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- EMDB-64387: PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module) -

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Basic information

Entry
Database: EMDB / ID: EMD-64387
TitlePvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)
Map data
Sample
  • Complex: PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)
    • Protein or peptide: PvdL
    • Protein or peptide: MbtH-like domain-containing protein
  • Ligand: 2,4-DIAMINOBUTYRIC ACID
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsNonribosomal peptide synthetase / LIGASE / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


pyoverdine biosynthetic process / monocarboxylic acid biosynthetic process / Actinobacterium-type cell wall biogenesis / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / lipid biosynthetic process / ligase activity / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process ...pyoverdine biosynthetic process / monocarboxylic acid biosynthetic process / Actinobacterium-type cell wall biogenesis / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / lipid biosynthetic process / ligase activity / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / fatty acid metabolic process / transferase activity / cytosol
Similarity search - Function
MbtH-like protein / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain ...MbtH-like protein / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
PvdL / MbtH-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsCao W / Wang J / Wang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2021YFA0910500 China
CitationJournal: Nat Synth / Year: 2026
Title: Analysis of heterocycle formation and stereochemical control by a non-ribosomal peptide synthetase condensation domain
Authors: Cao W / Wang J / Chen SL / Li D / Wang X / Deng Z / Liang J / Wang Z
History
DepositionApr 27, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64387.png

Downloads & links

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Map

FileDownload / File: emd_64387.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.012049202 - 0.041571394
Average (Standard dev.)-0.000008870823 (±0.0010317212)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_64387_additional_1.map
Projections & Slices
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Additional map: #1

Fileemd_64387_additional_2.map
Projections & Slices
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Half map: #2

Fileemd_64387_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_64387_half_map_2.map
Projections & Slices
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Sample components

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Entire : PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)

EntireName: PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)
Components
  • Complex: PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)
    • Protein or peptide: PvdL
    • Protein or peptide: MbtH-like domain-containing protein
  • Ligand: 2,4-DIAMINOBUTYRIC ACID
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)

SupramoleculeName: PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 186 kDa/nm

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Macromolecule #1: PvdL

MacromoleculeName: PvdL / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 172.528516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DSALTPIQHW FFDLPLARRE HWNQALLLQP RQAIDLGLLR KSLQRLVEQH DALRLAFRQV DGEWLAQHRP LREQELLWHV PVQSFDECA ELFAKAQRSL DLEQGPLLRA VLVDGPAGEQ RLLLAIHHLV VDGVSWRVLL EDLQQVYRQF AEGAEPALPA K TSAFRDWA ...String:
DSALTPIQHW FFDLPLARRE HWNQALLLQP RQAIDLGLLR KSLQRLVEQH DALRLAFRQV DGEWLAQHRP LREQELLWHV PVQSFDECA ELFAKAQRSL DLEQGPLLRA VLVDGPAGEQ RLLLAIHHLV VDGVSWRVLL EDLQQVYRQF AEGAEPALPA K TSAFRDWA GRLQAYAGSE SLREELGWWQ ARLGGQPVEW PCDRPQGDNR EALAESVSLR LDPQRTRQLL QQAPAAYRTQ VN DLLLTAL ARVLCRWSGQ PSTLVQLEGH GREALFDDID LTRSVGWFTS AYPLRLTPAQ SPGESIKAIK EQLRAVPHKG LGY GVLRYL ADPAVRQAMA ALPTAPITFN YLGQFDQSFA DALFQPLDQP TGPIHDEQAP LPNELSVDGQ VYGGELVLRW TYSR ERYDA RTVNELAQAY LAELQALIEH CLEDGAGGLT PSDFPLAQLS QAQLDALAVP AGEIEDVYPL TPMQEGLLLH TLLEP GTGI YYMQDRYRID SPLDPERFAA AWQAVVARHE ALRASFVWNA GETMLQVIHK PGRTRIEFLD WSELPEDGHE ERLQAL HKR EREAGFDLLE QPPFHLRLIR LGEARYWFMM SNHHILIDAW CRGLLMNDFF EIYSALGESR PANLPTPPRY RDYIAWL QR QDLEQSRRWW SESLRGFERP TLVPSDRPFL REHAGESGGM IVGDRYTRLD AADGARLREL AQRYQLTVNT FAQAAWAL T LRRFSGERDV LFGVTVAGRP VGMPEMQRTV GLFINSIPLR VQMPAAGQRC TVREWLNRLF ERNLELREHE HLPLVAIQE SSELPKGQPL FDSLFVFENA PVEVSVLDRA QSLNASSDSG RTHTNFPLTV VCYPGDDLGL HLSYDQRYFE APTVERLLGE FKRLLLALA DGFHGELEAL PLLGEDERDF LLDGCNRSAR DYPLEQGYVR LFEAQVAAHP QRIAASCLEQ RWSYAELNRR A NRLGHALR AAGVGIDQPV ALLAERGLDL LGMIVGSFKA GAGYLPLDPG HPTQRLTRIV ELSRTLVLVC TQACREQALA LF DELGCVD RPRLLVWDEI QQGEGAEHDP QVYSGPQNLA YVIYTSGSTG LPKGVMVEQA GMLNNQLSKV PYLELDENDV IAQ TASQSF DISVWQFLAA PLFGARVAIV PNAVAHDPQG LLAHVGEQGI TVLESVPSLI QGMLAEERQA LDGLRWMLPT GEAM PPELA RQWLKRYPRI GLVNAYGPAE CSDDVAFFRV DLASTESTYL PIGSPTDNNR LYLLGAGADD AFELVPLGAV GELCV AGTG VGRGYVGDPL RTAQAFVPHP FGAPGERLYR TGDLARRRAD GVLEYVGRID HQVKIRGFRI ELGEIEARLH ERADVR EAA VAVQEGANGK YLVGYLVPGE TPRSSADSPA GLMVEQGAWF ERIKQQLRAD LPDYMVPLHW LVLDRMPLNA NGKLDRK AL PALDIGQMQN QAYQAPRNEL EETLARIWAE VLKVERVGVF DNFFELGGH(4HH) LLATQIASRV QKALQRNVPL RAMF ECTTV EELASYIESL APSEI

UniProtKB: PvdL

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Macromolecule #2: MbtH-like domain-containing protein

MacromoleculeName: MbtH-like domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 7.28819 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DDIQFQVVVN HEEQYSIWPE YKEIPQGWRA AGKSGLKKDC LAYIEEVWTD MRPLSLRQHM D

UniProtKB: MbtH-like domain-containing protein

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Macromolecule #3: 2,4-DIAMINOBUTYRIC ACID

MacromoleculeName: 2,4-DIAMINOBUTYRIC ACID / type: ligand / ID: 3 / Number of copies: 2 / Formula: DAB
Molecular weightTheoretical: 118.134 Da
Chemical component information

ChemComp-DAB:
2,4-DIAMINOBUTYRIC ACID / inhibitor*YM

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*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: OTHER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165245
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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