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- PDB-7daa: Crystal structure of basigin complexed with anti-basigin Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7daa
TitleCrystal structure of basigin complexed with anti-basigin Fab fragment
Components
  • Heavy chain of antibody Fab fragment
  • Isoform 2 of Basigin
  • Light chain of antibody Fab fragment
KeywordsCHAPERONE / Basigin / Fab / antibody / complex
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / dendrite self-avoidance / acrosomal membrane / cell-cell adhesion mediator activity / endothelial tube morphogenesis / response to mercury ion / neural retina development / photoreceptor cell maintenance ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / dendrite self-avoidance / acrosomal membrane / cell-cell adhesion mediator activity / endothelial tube morphogenesis / response to mercury ion / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / D-mannose binding / homophilic cell-cell adhesion / odontogenesis of dentin-containing tooth / decidualization / positive regulation of vascular endothelial growth factor production / response to cAMP / photoreceptor outer segment / Integrin cell surface interactions / Degradation of the extracellular matrix / neutrophil chemotaxis / photoreceptor inner segment / embryo implantation / positive regulation of endothelial cell migration / axon guidance / protein localization to plasma membrane / response to peptide hormone / sarcolemma / positive regulation of interleukin-6 production / melanosome / signaling receptor activity / virus receptor activity / angiogenesis / basolateral plasma membrane / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / axon / focal adhesion / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsSakuragi, T. / Kanai, R. / Narita, H. / Onishi, E. / Miyazaki, T. / Baba, T. / Nakagawa, A. / Toyoshima, C. / Nagata, S.
Funding support Japan, 6items
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 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 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Basigin
L: Light chain of antibody Fab fragment
H: Heavy chain of antibody Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,49819
Polymers65,6993
Non-polymers1,79916
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-107 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.345, 247.352, 52.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: Antibody Light chain of antibody Fab fragment


Mass: 23319.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Heavy chain of antibody Fab fragment


Mass: 22786.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cd
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl (pH 8.0) buffer containing 0.1M sodium chloride, 0.1M cadmium chloride hemi(pentahydrate), 33% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.509→123.676 Å / Num. obs: 18245 / % possible obs: 86.3 % / Redundancy: 5.1 % / CC1/2: 0.993 / Net I/σ(I): 7.3
Reflection shellResolution: 2.509→2.706 Å / Num. unique obs: 571 / CC1/2: 0.476

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Processing

Software
NameVersionClassification
PHENIX1.19rc2_4022refinement
autoPROC1.0.5data processing
STARANISO2.3.36data processing
MOLREP11.7.03phasing
Coot0.9model building
XDSJan 31, 2020 BUILT=20200417data processing
pointless1.12.2data reduction
Aimless0.7.4data reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D9Z

7d9z


Resolution: 2.51→123.676 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2833 946 5.19 %
Rwork0.2278 --
obs0.2305 18231 68.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→123.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 16 0 3885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033956
X-RAY DIFFRACTIONf_angle_d0.5655388
X-RAY DIFFRACTIONf_dihedral_angle_d4.667552
X-RAY DIFFRACTIONf_chiral_restr0.043622
X-RAY DIFFRACTIONf_plane_restr0.004681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.640.551390.3435195X-RAY DIFFRACTION5
2.64-2.810.3425820.32761286X-RAY DIFFRACTION36
2.81-3.020.3611320.31262307X-RAY DIFFRACTION65
3.02-3.330.3571530.27872864X-RAY DIFFRACTION80
3.33-3.810.28891860.2383327X-RAY DIFFRACTION93
3.81-4.80.25541750.18573598X-RAY DIFFRACTION98
4.8-123.6760.24242090.2083708X-RAY DIFFRACTION98

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