<emd emdb_id="EMD-2884" 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>2015-02-08</deposition>
            <header_release>2015-04-01</header_release>
            <map_release>2016-01-13</map_release>
            <update>2016-02-17</update>
        </key_dates>
        <title>Cryo-Molecular electron tomography of PfEMP1-IT4Var60)</title>
        <authors_list>
            <author>Akhouri RR</author>
            <author>Goel S</author>
            <author>Furusho H</author>
            <author>Skoglund U</author>
            <author>Wahlgren M</author>
        </authors_list>
        <keywords>Malaria, Rosetting, PfEMP1</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Akhouri RR</author>
                    <author order="2">Goel S</author>
                    <author order="3">Furusho H</author>
                    <author order="4">Skoglund U</author>
                    <author order="5">Wahlgren M</author>
                    <title>Architecture of Human IgM in Complex with P. falciparum Erythrocyte Membrane Protein 1.</title>
                    <journal>CELL REP.</journal>
                    <volume>14</volume>
                    <first_page>723</first_page>
                    <last_page>736</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26776517</external_references>
                    <external_references type="DOI">doi:10.1016/j.celrep.2015.12.067</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>ectodomain of PfEMP1-IT4Var60</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>ectodomain of PfEMP1-IT4Var60</name>
                <details>the sample was monodisperse.</details>
                <oligomeric_state>Monomer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.358</experimental>
                    <theoretical units="MDa">0.280</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>PfEMP1</name>
                <natural_source database="NCBI">
                    <organism ncbi="5833">Plasmodium falciparum</organism>
                    <strain>FCR3S1.2</strain>
                    <synonym_organism>Malaria Parasite</synonym_organism>
                    <cellular_location>Infected erythrocyte membrane</cellular_location>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.358</experimental>
                    <theoretical units="MDa">0.280</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7227">Drosophila melanogaster</recombinant_organism>
                    <recombinant_cell>S2 cells</recombinant_cell>
                    <recombinant_plasmid>pMTBipV5HisA</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <concentration units="mg/mL">2</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>20mM Hepes, 200mM NaCl</details>
                    </buffer>
                    <grid>
                        <details>C-Flat (Copper grid with thin Carbon support)</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">78</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot for 4 seconds before plunging</method>
                    </vitrification>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.0007</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">0.0015</nominal_defocus_max>
                    <nominal_magnification>37000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">78</temperature_min>
                        <temperature_max units="K">100</temperature_max>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>FEI</name>
                        </energy_filter>
                    </specialist_optics>
                    <date>2013-09-13</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <number_real_images>281</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">40</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>LN2 cooled</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-70</min_angle>
                            <max_angle units="deg">70</max_angle>
                            <angle_increment units="deg">0.5</angle_increment>
                        </axis1>
                    </tilt_series>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <details>CTF correction and alignment using gold particles</details>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">20.0</resolution>
                    <software_list>
                        <software>
                            <name>COMET</name>
                        </software>
                    </software_list>
                    <number_images_used>281</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <details>each frame</details>
                </ctf_correction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1922">
        <file>emd_2884.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>62</col>
            <row>103</row>
            <sec>77</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>103</x>
            <y>62</y>
            <z>77</z>
        </spacing>
        <cell>
            <a units="&#8491;">140.554</a>
            <b units="&#8491;">233.50099</b>
            <c units="&#8491;">174.55899</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>0.00021451</minimum>
            <maximum>0.02836445</maximum>
            <average>0.00636834</average>
            <std>0.00430598</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.267</x>
            <y units="&#8491;">2.267</y>
            <z units="&#8491;">2.267</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.013</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of PfEMP1-IT4Var60 ectodomain</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2884::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_2884.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>