x 256 pix.
= 250.112 Å		0.98 Å/pix.
x 256 pix.
= 250.112 Å		0.98 Å/pix.
x 256 pix.
= 250.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.977 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.116
Minimum - Maximum-0.93301415 - 1.0585724
Average (Standard dev.)-0.0003470722 (±0.023963075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 250.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66127_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_66127_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of ClassIII Lanthipeptide modification enzyme T...

EntireName: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme TherKC mutant R685A.
Components
  • Complex: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme TherKC mutant R685A.
    • Protein or peptide: Lantibiotic
    • Protein or peptide: Protein kinase domain-containing protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme T...

SupramoleculeName: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme TherKC mutant R685A.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Thermoactinomyces sp. DSM 45892 (bacteria)

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Macromolecule #1: Lantibiotic

MacromoleculeName: Lantibiotic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermoactinomyces sp. DSM 45892 (bacteria)
Molecular weightTheoretical: 4.678253 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MNQVLDLQKL SQAESLEQPE IGWTPLTWTV TTALSTVSNN CK

UniProtKB: UNIPROTKB: A0A1H3JBM1

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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: Thermoactinomyces sp. DSM 45892 (bacteria)
Molecular weightTheoretical: 99.361719 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKGDMLYHSY LKRGSEYYGP HDKEESIKEF FIEDLKEDVV VVNEEESIWR YYEFKDRTLP EQGWKIHISA TMNEAEQVLA AVSKVLIKH KVAFKHIKNI ETLLEMNSKG ANRASSGKFI AVYPMDDNEF VHLLDALREE IQPYEKGPYI LNDKCWKNSN V YYRYGGFK ...String:
MKGDMLYHSY LKRGSEYYGP HDKEESIKEF FIEDLKEDVV VVNEEESIWR YYEFKDRTLP EQGWKIHISA TMNEAEQVLA AVSKVLIKH KVAFKHIKNI ETLLEMNSKG ANRASSGKFI AVYPMDDNEF VHLLDALREE IQPYEKGPYI LNDKCWKNSN V YYRYGGFK SIYNDKGELC IRDTKGELTV DERNPYYQAP DFVKEFDHYL DLLNDKPNNE DRENKLDLYN IETSLRFTNS GG IYLAERK SDNKKVIIKE ARPKAGLDGN SVDAVERQII ERNALKKLAN VKGIVNVLDH FKVWEHYFLV EECVEGMDLH SWI AINYPF MKSQSLDDYK IKIKKVLSQL VIIMEEMLDK DVAMGDLQPA NIMISEDLQV TLIDFETAKQ TNSQEKPGMA TTGF INSQI KTSGAMDWFA LQKIVRYSLL PVLTSECLDK YINENYYKWI RVNYGDDFYE FVKSMIQKCE DHLIDFGEET QRLDS VVNN FVMNNDILSI LEGLSDGIKA NLTGDIRLIN GDIRQYEHHD GKLNVLSGGS GAAIALARVG STNDEVHQWI TQYVLK NID TVKSAGLFTG TAGIAGMLYE NGYREESLDI FSKIDSSLND SDITLRSGLA GIGLALASFY LESLDSKYLE KAESIAV KI ENFLQEDNEI TVQDWKGIPI GLIDGWSGVS VFYSSLYAIT KNAKYYFRAV ELVARDLNKT VTDNKLGVLN TIDNSRRL L PYLSGGSIGI GVAIWYLIHV SGEEVFYEEL KLITNLSKIR ATVIGGLFDG AGSFLIIPPM MGKDQATYYS QTEDIIELL NLYLIDKKNY LSFPGQFSFR LSDDLFSGSS GIVLALKGIL NENPLYWLPI INIDKFYEDT RFNREKLVVM V

UniProtKB: UNIPROTKB: A0A1H3JBN8

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 174223
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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