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Asym./Biol. Unit (Jmol Viewer)

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Title :   L-SELECTIN LECTIN AND EGF DOMAINS

Authors :   P. Mehta, V. Oganesyan, S. Terzyan, T. Mather, R. P. Mcever

Date :   04 Mar 08 (Deposition) - 18 Mar 08 (Release) - 22 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   L-Selectin, Lectin, Egf, Cell Adhesion, Egf-Like Domain, Glycoprotein, Membrane, Sushi, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Mehta-D'Souza, A. G. Klopocki, V. Oganesyan, S. Terzyan, T. Mather Z. Li, S. R. Panicker, C. Zhu, R. P. Mcever
Glycan Bound To The Selectin Low Affinity State Engages Glu-88 To Stabilize The High Affinity State Under Force.
J. Biol. Chem. V. 292 2510 2017
PubMed-ID: 28011641 | Reference-DOI: 10.1074/JBC.M116.767186

Molecule 1 - L-SELECTIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Cell Line	:	OVARY CELLS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Plasmid	:	PEE14.1
	Expression System Strain	:	LEC 1
	Expression System Taxid	:	10029
	Expression System Vector Type	:	PLASMID
	Fragment	:	EGF DOMAIN (UNP RESIDUES 39-194)
	Gene	:	L-SELECTIN, SELL
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SELECTIN L (LYMPHOCYTE ADHESION MOLECULE 1), ISOFORM CRA_B, SELECTIN L, LYMPHOCYTE ADHESION MOLECULE 1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CA	1	Ligand/Ion	CALCIUM ION
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:46 , ASN A:66	BINDING SITE FOR RESIDUE NAG A 157
2	AC2	SOFTWARE	PHE A:44 , ARG A:46 , TYR A:48	BINDING SITE FOR RESIDUE NAG A 158
3	AC3	SOFTWARE	TYR A:94 , ARG A:97	BINDING SITE FOR RESIDUE MAN A 159
4	AC4	SOFTWARE	ARG A:97	BINDING SITE FOR RESIDUE BMA A 160
5	AC5	SOFTWARE	GLU A:80 , ASN A:82 , LYS A:84 , GLU A:88 , ASN A:105 , ASP A:106 , LYS A:111	BINDING SITE FOR RESIDUE MAN A 161
6	AC6	SOFTWARE	PHE A:18 , ASP A:21 , ASN A:22 , GLY A:79 , ASN A:82	BINDING SITE FOR RESIDUE NAG A 162
7	AC7	SOFTWARE	GLU A:80 , ASN A:82 , GLU A:88 , ASN A:105 , ASP A:106	BINDING SITE FOR RESIDUE CA A 163

Asymmetric/Biological Unit

No.	Residues
1	A:19	-	A:117
2	A:90	-	A:109
3	A:122	-	A:133
4	A:127	-	A:142
5	A:144	-	A:153

Asymmetric/Biological Unit

No.	Residues
1	Glu A:80	-	Pro A:81

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_019134	F	193	L	LYAM1_HUMAN	Polymorphism	1131498	A	F	155	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (4, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	LYAM1_HUMAN	128-155	1	A:90-117
2	EGF_3	PS50026	EGF-like domain profile.	LYAM1_HUMAN	156-192	1	A:118-154
3	EGF_1	PS00022	EGF-like domain signature 1.	LYAM1_HUMAN	180-191	1	A:142-153
4	EGF_2	PS01186	EGF-like domain signature 2.	LYAM1_HUMAN	180-191	1	A:142-153

(no "Exon" information available for 3CFW)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:156
 aligned with LYAM1_HUMAN | P14151 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:156
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      
          LYAM1_HUMAN    39 WTYHYSEKPMNWQRARRFCRDNYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVGTNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKAALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFV 194
               SCOP domains d3cfwa1 A:1-118 automated matches                                                                                     d3cfwa2 A:119-156 automated matches    SCOP domains
               CATH domains 3cfwA01 A:1-119 Mannose-Binding Protein A, subunit A                                                                   3cfwA02 A:120-156 Laminin             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhh.ee....hhhhhhhhhhhh......eee.eeee..eeee....................hhhhh..eeee..........eeee.....eeeeeee...........eeeeee..eeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------L- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------C_TYPE_LECTIN_1             EGF_3  PDB: A:118-154                -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------EGF_1       --- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------EGF_2       --- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cfw A   1 WTYHYSEKPMNWQRARRFCRDNYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVGTNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKAALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFV 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: C-type lectin-like (322)

Superfamily: C-type lectin-like (322)

Family: C-type lectin domain (182)

Protein domain: automated matches (16)

Human (Homo sapiens) [TaxId: 9606] (8)

d3cfwa1

A:1-118

Class: Small proteins (3458)

Fold: Knottins (small inhibitors, toxins, lectins) (761)

Superfamily: EGF/Laminin (347)

Family: automated matches (19)

Protein domain: automated matches (19)

Human (Homo sapiens) [TaxId: 9606] (17)

d3cfwa2

A:119-156

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Mannose-Binding Protein A; Chain A (180)

Homologous Superfamily: Mannose-Binding Protein A, subunit A (180)

Human (Homo sapiens) (80)

3cfwA01

A:1-119

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Laminin (270)

Homologous Superfamily: Laminin (263)

Human (Homo sapiens) (195)

3cfwA02

A:120-156

(no "Pfam Domain" information available for 3CFW)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LYAM1_HUMAN | P14151)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0050839	cell adhesion molecule binding	Interacting selectively and non-covalently with a cell adhesion molecule.
	GO:0043208	glycosphingolipid binding	Interacting selectively and non-covalently with glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0033198	response to ATP	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ATP (adenosine 5'-triphosphate) stimulus.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:80 - Pro A:81	[ RasMol ]

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	3cfw
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UniProtKB/Swiss-Prot
	LYAM1_HUMAN \| P14151	:	1kjb 2lgf 5vc1

1esl	E-SELECTIN LECTIN AND EGF DOMAINS
1g1q	P-SELECTIN LECTIN AND EGF DOMAINS
1g1r	P-SELECTIN LECTIN AND EGF DOMAINS WITH SIALYL LEWIS X
1g1s	P-SELECTIN LECTIN AND EGF DOMAINS WITH N-TERMINAL PEPTIDE OF PSGL-1
1g1t	E-SELECTIN LECTIN AND EGF DOMAINS WITH SIALYL LEWIS X

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (5, 5)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (4, 3)

Exons (0, 0)

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SCOP Domains (2, 2)

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Gene Ontology (16, 16)

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