<emd emdb_id="EMD-2572" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2014-02-10</deposition>
            <header_release>2014-03-12</header_release>
            <map_release>2014-04-30</map_release>
            <update>2014-04-30</update>
        </key_dates>
        <title>Cryo-EM structure of Plasmodium falciparum actin I</title>
        <authors_list>
            <author>Vahokoski J</author>
            <author>Bhargav SP</author>
            <author>Desfosses A</author>
            <author>Andreadaki M</author>
            <author>Kumpula E</author>
            <author>Ignatev A</author>
            <author>Martinez SM</author>
            <author>Lepper S</author>
            <author>Frischknecht F</author>
            <author>Siden-Kiamos I</author>
            <author>Sachse C</author>
            <author>Kursula I</author>
        </authors_list>
        <keywords>Plasmodium falciparum Actin I, malaria parasite</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Vahokoski J</author>
                    <author order="2">Bhargav SP</author>
                    <author order="3">Desfosses A</author>
                    <author order="4">Andreadaki M</author>
                    <author order="5">Kumpula E</author>
                    <author order="6">Ignatev A</author>
                    <author order="7">Martinez SM</author>
                    <author order="8">Lepper S</author>
                    <author order="9">Frischknecht F</author>
                    <author order="10">Siden-Kiamos I</author>
                    <author order="11">Sachse C</author>
                    <author order="12">Kursula I</author>
                    <title>Structural Differences Explain Diverse Functions of Plasmodium Actins</title>
                    <journal>PLOS PATHOG.</journal>
                    <volume>10</volume>
                    <first_page>e1004091</first_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24743229</external_references>
                    <external_references type="DOI">doi:10.1371/journal.ppat.1004091</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Plasmodium falciparum Actin I</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Plasmodium falciparum Actin I</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Plasmodium actin I</name>
                <natural_source database="NCBI">
                    <organism ncbi="5833">Plasmodium falciparum</organism>
                </natural_source>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
                    <recombinant_strain>Sf21</recombinant_strain>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q9U6U4</external_references>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>helicalArray</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">0.3</concentration>
                    <buffer>
                        <details>50 mM (pH 8.0) Tris-HCl, 500 mM KCl, 20 mM MgCl2, 50 mM DTT, and 10 mM ATP, JAS 5 uM</details>
                    </buffer>
                    <grid>
                        <details>glow-discharged holey carbon grids (Quantifoil R 2/2)</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">70</chamber_humidity>
                        <chamber_temperature units="K">120</chamber_temperature>
                        <instrument>LEICA EM GP</instrument>
                        <method>Polymerized samples were applied in 3-uL aliquots onto freshly glow-discharged holey carbon grids (Quantifoil R 2/2) at 295 K and 70% humidity and vitrified in liquid ethane using a Leica EM GP vitrification robot.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">7.0</nominal_defocus_max>
                    <nominal_magnification>69000.0</nominal_magnification>
                    <calibrated_magnification>69000.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2013-02-06</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>75</number_real_images>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>93 K</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>For 3D structure determination, segments were excised using a regular step size of 70 Angstrom, convolved by their respective CTF and further reconstructed as described (Sachse et al. 2007) using the software SPRING (Desfosses et al. 2014)</details>
                <ctf_correction>
                    <details>Each particle (convolved)</details>
                </ctf_correction>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">27.69</delta_z>
                            <delta_phi units="deg">167.52</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">25.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>SPRING</name>
                        </software>
                    </software_list>
                    <number_images_used>3513</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="939">
        <file>emd_2572.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>40</col>
            <row>40</row>
            <sec>150</sec>
        </dimensions>
        <origin>
            <col>-20</col>
            <row>-20</row>
            <sec>-75</sec>
        </origin>
        <spacing>
            <x>40</x>
            <y>40</y>
            <z>150</z>
        </spacing>
        <cell>
            <a units="&#8491;">176.48001</a>
            <b units="&#8491;">176.48001</b>
            <c units="&#8491;">661.80005</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-0.36687934</minimum>
            <maximum>1.25957727</maximum>
            <average>0.00141309</average>
            <std>0.21407938</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.412</x>
            <y units="&#8491;">4.412</y>
            <z units="&#8491;">4.412</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.125</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Cryo-EM structure of Plasmodium falciparum actin I</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2572::::</details>
    </map>
</emd>