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- PDB-7d9z: Crystal structure of anti-basigin Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7d9z
TitleCrystal structure of anti-basigin Fab fragment
Components
  • Heavy chain of antibody Fab fragment
  • Light chain of antibody Fab fragment
KeywordsIMMUNE SYSTEM / Fab / antibody / basigin
Function / homologyCITRATE ANION
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.123 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 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Light chain of antibody Fab fragment
H: Heavy chain of antibody Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6689
Polymers46,1062
Non-polymers5627
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-11 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.452, 53.048, 54.313
Angle α, β, γ (deg.)90.000, 105.047, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: 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.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: 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.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 698 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1% n-Octyl-beta-D-glucoside, 0.1M sodium citrate tribasic dihydrate, 22% PEG 3350

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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: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.123→78.924 Å / Num. obs: 139276 / % possible obs: 81.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.35 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 1.123→1.194 Å / Num. unique obs: 6905 / CC1/2: 0.575

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Processing

Software
NameVersionClassification
PHENIX1.19rc1_4016refinement
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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ma3

4ma3


Resolution: 1.123→36.4 Å / SU ML: 0.0836 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.0715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1503 6810 4.89 %
Rwork0.1209 132456 -
obs0.1223 139266 81.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.68 Å2
Refinement stepCycle: LAST / Resolution: 1.123→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 37 698 3906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00993556
X-RAY DIFFRACTIONf_angle_d1.17774895
X-RAY DIFFRACTIONf_chiral_restr0.0904562
X-RAY DIFFRACTIONf_plane_restr0.0087636
X-RAY DIFFRACTIONf_dihedral_angle_d13.08711269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.140.3332250.2559526X-RAY DIFFRACTION9.64
1.14-1.150.3109330.2418894X-RAY DIFFRACTION16.53
1.15-1.160.2462670.2271271X-RAY DIFFRACTION23.82
1.16-1.180.2433960.21361700X-RAY DIFFRACTION31.38
1.18-1.190.22541120.21422104X-RAY DIFFRACTION39.51
1.19-1.210.23111410.18522630X-RAY DIFFRACTION48.46
1.21-1.230.23861670.1753192X-RAY DIFFRACTION59.25
1.23-1.250.21592230.173783X-RAY DIFFRACTION70.68
1.25-1.270.21812170.16164286X-RAY DIFFRACTION79.42
1.27-1.290.18922430.15214746X-RAY DIFFRACTION88.54
1.29-1.310.17362620.13765131X-RAY DIFFRACTION95.6
1.31-1.330.17952190.13655419X-RAY DIFFRACTION99.33
1.33-1.360.17812940.13035437X-RAY DIFFRACTION99.91
1.36-1.390.15942820.12325331X-RAY DIFFRACTION99.89
1.39-1.420.15432880.11435312X-RAY DIFFRACTION99.73
1.42-1.450.14252970.10695377X-RAY DIFFRACTION99.65
1.45-1.480.15962880.10325366X-RAY DIFFRACTION99.42
1.48-1.520.13872910.09585342X-RAY DIFFRACTION99.35
1.52-1.570.13892840.09375370X-RAY DIFFRACTION99.21
1.57-1.620.13022830.09735338X-RAY DIFFRACTION98.96
1.62-1.680.1332970.10055348X-RAY DIFFRACTION99.14
1.68-1.750.14092360.10225364X-RAY DIFFRACTION99.04
1.75-1.820.13043050.09835422X-RAY DIFFRACTION99.77
1.82-1.920.12493080.10035356X-RAY DIFFRACTION99.68
1.92-2.040.12952700.10175424X-RAY DIFFRACTION99.53
2.04-2.20.14352650.10625393X-RAY DIFFRACTION99.19
2.2-2.420.17012510.11635406X-RAY DIFFRACTION98.83
2.42-2.770.15442450.12955395X-RAY DIFFRACTION98.34
2.77-3.490.15172580.13215382X-RAY DIFFRACTION98.04
3.49-36.40.14492630.1355411X-RAY DIFFRACTION96.46

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