7D9Z | pdb_00007d9z

Crystal structure of anti-basigin Fab fragment

PDB DOI: https://doi.org/10.2210/pdb7D9Z/pdb

Classification: IMMUNE SYSTEM
Organism(s): Oryctolagus cuniculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-10-14 Released: 2021-10-20
Deposition Author(s): Sakuragi, T., Kanai, R., Narita, H., Onishi, E., Miyazaki, T., Baba, T., Nakagawa, A., Toyoshima, C., Nagata, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free:
0.150 (Depositor), 0.151 (DCC)
R-Value Work:
0.121 (Depositor), 0.122 (DCC)
R-Value Observed:
0.122 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes.

Sakuragi, T., Kanai, R., Tsutsumi, A., Narita, H., Onishi, E., Nishino, K., Miyazaki, T., Baba, T., Kosako, H., Nakagawa, A., Kikkawa, M., Toyoshima, C., Nagata, S.

(2021) Nat Struct Mol Biol 28: 825-834

PubMed: 34625749 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-021-00665-8
Primary Citation Related Structures:
7D9Z, 7DAA, 7DCE

PubMed 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 3.8 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.

Organizational Affiliation

Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Japan.

Macromolecule Content

Total Structure Weight: 46.67 kDa
Atom Count: 4,153
Modeled Residue Count: 425
Deposited Residue Count: 435
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of antibody Fab fragment	A [auth L]	218	Oryctolagus cuniculus	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of antibody Fab fragment	B [auth H]	217	Oryctolagus cuniculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain I [auth H] MOL2 format, chain I [auth H] mmCIF format, chain I [auth H]	I [auth H]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain I [auth H] Interactions & Density Focus chain I [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H SDF format, chain G [auth H] SDF format, chain F [auth H] SDF format, chain E [auth H] SDF format, chain D [auth H] SDF format, chain C [auth L] MOL2 format, chain H MOL2 format, chain G [auth H] MOL2 format, chain F [auth H] MOL2 format, chain E [auth H] MOL2 format, chain D [auth H] MOL2 format, chain C [auth L] mmCIF format, chain H mmCIF format, chain G [auth H] mmCIF format, chain F [auth H] mmCIF format, chain E [auth H] mmCIF format, chain D [auth H] mmCIF format, chain C [auth L]	C [auth L] D [auth H] E [auth H] F [auth H] G [auth H] C [auth L], D [auth H], E [auth H], F [auth H], G [auth H], H	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Interactions & Density Focus chain C [auth L] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	B [auth H]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free: 0.150 (Depositor), 0.151 (DCC)
R-Value Work: 0.121 (Depositor), 0.122 (DCC)
R-Value Observed: 0.122 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.452	α = 90
b = 53.048	β = 105.047
c = 54.313	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
STARANISO	data processing
MOLREP	phasing
Coot	model building
XDS	data processing
pointless	data reduction
Aimless	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15H05785
Japan Society for the Promotion of Science (JSPS)	Japan	20K15731
Japan Science and Technology	Japan	JPMJCR14M4
Japan Agency for Medical Research and Development (AMED)	Japan	JP17am010172
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101072
Japan Agency for Medical Research and Development (AMED)	Japan	JP19am0101072