[English] 日本語
Yorodumi
- EMDB-44293: Cryo-EM structure of MraY in complex with analogue 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44293
TitleCryo-EM structure of MraY in complex with analogue 2
Map datamap
Sample
  • Complex: Complex of MraY AA dimer with nanobody bound
    • Protein or peptide: Phospho-N-acetylmuramoyl-pentapeptide-transferase
    • Protein or peptide: MraYAA nanobody
  • Ligand: (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{S})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid
  • Ligand: water
Keywordsinhibitor / antibiotics / TRANSFERASE
Function / homology
Function and homology information


phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division ...phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Phospho-N-acetylmuramoyl-pentapeptide transferase / Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site / Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 / MraY family signature 1. / MraY family signature 2. / Glycosyl transferase, family 4 / Glycosyl transferase family 4
Similarity search - Domain/homology
Phospho-N-acetylmuramoyl-pentapeptide-transferase
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsHao A / Lee S-Y
Funding support United States, 1 items
OrganizationGrant numberCountry
Other privateDuke Science Technology Scholar Fund United States
CitationJournal: Nat Commun / Year: 2024
Title: Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target.
Authors: Kazuki Yamamoto / Toyotaka Sato / Aili Hao / Kenta Asao / Rintaro Kaguchi / Shintaro Kusaka / Radhakrishnam Raju Ruddarraju / Daichi Kazamori / Kiki Seo / Satoshi Takahashi / Motohiro ...Authors: Kazuki Yamamoto / Toyotaka Sato / Aili Hao / Kenta Asao / Rintaro Kaguchi / Shintaro Kusaka / Radhakrishnam Raju Ruddarraju / Daichi Kazamori / Kiki Seo / Satoshi Takahashi / Motohiro Horiuchi / Shin-Ichi Yokota / Seok-Yong Lee / Satoshi Ichikawa /
Abstract: MraY (phospho-N-acetylmuramoyl-pentapeptide-transferase) inhibitory natural products are attractive molecules as candidates for a new class of antibacterial agents to combat antimicrobial-resistant ...MraY (phospho-N-acetylmuramoyl-pentapeptide-transferase) inhibitory natural products are attractive molecules as candidates for a new class of antibacterial agents to combat antimicrobial-resistant bacteria. Structural optimization of these natural products is required to improve their drug-like properties for therapeutic use. However, chemical modifications of these natural products are painstaking tasks due to complex synthetic processes, which is a bottleneck in advancing natural products to the clinic. Here, we develop a strategy for a comprehensive in situ evaluation of the build-up library, which enables us to streamline the preparation of the analogue library and directly assess its biological activities. We apply this approach to a series of MraY inhibitory natural products. Through construction and evaluation of the 686-compound library, we identify promising analogues that exhibit potent and broad-spectrum antibacterial activity against highly drug-resistant strains in vitro as well as in vivo in an acute thigh infection model. Structures of the MraY-analogue complexes reveal distinct interaction patterns, suggesting that these analogues represent MraY inhibitors with unique binding modes. We further demonstrate the generality of our strategy by applying it to tubulin-binding natural products to modulate their tubulin polymerization activities.
History
DepositionMar 26, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44293.png

Downloads & links

-
Map

FileDownload / File: emd_44293.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.619997 - 1.5667046
Average (Standard dev.)0.0015025014 (±0.035831407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half A

Fileemd_44293_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half B

Fileemd_44293_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of MraY AA dimer with nanobody bound

EntireName: Complex of MraY AA dimer with nanobody bound
Components
  • Complex: Complex of MraY AA dimer with nanobody bound
    • Protein or peptide: Phospho-N-acetylmuramoyl-pentapeptide-transferase
    • Protein or peptide: MraYAA nanobody
  • Ligand: (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{S})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid
  • Ligand: water

-
Supramolecule #1: Complex of MraY AA dimer with nanobody bound

SupramoleculeName: Complex of MraY AA dimer with nanobody bound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 200 KDa

-
Macromolecule #1: Phospho-N-acetylmuramoyl-pentapeptide-transferase

MacromoleculeName: Phospho-N-acetylmuramoyl-pentapeptide-transferase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: phospho-N-acetylmuramoyl-pentapeptide-transferase
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 40.954684 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPAVPRMLYQ LALLLKDYWF AFNVLKYITF RSFTAVLIAF FLTLVLSPSF INRLRKIQRL FGGYVREYTP ESHEVKKYTP TMGGIVILI VVTLSTLLLM RWDIKYTWVV LLSFLSFGTI GFWDDYVKLK NKKGISIKTK FLLQVLSASL ISVLIYYWAD I DTILYFPF ...String:
GPAVPRMLYQ LALLLKDYWF AFNVLKYITF RSFTAVLIAF FLTLVLSPSF INRLRKIQRL FGGYVREYTP ESHEVKKYTP TMGGIVILI VVTLSTLLLM RWDIKYTWVV LLSFLSFGTI GFWDDYVKLK NKKGISIKTK FLLQVLSASL ISVLIYYWAD I DTILYFPF FKELYVDLGV LYLPFAVFVI VGSANAVNLT DGLDGLAIGP AMTTATALGV VAYAVGHSKI AQYLNIPYVP YA GELTVFC FALVGAGLGF LWFNSFPAQM FMGDVGSLSI GASLATVALL TKSEFIFAVA AGVFVFETIS VILQIIYFRW TGG KRLFKR APFHHHLELN GLPEPKIVVR MWIISILLAI IAISMLKLR

UniProtKB: Phospho-N-acetylmuramoyl-pentapeptide-transferase

-
Macromolecule #2: MraYAA nanobody

MacromoleculeName: MraYAA nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.057651 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVPDVQLQES GGGLVQTGGS LTLSCATSGR SFSLYAMAWF RQAPGKEREF VAGVSRRGNT AYADAVKGRF TISRDNAANT VYLQMTSLK PEDTAVYFCA AFRVAVTTYT SQQANEYNYW GQGTQVTVSS LEHHHHHH

-
Macromolecule #3: (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bi...

MacromoleculeName: (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{S})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3- ...Name: (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{S})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid
type: ligand / ID: 3 / Number of copies: 2 / Formula: A1AI1
Molecular weightTheoretical: 934.127 Da

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration7.7 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris hydrochloride
150.0 mMNaClSodium chloride
5.0 mMDMdecyl-maltoside
2.0 mMDTTDithiothreitol

Details: 20mM Tris-HCl, 150mM NaCl, 2mM DTT, 5mM DM
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 4 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 2299 / Average exposure time: 4.6 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 277701
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC

-
Atomic model buiding 1

Initial modelPDB ID:

5ckr


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementOverall B value: 30
Output model

PDB-9b70:
Cryo-EM structure of MraY in complex with analogue 2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more