<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-14771">
    <admin>
        <current_status>
            <date>2024-07-24</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-04-13</deposition>
            <header_release>2022-12-07</header_release>
            <map_release>2022-12-07</map_release>
            <update>2024-07-24</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Not funded</funding_body>
            </grant_reference>
        </grant_support>
        <title>Amyloid fibril from human systemic AA amyloidosis (vascular variant)</title>
        <authors_list>
            <author>Banerjee S</author>
            <author>Schmidt M</author>
            <author>Faendrich M</author>
        </authors_list>
        <keywords>Amyloids, Vascular AA, SAA, Cryo-EM, PROTEIN FIBRIL</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0003-1705-1034" order="1">Banerjee S</author>
                    <author order="2">Baur J</author>
                    <author ORCID="0000-0002-6803-4755" order="3">Daniel C</author>
                    <author order="4">Pfeiffer PB</author>
                    <author order="5">Hitzenberger M</author>
                    <author order="6">Kuhn L</author>
                    <author ORCID="0000-0001-5697-2608" order="7">Wiese S</author>
                    <author order="8">Bijzet J</author>
                    <author order="9">Haupt C</author>
                    <author order="10">Amann KU</author>
                    <author ORCID="0000-0001-5163-2663" order="11">Zacharias M</author>
                    <author ORCID="0000-0003-1827-0482" order="12">Hazenberg BPC</author>
                    <author ORCID="0000-0003-1151-9986" order="13">Westermark GT</author>
                    <author ORCID="0000-0002-9442-460X" order="14">Schmidt M</author>
                    <author ORCID="0000-0003-2123-6816" order="15">Fandrich M</author>
                    <title>Amyloid fibril structure from the vascular variant of systemic AA amyloidosis.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>13</volume>
                    <first_page>7261</first_page>
                    <last_page>7261</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">36433936</external_references>
                    <external_references type="DOI">doi:10.1038/s41467-022-34636-4</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>7zky</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Amyloid fibril from human systemic AA amyloidosis (vascular variant)</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Amyloid fibril from human systemic AA amyloidosis (vascular variant)</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Amyloid protein A</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.007775502</theoretical>
                </molecular_weight>
                <number_of_copies>12</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>SFFSFLGEAFDGARDMWRAYSDMREANYIGSDKYFHARGNYDAAKRGPGGVWAAEAISDARENIQRFF</string>
                    <external_references type="UNIPROTKB">P0DJI8</external_references>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>helicalArray</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <buffer>
                        <ph>7.0</ph>
                    </buffer>
                    <grid>
                        <model>C-flat-1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">40</time>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>SPOT SCAN</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="µm">0.8</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.0</nominal_defocus_max>
                    <nominal_magnification>130000.0</nominal_magnification>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <average_exposure_time units="s">10.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">42.84</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="Å">4.75</delta_z>
                            <delta_phi units="deg">-1.63</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>SIMULTANEOUS ITERATIVE (SIRT)</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">2.56</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>77061</number_images_used>
                </final_reconstruction>
                <startup_model type_of_model="NONE"/>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </final_angle_assignment>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="67109">
        <file>emd_14771.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>256</col>
            <row>256</row>
            <sec>256</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="Å">266.24</a>
            <b units="Å">266.24</b>
            <c units="Å">266.24</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>-0.053856436</minimum>
            <maximum>0.14575852</maximum>
            <average>0.000722567</average>
            <std>0.005809631</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.04</x>
            <y units="Å">1.04</y>
            <z units="Å">1.04</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0163</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-14771::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>AB INITIO MODEL</refinement_protocol>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
