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Title :   HIGH-RESOLUTION STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN CD69

Authors :   P. Kolenko, J. Dohnalek, T. Skalova, J. Hasek, J. Duskova, O. Vanek, K. B

Date :   15 Jun 09 (Deposition) - 15 Dec 09 (Release) - 17 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.37

Chains :   Asym./Biol. Unit : A,B

Keywords :   C-Type Lectin-Like Domain, Disulfide Bond, Glycoprotein, Lectin, Membrane, Phosphoprotein, Signal-Anchor, Transmembrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Kolenko, T. Skalova, O. Vanek, A. Stepankova, J. Duskova, J. Hasek, K. Bezouska, J. Dohnalek
The High-Resolution Structure Of The Extracellular Domain O Human Cd69 Using A Novel Polymer
Acta Crystallogr. , Sect. F V. 65 1258 2009
PubMed-ID: 20054122 | Reference-DOI: 10.1107/S1744309109043152

Molecule 1 - EARLY ACTIVATION ANTIGEN CD69
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSETB
	Expression System Strain	:	BL21-(DE3) RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN, UNP RESIDUES 70-199
	Gene	:	CD69
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	EARLY T-CELL ACTIVATION ANTIGEN P60, GP32/28, LEU-23, MLR-3, EA1, BL-AC/P26, ACTIVATION INDUCER MOLECULE, AIM

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CL	5	Ligand/Ion	CHLORIDE ION
2	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:103 , HOH A:300 , LYS B:103	BINDING SITE FOR RESIDUE CL A 201
2	AC2	SOFTWARE	TRP A:155 , LYS A:159 , PHE A:161 , ASN A:162 , TRP A:164 , HOH A:269	BINDING SITE FOR RESIDUE CL A 202
3	AC3	SOFTWARE	SER A:100 , THR A:101 , HOH A:280 , HOH A:284	BINDING SITE FOR RESIDUE CL A 203
4	AC4	SOFTWARE	TRP B:155 , PHE B:161 , ASN B:162 , TRP B:164 , HOH B:283 , HOH B:316	BINDING SITE FOR RESIDUE CL B 201
5	AC5	SOFTWARE	THR B:101	BINDING SITE FOR RESIDUE CL B 202
6	AC6	SOFTWARE	GLY A:91 , HOH A:213 , HOH A:214 , SER B:86 , TRP B:89	BINDING SITE FOR RESIDUE NA B 203

Asymmetric/Biological Unit

No.	Residues
1	A:85	-	A:96
2	A:113	-	A:194
3	A:173	-	A:186
4	B:85	-	B:96
5	B:113	-	B:194
6	B:173	-	B:186

(no "Cis Peptide Bond" information available for 3HUP)

(no "SAP(SNP)/Variant" information available for 3HUP)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	CD69_HUMAN	92-195	2	A:92-195 B:92-195

Asymmetric/Biological Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000228434	1	ENSE00000821823	chr12:9913497-9913353	145	CD69_HUMAN	1-22	22	0	-	-
1.2	ENST00000228434	2	ENSE00000718673	chr12:9909015-9908893	123	CD69_HUMAN	22-63	42	0	-	-
1.3a	ENST00000228434	3a	ENSE00000718665	chr12:9907857-9907658	200	CD69_HUMAN	63-129	67	2	A:79-129 B:82-129	51 48
1.4	ENST00000228434	4	ENSE00000718659	chr12:9907286-9907183	104	CD69_HUMAN	130-164	35	2	A:130-164 B:130-164	35 35
1.5	ENST00000228434	5	ENSE00000821822	chr12:9906185-9905082	1104	CD69_HUMAN	164-199	36	2	A:164-199 B:164-199	36 36

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
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Chain A from PDB  Type:PROTEIN  Length:121
 aligned with CD69_HUMAN | Q07108 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:121
                                    88        98       108       118       128       138       148       158       168       178       188       198 
           CD69_HUMAN    79 DSHVSSCSEDWVGYQRKCYFISTVKRSWTSAQNACSEHGATLAVIDSEKDMNFLKRYAGREEHWVGLKKEPGHPWKWSNGKEFNNWFNVTGSDKCVFLKNTEVSSMECEKNLYWICNKPYK 199
               SCOP domains d3hupa_ A: automated matches                                                                                              SCOP domains
               CATH domains 3hupA00 A:79-199 Mannose-Binding Protein A, subunit A                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhh...eeeeeee.....eee.................eeeee..eeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------C_TYPE_LECTIN_2  PDB: A:92-195 UniProt: 92-195                                                          ---- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:79-129 UniProt: 63-129           Exon 1.4  PDB: A:130-164           ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.5  PDB: A:164-199             Transcript 1 (2)
                 3hup A  79 DSHVSSCSEDWVGYQRKCYFISTVKRSWTSAQNACSEHGATLAVIDSEKDMNFLKRYAGREEHWVGLKKEPGHPWKWSNGKEFNNWFNVTGSDKCVFLKNTEVSSMECEKNLYWICNKPYK 199
                                    88        98       108       118       128       138       148       158       168       178       188       198

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with CD69_HUMAN | Q07108 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:118
                                    91       101       111       121       131       141       151       161       171       181       191        
           CD69_HUMAN    82 VSSCSEDWVGYQRKCYFISTVKRSWTSAQNACSEHGATLAVIDSEKDMNFLKRYAGREEHWVGLKKEPGHPWKWSNGKEFNNWFNVTGSDKCVFLKNTEVSSMECEKNLYWICNKPYK 199
               SCOP domains d3hupb_ B: automated matches                                                                                           SCOP domains
               CATH domains 3hupB00 B:82-199 Mannose-Binding Protein A, subunit A                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhh...eeeeee.......ee.................eeeee..eeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------C_TYPE_LECTIN_2  PDB: B:92-195 UniProt: 92-195                                                          ---- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: B:82-129 UniProt: 63-129        Exon 1.4  PDB: B:130-164           ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------Exon 1.5  PDB: B:164-199             Transcript 1 (2)
                 3hup B  82 VSSCSEDWVGYQRKCYFISTVKRSWTSAQNACSEHGATLAVIDSEKDMNFLKRYAGREEHWVGLKKEPGHPWKWSNGKEFNNWFNVTGSDKCVFLKNTEVSSMECEKNLYWICNKPYK 199
                                    91       101       111       121       131       141       151       161       171       181       191

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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

1a	d3hupa_	A:
1b	d3hupb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

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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)

1a	3hupA00	A:79-199
1b	3hupB00	B:82-199

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CD69_HUMAN | Q07108)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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: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).
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
	GO:0035690	cellular response to drug	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	CD69_HUMAN \| Q07108
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	CD69_HUMAN \| Q07108	:	1e87 1e8i 1fm5 3cck

1e87	THE SAME PROTEIN IN A DIFFERENT SPACE GROUP.
1e8i	THE SAME PROTEIN IN A DIFFERENT SPACE GROUP.
1fm5	THE SAME PROTEIN IN A DIFFERENT SPACE GROUP.
3cck	ISOMORPHOUS STRUCTURE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (3, 6)

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Gene Ontology (10, 10)

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