<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-2471" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>HPUB</code>
            </status>
        </status_history_list>
        <current_status>
            <code>OBS</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2013-09-19</deposition>
            <header_release>2013-10-16</header_release>
            <obsolete>2015-01-14</obsolete>
            <update>2015-01-14</update>
        </key_dates>
        <title>Cryo-EM structures of archaeal translation initiation complexes</title>
        <authors_list>
            <author>Coureux P-D</author>
            <author>Schmitt E</author>
            <author>Monestier A</author>
            <author>Larquet E</author>
            <author>Cladiere L</author>
            <author>Devaux Z</author>
            <author>Jonic S</author>
            <author>Myasnikov A</author>
            <author>Menetret J-F</author>
            <author>Klaholz B</author>
            <author>Mechulam Y</author>
        </authors_list>
        <keywords>Translation initiation, archaea</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Coureux P-D</author>
                    <author order="2">Schmitt E</author>
                    <author order="3">Monestier A</author>
                    <author order="4">Larquet E</author>
                    <author order="5">Cladiere L</author>
                    <author order="6">Devaux Z</author>
                    <author order="7">Jonic S</author>
                    <author order="8">Myasnikov A</author>
                    <author order="9">Menetret J-F</author>
                    <author order="10">Klaholz B</author>
                    <author order="11">Mechulam Y</author>
                    <title>Cryo-EM structures of archaeal translation initiation complexes</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>4c7c</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Pyrococcus abyssi 30S subunit with aIF1A, aIF1, aIF2, tRNAi and mRNA</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Pyrococcus abyssi 30S subunit with aIF1A, aIF1, aIF2, tRNAi and mRNA</name>
                <number_unique_components>6</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>Archaeal 30S subunit</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="29292">Pyrococcus abyssi</organism>
                </natural_source>
                <recombinant_expression database="NCBI"/>
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>aIF1</name>
                <natural_source database="NCBI">
                    <organism ncbi="29292">Pyrococcus abyssi</organism>
                </natural_source>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <sequence/>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>aIF2</name>
                <natural_source database="NCBI">
                    <organism ncbi="29292">Pyrococcus abyssi</organism>
                </natural_source>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <sequence/>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>aIF1A</name>
                <natural_source database="NCBI">
                    <organism ncbi="29292">Pyrococcus abyssi</organism>
                </natural_source>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <sequence/>
            </protein_or_peptide>
            <rna macromolecule_id="4">
                <name synonym="tRNA">Transfer RNA</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                </natural_source>
                <classification>TRANSFER</classification>
                <structure>DOUBLE HELIX</structure>
                <synthetic_flag>false</synthetic_flag>
            </rna>
            <rna macromolecule_id="5">
                <name synonym="mRNA">messenger RNA</name>
                <natural_source database="NCBI">
                    <organism ncbi="29292">Pyrococcus abyssi</organism>
                </natural_source>
                <classification>OTHER</classification>
                <structure>SINGLE STRANDED</structure>
                <synthetic_flag>true</synthetic_flag>
            </rna>
        </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">0.2</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>10 mM Hepes pH 7.5, 100 mM NH4Cl, 10 mM MgAcetate, 3 mM 2-mercaptoethanol</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">100</acceleration_voltage>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2011-12-12</date>
                    <image_recording_list>
                        <image_recording>
                            <digitization_details>
                                <sampling_interval units="µm">2</sampling_interval>
                            </digitization_details>
                            <number_real_images>3008</number_real_images>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <number_images_used>27000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="34649">
        <file>emd_2471.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>207</col>
            <row>207</row>
            <sec>207</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>207</x>
            <y>207</y>
            <z>207</z>
        </spacing>
        <cell>
            <a units="Å">376.74002</a>
            <b units="Å">376.74002</b>
            <c units="Å">376.74002</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>-0.0359138</minimum>
            <maximum>0.10863522</maximum>
            <average>0.00030886</average>
            <std>0.00935727</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.82</x>
            <y units="Å">1.82</y>
            <z units="Å">1.82</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.008</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>IC1 map</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2471::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3j20</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
            <modelling>
                <initial_model>
                    <access_code>3V11</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
