1QA9 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF A HETEROPHILIC ADHESION COMPLEX BETWEEN THE HUMAN CD2 AND CD58(LFA-3) COUNTER-RECEPTORS

Authors :   J. -H. Wang, A. Smolyar, K. Tan, J. -H. Liu, M. Kim, Z. J. Sun, G. Wagner, E. L. Reinherz

Date :   13 Apr 99 (Deposition) - 29 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Cell Adhesion, Ig-Like Domain, Cd2, Cd58, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. H. Wang, A. Smolyar, K. Tan, J. H. Liu, M. Kim, Z. Y. Sun, G. Wagner, E. L. Reinherz
Structure Of A Heterophilic Adhesion Complex Between The Human Cd2 And Cd58 (Lfa-3) Counterreceptors.
Cell(Cambridge, Mass. ) V. 97 791 1999
PubMed-ID: 10380930 | Reference-DOI: 10.1016/S0092-8674(00)80790-4
(for further references see the PDB file header)

Molecule 1 - HUMAN CD2 PROTEIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL ADHESION DOMAIN OF CD2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - HUMAN CD58 PROTEIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL ADHESION DOMAIN OF CD58
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1QA9)

(no "Site" information available for 1QA9)

(no "SS Bond" information available for 1QA9)

(no "Cis Peptide Bond" information available for 1QA9)

(no "SAP(SNP)/Variant" information available for 1QA9)

(no "PROSITE Motif" information available for 1QA9)

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000369478	1a	ENSE00001450130	chr1:117297007-117297175	169	CD2_HUMAN	1-21	21	0	-	-
1.2a	ENST00000369478	2a	ENSE00000785006	chr1:117297253-117297573	321	CD2_HUMAN	21-128	108	2	A:4-104 C:4-104	101 101
1.3	ENST00000369478	3	ENSE00000785007	chr1:117303024-117303254	231	CD2_HUMAN	128-205	78	2	A:104-105 C:104-105	2 2
1.4	ENST00000369478	4	ENSE00000785008	chr1:117307106-117307228	123	CD2_HUMAN	205-246	42	0	-	-
1.5	ENST00000369478	5	ENSE00001141790	chr1:117311086-117311850	765	CD2_HUMAN	246-351	106	0	-	-

2.1a	ENST00000369489	1a	ENSE00000957936	chr1:117113661-117113525	137	LFA3_HUMAN	1-24	24	0	-	-
2.2a	ENST00000369489	2a	ENSE00001158370	chr1:117087226-117086933	294	LFA3_HUMAN	24-122	99	2	B:1-94 D:1-94	94 94
2.3	ENST00000369489	3	ENSE00000957938	chr1:117078850-117078587	264	LFA3_HUMAN	122-210	89	2	B:94-95 D:94-95	2 2
2.4a	ENST00000369489	4a	ENSE00000913430	chr1:117064605-117064528	78	LFA3_HUMAN	210-236	27	0	-	-
2.5b	ENST00000369489	5b	ENSE00002192029	chr1:117061889-117061853	37	LFA3_HUMAN	236-248	13	0	-	-
2.6b	ENST00000369489	6b	ENSE00001728169	chr1:117057444-117057157	288	LFA3_HUMAN	248-250	3	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:102
 aligned with CD2_HUMAN | P06729 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:102
                                    37        47        57        67        77        87        97       107       117       127  
            CD2_HUMAN    28 TNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTYKLFKNGTLKIKHLKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQER 129
               SCOP domains d1qa9a_ A: CD2, first domain                                                                           SCOP domains
               CATH domains 1qa9A00 A:4-105 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee....eee..........eeeeeeee.......eeee.....ee....eeee...eeee.........eeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:4-104 UniProt: 21-128 [INCOMPLETE]                                                 - Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 1qa9 A   4 TNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTYELLKNGALKIKHLKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQER 105
                                    13        23        33        43        53        63        73        83        93       103

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with LFA3_HUMAN | P19256 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:95
                                    38        48        58        68        78        88        98       108       118     
           LFA3_HUMAN    29 FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTIYNLTSSDEDEYEMESPNITDTMKFFLYVLES 123
               SCOP domains d1qa9b_ B: CD2-binding domain of CD58, N-terminal domain                                        SCOP domains
               CATH domains 1qa9B00 B:1-95 Immunoglobulins                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eee..........eeeee..eeeeee....eee.hhhh..eee......eee.........eeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.2a  PDB: B:1-94 UniProt: 24-122 [INCOMPLETE]                                           - Transcript 2 (1)
           Transcript 2 (2) ---------------------------------------------------------------------------------------------2. Transcript 2 (2)
                 1qa9 B   1 SSQQIYGVKYGNVTFHVPSNQPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTKSGSLTIYNLTSSDEDEYEMESPNITDSMKFFLYVGES  95
                                    10        20        30        40        50        60        70        80        90

Chain C from PDB  Type:PROTEIN  Length:102
 aligned with CD2_HUMAN | P06729 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:102
                                    37        47        57        67        77        87        97       107       117       127  
            CD2_HUMAN    28 TNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTYKLFKNGTLKIKHLKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQER 129
               SCOP domains d1qa9c_ C: CD2, first domain                                                                           SCOP domains
               CATH domains 1qa9C00 C:4-105 Immunoglobulins                                                                        CATH domains
           Pfam domains (1) V-set-1qa9C01 C:4-105                                                                                  Pfam domains (1)
           Pfam domains (2) V-set-1qa9C02 C:4-105                                                                                  Pfam domains (2)
         Sec.struct. author ....eeeee....eee..........eeeeeeee.....eeeeee....eee....eeee...eeee.........eeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: C:4-104 UniProt: 21-128 [INCOMPLETE]                                                 - Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 1qa9 C   4 TNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTYELLKNGALKIKHLKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQER 105
                                    13        23        33        43        53        63        73        83        93       103

Chain D from PDB  Type:PROTEIN  Length:95
 aligned with LFA3_HUMAN | P19256 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:95
                                    38        48        58        68        78        88        98       108       118     
           LFA3_HUMAN    29 FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTIYNLTSSDEDEYEMESPNITDTMKFFLYVLES 123
               SCOP domains d1qa9d_ D: CD2-binding domain of CD58, N-terminal domain                                        SCOP domains
               CATH domains 1qa9D00 D:1-95 Immunoglobulins                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeee...........eee....eee.........hhhhh..eee......eeee........eeeee........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.2a  PDB: D:1-94 UniProt: 24-122 [INCOMPLETE]                                           - Transcript 2 (1)
           Transcript 2 (2) ---------------------------------------------------------------------------------------------2. Transcript 2 (2)
                 1qa9 D   1 SSQQIYGVKYGNVTFHVPSNQPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTKSGSLTIYNLTSSDEDEYEMESPNITDSMKFFLYVGES  95
                                    10        20        30        40        50        60        70        80        90

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: V set domains (antibody variable domain-like) (1919)

Protein domain: CD2, first domain (9)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d1qa9a_	A:
1b	d1qa9c_	C:

Protein domain: CD2-binding domain of CD58, N-terminal domain (3)

Human (Homo sapiens) [TaxId: 9606] (3)

2a	d1qa9b_	B:
2b	d1qa9d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	1qa9B00	B:1-95
1b	1qa9D00	D:1-95
1c	1qa9A00	A:4-105
1d	1qa9C00	C:4-105

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: V-set (144)

Homo sapiens (Human) (61)

1a	V-set-1qa9C01	C:4-105
1b	V-set-1qa9C02	C:4-105

Asymmetric Unit(hide GO term definitions)

Chain A,C (CD2_HUMAN | P06729)

molecular function
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0042110	T cell activation	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	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:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0034113	heterotypic cell-cell adhesion	The attachment of a cell to a cell of a different type via adhesion molecules.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0001766	membrane raft polarization	The clustering and aggregation of membrane rafts at a single cellular pole during activation of particular cell types, such as lymphocytes.
	GO:0030101	natural killer cell activation	The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor.
	GO:1902715	positive regulation of interferon-gamma secretion	Any process that activates or increases the frequency, rate or extent of interferon-gamma secretion.
	GO:2000484	positive regulation of interleukin-8 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-8 secretion.
	GO:0030887	positive regulation of myeloid dendritic cell activation	Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation.
	GO:0032760	positive regulation of tumor necrosis factor production	Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
	GO:0045580	regulation of T cell differentiation	Any process that modulates the frequency, rate or extent of T cell differentiation.
	GO:0016337	single organismal cell-cell adhesion	The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
cellular component
	GO:0046658	anchored component of plasma membrane	The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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.

Chain B,D (LFA3_HUMAN | P19256)

molecular function
	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:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
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:0071346	cellular response to interferon-gamma	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 an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far.
	GO:0071356	cellular response to tumor necrosis factor	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 tumor necrosis factor stimulus.
	GO:0034113	heterotypic cell-cell adhesion	The attachment of a cell to a cell of a different type via adhesion molecules.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:2000484	positive regulation of interleukin-8 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-8 secretion.
	GO:0016337	single organismal cell-cell adhesion	The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
cellular component
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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 Unit
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	1qa9
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	LFA3_HUMAN \| P19256
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UniProtKB/Swiss-Prot
	CD2_HUMAN \| P06729	:	1cdb 1gya 1hnf 1l2z 2j6o 2j7i
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(no "Related Entries Specified in the PDB File" available for 1QA9)

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Exons (4, 8)

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SCOP Domains (2, 4)

CATH Domains (1, 4)

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