<emd emdb_id="EMD-5938" 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>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2014-03-28</deposition>
            <header_release>2014-04-09</header_release>
            <map_release>2014-04-09</map_release>
            <update>2014-05-14</update>
        </key_dates>
        <title>Electron cryo-microscopy of the Moloney murine leukemia virus furin precursor Env in its native form in complex with 83A25 Fab</title>
        <authors_list>
            <author>Sjoberg M</author>
            <author>Wu SR</author>
            <author>Loving R</author>
            <author>Rantalainen K</author>
            <author>Lindqvist B</author>
            <author>Garoff H</author>
        </authors_list>
        <keywords>Furin precursor, Moloney murine leukemia virus, Env maturation, 83A25 Fab</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sjoberg M</author>
                    <author order="2">Wu SR</author>
                    <author order="3">Loving R</author>
                    <author order="4">Rantalainen K</author>
                    <author order="5">Lindqvist B</author>
                    <author order="6">Garoff H</author>
                    <title>Furin cleavage of the Moloney murine leukemia virus Env precursor reorganizes the spike structure.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>111</volume>
                    <first_page>6034</first_page>
                    <last_page>6039</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24711391</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1317972111</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Native form of furin cleavage deficient mutant (R466G/K468G) Env of Moloney murine leukemia virus in complex with 83A25 Fab</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Native form of furin cleavage deficient mutant (R466G/K468G) Env of Moloney murine leukemia virus in complex with 83A25 Fab</name>
                <details>Affinity purified, gradient separated protein in 0.05% Triton X-100</details>
                <oligomeric_state>trimer</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.6</experimental>
                    <theoretical units="MDa">0.4</theoretical>
                    <method>Estimated from Blue native PAGE</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Furin precursor">gp90</name>
                <natural_source database="NCBI">
                    <organism ncbi="11801">Moloney murine leukemia virus</organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.5</experimental>
                    <theoretical units="MDa">0.27</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <oligomeric_state>Trimer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>monoclonal antibody 83A25 Fab</name>
                <natural_source database="NCBI">
                    <organism ncbi="10114">Rattus</organism>
                    <synonym_organism>rat</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.05</experimental>
                    <theoretical units="MDa">0.05</theoretical>
                </molecular_weight>
                <details>2-3 Fab molecules bind to the gp90 trimer.</details>
                <number_of_copies>3</number_of_copies>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">0.1</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>50 mM HEPES, 100 mM NaCl, 1.8 mM CaCl2, pH 7.4</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>The specimen was stained with 2% uranyl acetate (UA).</details>
                    </staining>
                    <grid>
                        <details>400 mesh regular continuous carbon grid, glow discharged</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2100F</microscope>
                    <illumination_mode>SPOT SCAN</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">2.048</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.072</nominal_defocus_max>
                    <nominal_magnification>43200.0</nominal_magnification>
                    <calibrated_magnification>43200.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected using online FFT.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2013-07-05</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">3.5</sampling_interval>
                            </digitization_details>
                            <number_real_images>60</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">9</average_electron_dose_per_image>
                            <bits_per_pixel>14.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected using a semi-automatic selection program in EMAN.</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">26.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN1, EMAN2</name>
                        </software>
                    </software_list>
                    <details>Final maps were calculated from three averaged datasets. The particles were selected using an automatic selection program. Damaged particles were removed by visual inspection.</details>
                    <number_images_used>9374</number_images_used>
                </final_reconstruction>
                <final_angle_assignment>
                    <details>EMAN</details>
                </final_angle_assignment>
                <final_two_d_classification>
                    <number_classes>20</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1025">
        <file>emd_5938.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>64</col>
            <row>64</row>
            <sec>64</sec>
        </dimensions>
        <origin>
            <col>-32</col>
            <row>-32</row>
            <sec>-32</sec>
        </origin>
        <spacing>
            <x>64</x>
            <y>64</y>
            <z>64</z>
        </spacing>
        <cell>
            <a units="&#8491;">224.0</a>
            <b units="&#8491;">224.0</b>
            <c units="&#8491;">224.0</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>-3.59785509</minimum>
            <maximum>13.54157925</maximum>
            <average>0.06688309</average>
            <std>1.77408254</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">3.5</x>
            <y units="&#8491;">3.5</y>
            <z units="&#8491;">3.5</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>7.4</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of the native furin cleavage deficient mutant (R466G/K468G) Env of Moloney murine leukemia virus in complex with the 83A25 Fab</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5938::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1MQK</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Atomic structure of the Fv fragment of the monoclonal Ab 7E2 against the Paracoccus denitrificans cytochrome c oxidase was fitted into the density map.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>