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- EMDB-39714: Cryo-EM structure of trimer HtmB2-CT -

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Basic information

Entry
Database: EMDB / ID: EMD-39714
TitleCryo-EM structure of trimer HtmB2-CT
Map data
Sample
  • Complex: trimer of HtmB2-CT
    • Protein or peptide: special condensation domain in NRPS
KeywordsDimer of special condensation domain of NRPS / BIOSYNTHETIC PROTEIN
Biological speciesStreptomyces (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsSun YH / Zhang ZY / Mei Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800052 China
CitationJournal: Angew Chem Int Ed Engl / Year: 2025
Title: Formation of the Diketopiperazine Moiety by a Distinct Condensation-Like Domain in Hangtaimycin Biosynthesis.
Authors: Qing Mei / Shijuan Wu / Minghe Luo / Shunjia Ji / Jiayi Guo / Chuan Dong / Guo Sun / Jian Wang / Zixin Deng / Yi-Lei Zhao / Zhengyu Zhang / Yuhui Sun /
Abstract: Non-ribosomal peptide synthetases (NRPSs) are key enzymes in pharmaceutical synthesis, with condensation (C) domains catalyzing amide bond formation between aminoacyl substrates. However, recent ...Non-ribosomal peptide synthetases (NRPSs) are key enzymes in pharmaceutical synthesis, with condensation (C) domains catalyzing amide bond formation between aminoacyl substrates. However, recent research has elucidated that the catalytic capabilities of C domains extend beyond the traditional formation of peptide bonds. In this study, we elucidate the cyclization mechanism of the NRPS-derived natural products hangtaimycin (HTM), characterized by the formation of a 2,5-diketopiperazine (DKP) moiety which involves an intramolecular vinylamide-mediated nucleophilic attack instead of an N-terminal amino group. This cyclization is catalyzed by a terminal condensation-like (C) domain within the NRPS enzyme HtmB2. We investigated the evolutionary specificity of the HtmB2-C within Streptomyces spectabilis CCTCC M2017417. Employing a multidisciplinary analytical approach, we have delineated the molecular underpinnings of DKP formation within the HTM biosynthesis. This process is facilitated by residue R2776, which modulates the formation of reactive species and stabilizes the amidate through electrostatic interactions. Besides, we found a positive correlation between the alkaline strength of the residue at position 2776 and the activity of HtmB2-C. Our study elucidates the formation mechanism of DKPs in NRPS-derived natural products, thereby bridging a critical gap in the structural and mechanistic understanding of this field.
History
DepositionApr 10, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39714.png

Downloads & links

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Map

FileDownload / File: emd_39714.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.16
Minimum - Maximum-1.7771297 - 2.3038573
Average (Standard dev.)-0.00015199419 (±0.04777754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39714_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_39714_half_map_1.map
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Half map: Author stated: During our parsing of the data...

Fileemd_39714_half_map_2.map
AnnotationAuthor stated: During our parsing of the data using Cryosparc, there were no issues with FSC data based on the parameters of the original map.
Projections & Slices
AxesZYX

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Sample components

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Entire : trimer of HtmB2-CT

EntireName: trimer of HtmB2-CT
Components
  • Complex: trimer of HtmB2-CT
    • Protein or peptide: special condensation domain in NRPS

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Supramolecule #1: trimer of HtmB2-CT

SupramoleculeName: trimer of HtmB2-CT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces (bacteria)

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Macromolecule #1: special condensation domain in NRPS

MacromoleculeName: special condensation domain in NRPS / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces (bacteria)
Molecular weightTheoretical: 61.822629 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MKEVYVAPRT ATERVLCRLV QDVLDLDRVG LQDGFFDLGG HSLLATRLTI RVKQETGKEL PLQSILAGA TLGELAAALD AADGGTSDGA VPLVPVTGPG EESPLSCQQS ELWFLNQRAH LGSSYDNVQM AYRVIGPLDR Q AYARAFEG ...String:
MGSSHHHHHH SSGLVPRGSH MKEVYVAPRT ATERVLCRLV QDVLDLDRVG LQDGFFDLGG HSLLATRLTI RVKQETGKEL PLQSILAGA TLGELAAALD AADGGTSDGA VPLVPVTGPG EESPLSCQQS ELWFLNQRAH LGSSYDNVQM AYRVIGPLDR Q AYARAFEG LVARHAVLRT SYLRRGDTYV QKVNDTTGFA VAFEDVTGDS AVTEFLRAER PRPFDPADRH MLRVHILTLT PY EHVAVVT RPWGIFDGWS TGVFIAELNA LYQALSRGDE PSLPELPVQY ADFAHWQRRT FDADARARQQ AYWRAQLADL PSC TALRTD YRRPEAKSYQ GSSVEVNVPA AVLDQLKRVS KERGGTLYMT LLSAFATLLG AHTDDRELAI GSPVTNRPRP ELER LVGYF INVLVMRLDV RPEQAFDDLL AQAQRVTAAA HEHKEVPFAD LVRDLVPEPD PAYSPLFQVM FNLVPAVEAA PPGAA DPGA LGFVPLPTDS GTAKFDLNLV VRETPDGLRG YLEYSTDLYA RSTVRSMAAT YERLLLKIVT QPGASLARLR EAAADG GAG

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 8.0 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: 1.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 471903
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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