[English] 日本語
Yorodumi
- PDB-9org: MicroED structure of apo-form CTX-M-14 beta-lactamase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9org
TitleMicroED structure of apo-form CTX-M-14 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / enzyme / beta-lactamase / MicroED
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.5 Å
AuthorsVlahakis, N. / Rodriguez, J.A. / Jacobs, L.M.C. / Chen, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
Howard Hughes Medical Institute (HHMI)HHMI-EPI United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Combining MicroED and native mass spectrometry for structural discovery of enzyme-small molecule complexes.
Authors: Niko W Vlahakis / Cameron W Flowers / Mengting Liu / Matthew P Agdanowski / Samuel Johnson / Jacob A Summers / Lian M C Jacobs / Catherine Keyser / Phoebe Russell / Samuel L Rose / Julien ...Authors: Niko W Vlahakis / Cameron W Flowers / Mengting Liu / Matthew P Agdanowski / Samuel Johnson / Jacob A Summers / Lian M C Jacobs / Catherine Keyser / Phoebe Russell / Samuel L Rose / Julien Orlans / Nima Adhami / Yu Chen / Michael R Sawaya / Shibom Basu / Daniele de Sanctis / Yu Chen / Soichi Wakatsuki / Hosea M Nelson / Joseph A Loo / Yi Tang / Jose A Rodriguez /
Abstract: With the goal of accelerating the discovery of small molecule-protein complexes, we leverage fast, low-dose, event-based electron counting microcrystal electron diffraction (MicroED) data collection ...With the goal of accelerating the discovery of small molecule-protein complexes, we leverage fast, low-dose, event-based electron counting microcrystal electron diffraction (MicroED) data collection and native mass spectrometry. This approach, which we term electron diffraction with native mass spectrometry (ED-MS), allows assignment of protein target structures bound to ligands with data obtained from crystal slurries soaked with mixtures of known inhibitors and crude biosynthetic reactions. This extends to libraries of printed ligands dispensed directly onto TEM grids for later soaking with microcrystal slurries, and complexes with noncovalent ligands. ED-MS resolves structures of the natural product, epoxide-based cysteine protease inhibitor E-64, and its biosynthetic analogs bound to the model cysteine protease, papain. It further identifies papain binding to its preferred natural products, by showing that two analogs of E-64 outcompete others in binding to papain crystals, and by detecting papain bound to E-64 and an analog from crude biosynthetic reactions, without purification. ED-MS also resolves binding of the CTX-M-14 β-lactamase, a target of active drug development, to the non-β-lactam inhibitor, avibactam, alone or in a cocktail of unrelated compounds. These results illustrate the utility of ED-MS for natural product ligand discovery and for structure-based screening of small molecule binders to macromolecular targets, promising utility for drug discovery.
History
DepositionMay 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)56,0012
Polymers56,0012
Non-polymers00
Water21612
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,0011
Polymers28,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,0011
Polymers28,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.870, 107.270, 47.620
Angle α, β, γ (deg.)90.00, 101.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-lactamase


Mass: 28000.547 Da / Num. of mol.: 2 / Fragment: UNP residues 23-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, AM340_ ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, AM340_28340, AM465_01285, AM465_06510, AM465_23360, APT94_14605, BEN53_26220, BJJ90_27545, BK334_27290, BOH76_00730, BON63_16015, BON65_15195, BON66_01305, BON69_22545, BON72_03470, BON75_10525, BON76_14325, BON83_15455, BON86_08515, BON91_02075, BON92_04750, BON94_23850, BON95_01680, BON96_03940, BON98_23175, BXT93_06855, C5N07_28500, CDL37_21060, CR538_26855, DW236_20870, E4K51_21070, EIA08_25160, EIA21_26975, ELT23_05930, ELV24_09995, ELX61_24095, EST51_15935, EST51_18575, EST51_22260, EST51_22365, ETN48_p0088, FNJ69_13810, FTV90_03295, GE096_24920, GE096_25355, GQE36_23945, HGR36_01450, HGR36_27140, HHH24_004455, HHH24_005319, HJI79_003882, HJI79_004995, HK427_004976, HK427_005087, HL152_24835, HL152_25835, HL563_21800, HL563_23665, HLT96_25270, HLT96_28700, HLU13_27785, HLY53_18605, HLY53_26190, HLZ85_26065, HMW26_20895, HMW26_29355, HNC73_28650, HNC75_27190, HNC75_29165, HNC80_26145, HNC80_27675, HNC88_26185, HNC88_27880, HND23_26750, HND23_28285, HNV91_23425, HNV91_24920, HNV94_24095, HNV94_27845, pCT_085, pHK01_011, RCS103_P0010, RCS30_P0082, RCS56_P0085, RCS60_P0031, RCS63_P0006, RCS65_P0008, RCS66_P0053, SAMEA4362930_00013, SAMEA4363083_00099, SAMEA4370290_00046, WP4S18E07_P40650, WP7S17E01_P10270, WP7S18E09_37980
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L5C7, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

-
Sample preparation

ComponentName: CTX-M_14 beta-lactamase / Type: COMPLEX
Details: Crystals were grown by hanging-drop vapor diffusion from drops of 25.7 mg/mL CTX-M-14 mixed 1:1 with crystallization solution (1.4 M potassium phosphate pH 7.9)
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
EM crystal formationDetails: Crystals were grown by hanging-drop vapor diffusion from drops of 25.7 mg/mL CTX-M-14 mixed 1:1 with crystallization solution (1.4 M potassium phosphate pH 7.9)
Temperature: 293 K
Buffer solutionpH: 7.9 / Details: 1.4 M potassium phosphate pH 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Crystals were grown by hanging-drop vapor diffusion from drops of 25.7 mg/mL CTX-M-14 mixed 1:1 with crystallization solution (1.4 M potassium phosphate pH 7.9)
VitrificationCryogen name: ETHANE

-
Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: TFS TALOS F200C
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / C2 aperture diameter: 70 µm
Specimen holderTemperature (max): 100 K / Temperature (min): 100 K
Image recordingElectron dose: 0.09 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)
EM diffraction shellResolution: 2.5→2.6 Å / Fourier space coverage: 86.8 % / Multiplicity: 8.19 / Num. of structure factors: 1437 / Phase residual: 28.9 °
EM diffraction statsFourier space coverage: 87.8 % / High resolution: 2.5 Å / Num. of intensities measured: 113750 / Num. of structure factors: 13467 / Phase error rejection criteria: NONE / Rmerge: 0.387

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
EM 3D crystal entity∠α: 90 ° / ∠β: 101.371 ° / ∠γ: 90 ° / A: 44.87 Å / B: 107.27 Å / C: 47.62 Å / Space group name: P21 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution: 2.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingPDB-ID: 1YLT

1ylt


Accession code: 1YLT / Source name: PDB / Type: experimental model
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.99 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 1345 10.01 %
Rwork0.2088 --
obs0.2118 13439 87.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0043980
ELECTRON CRYSTALLOGRAPHYf_angle_d0.9795420
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d5.995566
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.053644
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.007715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.331300.28421167ELECTRON CRYSTALLOGRAPHY87
2.59-2.690.2871360.27681226ELECTRON CRYSTALLOGRAPHY89
2.69-2.820.30081360.26911222ELECTRON CRYSTALLOGRAPHY89
2.82-2.960.31341340.26061208ELECTRON CRYSTALLOGRAPHY88
2.96-3.150.27321360.25531217ELECTRON CRYSTALLOGRAPHY89
3.15-3.390.25071360.221224ELECTRON CRYSTALLOGRAPHY88
3.39-3.730.24321350.18351218ELECTRON CRYSTALLOGRAPHY88
3.73-4.270.19981330.16891195ELECTRON CRYSTALLOGRAPHY87
4.27-5.380.16331350.15061217ELECTRON CRYSTALLOGRAPHY87
5.39-43.990.20551340.1861200ELECTRON CRYSTALLOGRAPHY86

+
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://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