You are here: Home / Infrastructures / Res. Infrastructure
Czech Infrastructure for Integrative Structural Biology (CIISB)
Identification
Hosting Legal Entity
Masaryk University
Location
Kamenice 753/5, CEITEC MU, Structural Biology Programme, Brno, PO: 625 00 (Czech Republic)
Structure
Type Of RI
Distributed
Coordinating Country
Czech Republic
Participating Countries
Czech Republic
Nodes
Provider Country:
Czech Republic
Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec
Status
Status
Current Status:
Being upgraded since 2017
Timeline
Being upgraded since 2017 to 2019
Operational since 2016
Under construction since 2011 to 2015
Scientific Description
A gateway to realm of structural data for biochemists, biophysicists, molecular biologist, and all scientists whose research benefits from accurate structure determination of biological macromolecules, assemblies, and complex molecular machineries at atomic resolution.
The goal of the CIISB research infrastructure is to offer access to technologies for a variety of users from both the academic and the industrial community (pharmaceutical, biotechnology and agricultural companies) from the Czech Republic and other countries.
CIISB expertise covers a wide range of topics in cellular and molecular structural biology and secures necessary support for external users in all stages of project implementation, from sample preparation, data acquisition, up to data processing and evaluation.

RI Keywords
NMR, Protein crystallization, Data acquisition, Open-access infrastructure, Spectroscopy, Diffraction, Proteomics, 3D cryo-EM, Data processing, Sample preparation
Classifications
RI Category
Structural Biology Facilities
Scientific Domain
Biological and Medical Sciences
ESFRI Domain
Health and Food
Services
Biomolecular Interactions and Crystallization

Calorimetric measurement of protein-ligand interaction (Standard titration method, Single injection method) Competitive-based measurement - low or high affinity interactions Data evaluation - thermodynamic parameters determination using curve fitting models: One set of binding site, Two sets of binding sites Eventuality of manual data evaluation using fitting models: Sequential binding sites, Competitive binding, Dissociation

Crystallisation of proteins and nucleic acids

Classical and robotic crystallogenesis with remote experiment monitoring in three dedicated laboratories with strictly controlled temperature regimes with full backup. Automated screening of variation of crystallization conditions and its effects. Anaerobic crystallization and manipulation of biomacromolecules.

Cryo-electron Microscopy and Tomography

The cryo-EM core facility provides access and support to collect cryo-electron microscopy images for both single particle as well as for electron tomography applications. Furthermore, the facility provides support for sample preparation, namely plunge freezing of purified protein complexes as well as cryo-FIB lamella milling for thick biological objects such as cells. Additional support is given in experiment design, setting up data collection and data analysis (i.e. image processing). Interested non-specialists could receive training in using the electron microscopes or develop a collaboration with the CryoEM research group, particularly in these areas: high-resolution structure determination of macromolecular complexes and assemblies structural studies of intracellular compartments and host-pathogen interactions time-resolved electron microscopy of transient macromolecular complexes

Proteomics

Analysis of intact proteins; protein identification (incl. protein complexes, de novo sequencing); identification of protein modifications; absolute and relative protein quantification

Nuclear Magnetic Resonance (NMR) Spectroscopy

Besides providing the access to the spectrometers, the core facility offers consultations on the choice of suitable NMR measurements, support in setup and running the experiments, processing the data and evaluation of the results. The facility can run the latest multidimensional measurements using non-uniform sampling methods and direct carbon detection. In collaboration with the research groups of Protein Structure and Dynamics and Structural Biology of Gene Regulation, the users can in collaborative projects utilize the expertise of the groups in studies of the structures, dynamics and interactions of proteins and nucleic acids, including the use of available hardware and software.

Nanobiotechnology

The imaging of biomolecules, cells and other biological structures and objects is realized in aqueous solution or in the dry state. The carrier materials for sample deposition range from ultra flat mica slides suitable for atomic resolution to highly oriented graphite, gold, silicon, glass and polymers as polystyrene petri dishes. Different scanning tips with appropriate sharpness and cantilevers with a wide range of force constants.

Structural Mass Spectrometry

The utilization of high-resolution mass spectrometry (15T FT-ICR MS) to determine the composition of molecules (metabolites, nucleic acid, proteins, and carbohydrates) based on accurate mass measurements and fragment pattern. FT-ICR MS is equipped with atmospheric pressure ionization technique (electrospray) and various types of vacuum ionization techniques (laser desorption, matrix-assisted laser desorption). FT-ICR MS is able to perform sustained off-resonance irradiation, collision-induced and electron transfer/capture dissociations. Mass spectrometric cutting-edge analysis of post-translational modifications, and of structural states of proteins and complexes in solution. Combination of covalent surface labeling, isotope (H/D) exchange, chemical cross-linking.

Biophysical techniques

All services at CMS (Centre of Molecular Structure of BIOCEV) are available both to unexperienced users and to experienced users (that do not require the assistance of the scientist in charge). Biophysical core research facilities offer a range of services, including investigations of biomolecular interactions, of structure, stability and conformation of DNA and proteins, determination of hydrodynamic radii, zeta potential and electrophoretic mobility of molecules, together with crystallization screens.

Diffraction techniques

Bruker D8 Venture diffractometer with a high-flux liquid Gallium X-ray source MetalJet D2, Photon II detector and Kappa goniometer. The diffractometer is used (at CMS) for X-ray diffraction of biomolecular crystals. ISX stage for D8 Venture – motorized stage for in-situ X-ray diffraction experiments, enabling screening of diffraction properties in crystallization trays.

X-ray Diffraction and Bio-SAXS Characterisation

Basic characterization of solution of biological macromolecules by SAXS Determination of a low resolution 3-D shape of biological macromolecules by SAXS SAXS characterization of non-biological nanostructures Test of a diffraction quality of protein crystals, derivatives, cryoprotectants etc prior data collection Collection of diffraction data with crystals of biological macromolecules Data collection and solving of the crystal structures with non-biological single crystals Collection of high angle diffraction data with non-biological single crystals Collection of diffraction data with small and/or weekly diffracting non-biological single crystals

Equipment
Scanning probe microscope - Ntegra Vita / Solaris (NTMDT)
Formulatrix RI1000 crystallisation hotel

Formulatrix RI1000 crystallisation hotel - a crystallisation plate storage and automated crystallization monitoring enclosure allowing remote access to crystallization images

Automated system SolverNEXT (NTMDT)
CD spectrometer Jasco 850 equipped with fluorescence detecto
Rigaku BioSAXS-1000 SAXS camera

Rigaku BioSAXS-1000 SAXS camera for small angle X-ray scattering from solutions of biological macromolecules

Hybrid mass spectrometer (Q-LIT) with quadrupole and linear ion trap and liquid chromatography system
Monolith NT. LabelFree thermophoresis
Vitrification robot Vitrobot Mark IV
Applied Photophysics circular dichroism (CD) spectrometer Chirascan Plus
Crystallization robot Mosquito and Tecan Evo 150
MALDI-TOF/TOF mass spectrometer
Monolith NT.150 microscale thermophoresis (MST)
Rigaku HighFlux HomeLab™ universal, dual wavelength (Mo-Kα and Cu-Kα) diffractometer
Bruker Daltonics 15T-Solarix XR FT-ICR mass spectrometer, with electrospray and MALDI ion sources
Ink-jet based deposition system S3 (Scienion)
Prometheus NT.48 DSF assay
BioRad ProteOn XPR36 interaction array instrument
NMR spectrometer for high-resolution spectroscopy in liquids and solids (500 MHz and 700 MHz)
ISX stage for D8 Venture

motorized stage for in-situ X-ray diffraction experiments, enabling screening of diffraction properties in crystallization trays

Agilent Technologies 1200 HPLC system

Agilent Technologies 1200 HPLC system (usually coupled to the 15T-SolariX XR mass spectrometer) for the separation of complex peptide mixtures, proteins and metabolites

DLS Dynapro Plate Reader, DelsaMax
Bruker D8 Venture diffractometer with a high-flux liquid Gallium X-ray source MetalJet D2, Photon II detector and Kappa goniometer
NMR spectrometer for high-resolution spectroscopy in liquids (600 MHz, 700 MHz, 850 MHz and 950 MHz)
SPR BiaCore 3000
High-resolution mass spectrometer (FTMS) with Orbitrap
FEI Titan Krios

FEI Titan Krios – high-end transmission electron microscope operating at 80 - 300 kV equipped with Schottky field emission gun (XFEG) providing highly coherent electron beam with ultimate stability. The microscope is equipped with hole free Volta phase plate for increase of contrast, Thermo Fisher Scientific Falcon3EC direct electron detector, and Gatan K2 direct electron detector positioned at the end of post-column imaging energy filter (GIF Quantum LS imaging filter). Automated collection of single particle analysis data can be performed with EPU software, cryo-electron tomography data can be acquired using Tomography4 or SerialEM software

Spectrolight 600

Spectrolight 600 - in drop dynamic light scattering measurements in Terasaki 72-well plates

Rigaku HighFlux HomeLab™

Robotized macromolecular diffraction system with ACTOR sample changer optimized for work at Cu-Kα wavelength

NMR spectrometer for high-resolution spectroscopy in liquids (600 MHz, 700 MHz, 850 MHz and 950 MHz)
UV/visible spectrophotometer with temperature control Analytic Jena Specord 50 Plus
Microcal iTC200 highly sensitive, low volume isothermal titration calorimeter
FEI Tecnai F20

Transmission electron microscope operating at 20–200 kV equipped with Schottky field emission gun (SFEG), and a FEI Eagle 4k x 4k CCD camera. Sample is inserted using either side-entry cryo-holders (Gatan 626 and Gatan 914) or room-temperature side-entry holders. The microscope is well suited for optimization of cryoEM samples and automated data collection by single particle analysis or (cryo-)electron tomography

Malvern Zetasizer Nano ZS90
ForceRobot 300 (JPK)
Leica microscope with polarizing filter • Temperature optimizer for crystallization TG40 for 5 different temperatures
SPR BiaCore 3000
Atomic force microscope NanoWizzard3 (JPK)
Analytical ultracentrifuge ProteomLab XLI
Microcal VP-DSC highly sensitive differential scanning calorimeter
ArtRobbins Gryphon dropsetter

ArtRobbins Gryphon dropsetter - a multi-channel (96 channels) pipetting robot for the easy set-up of nanodrop crystallisation plates

FEI Versa3D

small dual beam microscope (SEM/FIB) equipped with a Quorum Technologies PP3010T cryo-preparation system for delivery of vitrified samples into the microscope. System is optimal for preparation of thin lamellas from vitrified cells for the purposes of in situ structural biology studies Conventional cryoEM microscope FEI F20 (200 kV) equipped with a CCD camera and a dual beam FIB/SEM instrument (Versa3D) for micromachining of thin lamellas of vitrified cells usable for electron tomography

Calorimeters AutoITC200, VP-ITC, VP-DSC
Automated Desktop UV Minstrel + Gallery Hotel 160 for inspection of screening plates
Access
Access Type
Physical, Mail-in, Remote
Access Mode
Market Driven, Excellence Driven
Users
Number of Users
Number Year
530 2017
Users Definition
Teams of individual researchers
User Demographics
National Users - 95.0% in 2017
European Users - 5.0% in 2017
National Users - 94.0% in 2016
European Users - 6.0% in 2016
Collaborations
ESFRI
RI is a node of an ESFRI project
Networks
INSTRUCT
Date of last update: 13/03/2019