7DCE | pdb_00007dce

Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054855	3000071	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	I-set_7	e7dceB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_7	ECOD (1.6)
C [auth H]	V-set_8	e7dceH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	C1-set_1	e7dceH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D [auth L]	C1-set_4	e7dceL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth L]	V-set	e7dceL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H]	Heavy Chain	IGHV1	-	isoform 2 of basigin \| xk-related protein 8	SAbDab (2025-04-11)
D [auth L]	Light Chain	IGKV1	Kappa	isoform 2 of basigin \| xk-related protein 8	SAbDab (2025-04-11)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain
B [auth X]	PF09815	XK-related protein (XK-related)	XK-related protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Isoform 2 of Basigin	protein binding binding virus receptor activity exogenous protein binding molecular transducer activity signaling receptor activity D-mannose binding monosaccharide binding carbohydrate binding small molecule binding cell adhesion molecule binding cadherin binding	response to mercury ion response to stimulus response to metal ion response to chemical response to hormone response to endogenous stimulus response to peptide hormone response to oxygen-containing compound response to nitrogen compound positive regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process endothelial cell migration response to mercury ion response to stimulus response to metal ion response to chemical response to hormone response to endogenous stimulus response to peptide hormone response to oxygen-containing compound response to nitrogen compound positive regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process endothelial cell migration biological regulation positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration cellular process cell motility locomotion positive regulation of cellular process multicellular organismal process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression vascular endothelial growth factor production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process developmental process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development odontogenesis of dentin-containing tooth odontogenesis animal organ development animal organ morphogenesis interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization transport matrix metallopeptidase secretion positive regulation of matrix metallopeptidase secretion positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport localization secretion by cell regulation of secretion by cell positive regulation of secretion cellular macromolecule localization regulation of matrix metallopeptidase secretion secretion regulation of transport establishment of protein localization to extracellular region regulation of establishment of protein localization export from cell regulation of protein transport protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization cell chemotaxis cellular response to stimulus chemotaxis neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis myeloid leukocyte migration leukocyte chemotaxis protein localization to cell periphery protein localization to plasma membrane localization within membrane protein localization to membrane epithelium development endothelium development morphogenesis of an endothelium endothelial tube morphogenesis morphogenesis of an epithelium tissue development tissue morphogenesis epithelial tube morphogenesis multi-multicellular organism process reproductive process female pregnancy embryo implantation multi-organism reproductive process cell surface receptor signaling pathway signaling signal transduction cell communication multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis retina homeostasis photoreceptor cell maintenance placenta development maternal process involved in female pregnancy multicellular organismal reproductive process developmental process involved in reproduction maternal placenta development decidualization biological process involved in interspecies interaction between organisms positive regulation of viral life cycle positive regulation of viral process viral life cycle modulation by symbiont of entry into host biological process involved in interaction with host biological process involved in symbiotic interaction regulation of viral entry into host cell regulation of viral life cycle regulation of viral process symbiont entry into host cell viral process symbiont entry into host positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction response to organophosphorus response to purine-containing compound response to cAMP sensory organ development eye development retina development in camera-type eye visual system development neural retina development camera-type eye development sensory system development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle anchoring junction cell junction focal adhesion cell-substrate junction membrane pigment granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle anchoring junction cell junction focal adhesion cell-substrate junction membrane pigment granule intracellular vesicle melanosome cytoplasmic vesicle vesicle photoreceptor inner segment extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell periphery sarcolemma plasma membrane basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane non-motile cilium 9+0 non-motile cilium cilium neuron projection photoreceptor outer segment plasma membrane bounded cell projection cell projection photoreceptor cell cilium organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane endosome Golgi membrane Golgi apparatus bounding membrane of organelle acrosomal vesicle acrosomal membrane cytoplasmic vesicle membrane vesicle membrane secretory granule secretory vesicle secretory granule membrane
B [auth X]	XK-related protein 8	lipid transporter activity intramembrane lipid transporter activity transporter activity phospholipid scramblase activity phospholipid transporter activity	phospholipid translocation transport phospholipid transport plasma membrane phospholipid scrambling cellular component organization localization execution phase of apoptosis phosphatidylserine exposure on apoptotic cell surface plasma membrane organization cellular component organization or biogenesis regulation of biological quality endomembrane system organization membrane organization biological regulation phospholipid translocation transport phospholipid transport plasma membrane phospholipid scrambling cellular component organization localization execution phase of apoptosis phosphatidylserine exposure on apoptotic cell surface plasma membrane organization cellular component organization or biogenesis regulation of biological quality endomembrane system organization membrane organization biological regulation lipid localization lipid transport cell death lipid translocation establishment of localization regulation of membrane lipid distribution macromolecule localization cellular process apoptotic process programmed cell death organophosphate ester transport developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development regulation of myoblast differentiation myoblast differentiation positive regulation of cellular process apoptotic process involved in development import into cell vesicle-mediated transport engulfment of apoptotic cell phagocytosis, engulfment membrane invagination phagocytosis apoptotic cell clearance endocytosis plasma membrane invagination immune system development multicellular organism development multicellular organismal process tolerance induction to self antigen immune system process tolerance induction system development homeostatic process neutrophil clearance neutrophil homeostasis multicellular organismal-level homeostasis leukocyte homeostasis homeostasis of number of cells myeloid cell homeostasis cellular localization establishment of localization in cell	cellular anatomical structure intracellular anatomical structure perinuclear region of cytoplasm cytoplasm cell periphery plasma membrane membrane
C [auth H]	Heavy chain of Fab fragment	-	-	-
D [auth L]	Light chain of Fab fragment	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth B]	IPR003598	Immunoglobulin subtype 2	Domain
A [auth B]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth B]	IPR007110	Immunoglobulin-like domain	Domain
B [auth X]	IPR018629	XK-related protein	Family
B [auth X]	IPR050895	XK-related phospholipid scramblase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	Pharos: P35613	Neoplasm Metastasis amyotrophic lateral sclerosis type 1 rheumatoid arthritis COVID-19 Down syndrome large cell medulloblastoma schizophrenia Crohn disease malignant ependymoma plasma cell myeloma ulcerative colitis atypical teratoid rhabdoid tumor dermatomyositis glioblastoma ovarian cancer

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth B], B [auth X]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth B], B [auth X]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B], B [auth X]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	XKR Family of Proteins	Xkr8 scramblase in complex with basigin

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.