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- PDB-7dce: Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7dce
TitleCryo-EM structure of human XKR8-basigin complex bound to Fab fragment
Components
  • Heavy chain of Fab fragment
  • Isoform 2 of Basigin
  • Light chain of Fab fragment
  • XK-related protein 8
KeywordsTRANSPORT PROTEIN / XKR8 / basigin / scramblase / phospholipid
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / phosphatidylserine exposure on apoptotic cell surface / tolerance induction to self antigen / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / phospholipid scramblase activity / neutrophil clearance / response to mercury ion / engulfment of apoptotic cell ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / phosphatidylserine exposure on apoptotic cell surface / tolerance induction to self antigen / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / phospholipid scramblase activity / neutrophil clearance / response to mercury ion / engulfment of apoptotic cell / endothelial tube morphogenesis / neural retina development / apoptotic process involved in development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / D-mannose binding / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / Integrin cell surface interactions / positive regulation of myoblast differentiation / response to cAMP / neutrophil chemotaxis / embryo implantation / Degradation of the extracellular matrix / photoreceptor inner segment / positive regulation of endothelial cell migration / establishment of localization in cell / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / signaling receptor activity / virus receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / perinuclear region of cytoplasm / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
XK-related protein / : / XK-related protein / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...XK-related protein / : / XK-related protein / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Basigin / XK-related protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSakuragi, T. / Kanai, R. / Tsutsumi, A. / Narita, H. / Onishi, E. / Miyazaki, T. / Baba, T. / Nakagawa, A. / Kikkawa, M. / Toyoshima, C. / Nagata, S.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H05785 Japan
Japan Society for the Promotion of Science (JSPS)20K15731 Japan
Japan Science and TechnologyJPMJCR14M1 Japan
Japan Science and TechnologyJPMJCR14M4 Japan
Japan Agency for Medical Research and Development (AMED)JP17am010172 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101072 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101072 Japan
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes.
Authors: Takaharu Sakuragi / Ryuta Kanai / Akihisa Tsutsumi / Hirotaka Narita / Eriko Onishi / Kohei Nishino / Takuya Miyazaki / Takeshi Baba / Hidetaka Kosako / Atsushi Nakagawa / Masahide Kikkawa / ...Authors: Takaharu Sakuragi / Ryuta Kanai / Akihisa Tsutsumi / Hirotaka Narita / Eriko Onishi / Kohei Nishino / Takuya Miyazaki / Takeshi Baba / Hidetaka Kosako / Atsushi Nakagawa / Masahide Kikkawa / Chikashi Toyoshima / Shigekazu Nagata /
Abstract: Xkr8-Basigin is a plasma membrane phospholipid scramblase activated by kinases or caspases. We combined cryo-EM and X-ray crystallography to investigate its structure at an overall resolution of 3. ...Xkr8-Basigin is a plasma membrane phospholipid scramblase activated by kinases or caspases. We combined cryo-EM and X-ray crystallography to investigate its structure at an overall resolution of 3.8 Å. Its membrane-spanning region carrying 22 charged amino acids adopts a cuboid-like structure stabilized by salt bridges between hydrophilic residues in transmembrane helices. Phosphatidylcholine binding was observed in a hydrophobic cleft on the surface exposed to the outer leaflet of the plasma membrane. Six charged residues placed from top to bottom inside the molecule were essential for scrambling phospholipids in inward and outward directions, apparently providing a pathway for their translocation. A tryptophan residue was present between the head group of phosphatidylcholine and the extracellular end of the path. Its mutation to alanine made the Xkr8-Basigin complex constitutively active, indicating that it plays a vital role in regulating its scramblase activity. The structure of Xkr8-Basigin provides insights into the molecular mechanisms underlying phospholipid scrambling.
History
DepositionOct 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 2.0Jan 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_imaging / em_software / entity_src_gen / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet_range
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min ..._em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Polymer geometry / Provider: author / Type: Coordinate replacement

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Structure visualization

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Assembly

Deposited unit
B: Isoform 2 of Basigin
X: XK-related protein 8
H: Heavy chain of Fab fragment
L: Light chain of Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4825
Polymers111,7004
Non-polymers7821
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoform 2 of Basigin / 5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / ...5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / Hepatoma-associated antigen / HAb18G / Leukocyte activation antigen M6 / OK blood group antigen / Tumor cell-derived collagenase stimulatory factor / TCSF


Mass: 19592.814 Da / Num. of mol.: 1 / Mutation: N152Q, N186Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BSG, UNQ6505/PRO21383 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35613
#2: Protein XK-related protein 8 / hXkr8


Mass: 45975.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XKR8, XRG8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H6D3
#3: Antibody Heavy chain of Fab fragment


Mass: 22869.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#4: Antibody Light chain of Fab fragment


Mass: 23261.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#5: Chemical ChemComp-DLP / 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DI-LINOLEOYL-3-SN-PHOSPHATIDYLCHOLINE


Mass: 782.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1human XKR8-basigin complex bound to Fab fragmentCOMPLEX#1-#40MULTIPLE SOURCES
2human XKR8-basigin complexCOMPLEX#1-#21RECOMBINANT
3Fab fragmentCOMPLEX#3-#41RECOMBINANT
Molecular weightValue: 0.11 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Oryctolagus cuniculus (rabbit)9986
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Homo sapiens (human)9606
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62124 / Symmetry type: POINT

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