2P26 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF THE PHE2 AND PHE3 FRAGMENTS OF THE INTEGRIN BETA2 SUBUNIT

Authors :   M. Shi, S. Y. Foo, S. M. Tan, E. P. Mitchell, S. K. A. Law, J. Lescar

Date :   06 Mar 07 (Deposition) - 14 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A

Keywords :   Integrin Beta2 Subunit, Hybrid Domain, Psi Domain, I-Egf Domains, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Shi, S. Y. Foo, S. M. Tan, E. P. Mitchell, S. K. A. Law, J. Lescar
A Structural Hypothesis For The Transition Between Bent And Extended Conformations Of The Leukocyte Beta2 Integrins
J. Biol. Chem. V. 282 30198 2007
PubMed-ID: 17673459 | Reference-DOI: 10.1074/JBC.M701670200

Molecule 1 - INTEGRIN BETA-2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293_GNTI
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PIRES2-EGFP
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	PHE2 AND PHE3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CELL SURFACE ADHESION GLYCOPROTEINS LFA- 1/CR3/P150,95 SUBUNIT BETA, COMPLEMENT RECEPTOR C3 SUBUNIT BETA, CD18 ANTIGEN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:94 , PHE A:363 , GLN A:390 , HOH A:593 , HOH A:695 , HOH A:733	BINDING SITE FOR RESIDUE NAG A 301
2	AC2	SOFTWARE	SER A:435 , HIS A:438 , LYS A:440 , ASN A:479 , HOH A:558 , HOH A:771	BINDING SITE FOR RESIDUE NAG A 302
3	AC3	SOFTWARE	ASN A:28 , ASN A:458 , ASN A:480 , HOH A:693 , HOH A:739	BINDING SITE FOR RESIDUE NAG A 303

Asymmetric/Biological Unit

No.	Residues
1	A:3	-	A:21
2	A:11	-	A:425
3	A:14	-	A:40
4	A:24	-	A:51
5	A:364	-	A:378
6	A:398	-	A:423
7	A:427	-	A:445
8	A:437	-	A:448
9	A:450	-	A:459
10	A:461	-	A:492
11	A:475	-	A:490
12	A:484	-	A:495
13	A:497	-	A:512

Asymmetric/Biological Unit

No.	Residues
1	Gln A:1	-	Glu A:2
2	Gly A:71	-	Gly A:72
3	Ser A:77	-	Pro A:78
4	Leu A:341	-	Ser A:342
5	Asn A:366	-	Gly A:367
6	Pro A:503	-	Gly A:504

(no "SAP(SNP)/Variant" information available for 2P26)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_1	PS00022	EGF-like domain signature 1.	ITB2_HUMAN	470-481 562-573	1	A:448-459 -
2	EGF_2	PS01186	EGF-like domain signature 2.	ITB2_HUMAN	470-483 562-575 601-615	1	A:448-461 - -
3	INTEGRIN_BETA	PS00243	Integrins beta chain cysteine-rich domain signature.	ITB2_HUMAN	506-519 549-564 590-603	1	A:484-497 - -

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000397850	2a	ENSE00002097953	chr21:46348788-46348569	220	ITB2_HUMAN	-	0	0	-	-
1.3b	ENST00000397850	3b	ENSE00001530484	chr21:46340965-46340736	230	ITB2_HUMAN	-	0	0	-	-
1.7b	ENST00000397850	7b	ENSE00002161928	chr21:46330700-46330640	61	ITB2_HUMAN	1-20	20	0	-	-
1.7i	ENST00000397850	7i	ENSE00002166383	chr21:46330287-46330199	89	ITB2_HUMAN	20-49	30	1	A:1-27	27
1.10c	ENST00000397850	10c	ENSE00001050919	chr21:46327010-46326830	181	ITB2_HUMAN	50-110	61	1	A:28-88	61
1.11e	ENST00000397850	11e	ENSE00002202060	chr21:46323450-46323280	171	ITB2_HUMAN	110-167	58	1	A:88-100	13
1.12b	ENST00000397850	12b	ENSE00001050930	chr21:46321648-46321407	242	ITB2_HUMAN	167-247	81	0	-	-
1.13	ENST00000397850	13	ENSE00001314546	chr21:46320390-46320235	156	ITB2_HUMAN	248-299	52	0	-	-
1.14	ENST00000397850	14	ENSE00002181070	chr21:46319077-46318982	96	ITB2_HUMAN	300-331	32	0	-	-
1.15a	ENST00000397850	15a	ENSE00001280312	chr21:46314975-46314886	90	ITB2_HUMAN	332-361	30	0	-	-
1.15d	ENST00000397850	15d	ENSE00001280354	chr21:46313459-46313319	141	ITB2_HUMAN	362-408	47	1	A:340-386	47
1.16	ENST00000397850	16	ENSE00001280307	chr21:46311911-46311724	188	ITB2_HUMAN	409-471	63	1	A:387-449	63
1.17	ENST00000397850	17	ENSE00001280195	chr21:46310137-46309893	245	ITB2_HUMAN	471-553	83	1	A:449-519	71
1.18	ENST00000397850	18	ENSE00001280299	chr21:46309410-46309191	220	ITB2_HUMAN	553-626	74	0	-	-
1.19b	ENST00000397850	19b	ENSE00001050945	chr21:46308810-46308608	203	ITB2_HUMAN	626-694	69	0	-	-
1.20	ENST00000397850	20	ENSE00001280183	chr21:46306817-46306651	167	ITB2_HUMAN	694-749	56	0	-	-
1.21c	ENST00000397850	21c	ENSE00001280374	chr21:46306345-46305868	478	ITB2_HUMAN	750-769	20	0	-	-

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:280
 aligned with ITB2_HUMAN | P05107 from UniProtKB/Swiss-Prot  Length:769

    Alignment length:519
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532         
           ITB2_HUMAN    23 QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDDLRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFATDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAVTSRMVKTYEKLTEIIPKSAVGELSEDSSNVVQLIKNAYNKLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINC 541
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------Integrin_beta-2p26A01 A:10-425                                                                                                                                                                                                                                                                                                                                                                                                  ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh.....eee..........hhhh.eehhhhhhhh..hhh.ee....eeeee.........ee..eeeeee.....eeeeeee...-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.....eeeee......eeeeeeee.....eeeee..eee........eeeeeeeee......eeeeeee......eeeeeee.............hhhhh.eeee..eeee...ee.....ee....hhhhhhhh.......hhhhh.eeee..eeee........eee.....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_2         ----------------------INTEGRIN_BETA ---------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_1       ------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.7i  PDB: A:1-27     Exon 1.10c  PDB: A:28-88 UniProt: 50-110                     --------------------------------------------------------Exon 1.12b  PDB: - UniProt: 167-247                                              Exon 1.13  PDB: - UniProt: 248-299                  Exon 1.14  PDB: -               Exon 1.15a  PDB: -            Exon 1.15d  PDB: A:340-386 UniProt: 362-408    Exon 1.16  PDB: A:387-449 UniProt: 409-471                     ---------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------Exon 1.11e  PDB: A:88-100 UniProt: 110-167 [INCOMPLETE]   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.17  PDB: A:449-519 UniProt: 471-553 [INCOMPLETE]                 Transcript 1 (2)
                 2p26 A   1 QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCEHHHHHH 519
                                    10        20        30        40        50        60        70        80        90       100         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510         
                                                                                                                             100                                                                                                                                                                                                                                             340

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 '\|'

(no "SCOP Domain" information available for 2P26)

(no "CATH Domain" information available for 2P26)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Integrin_beta] (18)

Family: Integrin_beta (18)

Homo sapiens (Human) (18)

Integrin_beta-2p26A01

A:10-425

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ITB2_HUMAN | P05107)

molecular function
	GO:0030369	ICAM-3 receptor activity	Combining with ICAM-3, intercellular adhesion molecule 3, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. ICAM-3, or CD50, are constitutively expressed on monocytes, granulocytes and lymphocytes; on physiological stimulation, they become transiently phosphorylated on serine residues.
	GO:0050839	cell adhesion molecule binding	Interacting selectively and non-covalently with a cell adhesion molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	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:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0007160	cell-matrix adhesion	The binding of a cell to the extracellular matrix via adhesion molecules.
	GO:0045123	cellular extravasation	The migration of a leukocyte from the blood vessels into the surrounding tissue.
	GO:0071404	cellular response to low-density lipoprotein particle stimulus	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 low-density lipoprotein particle stimulus.
	GO:0035987	endodermal cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
	GO:0043542	endothelial cell migration	The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0034113	heterotypic cell-cell adhesion	The attachment of a cell to a cell of a different type via adhesion molecules.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0007229	integrin-mediated signaling pathway	A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0007159	leukocyte cell-cell adhesion	The attachment of a leukocyte to another cell via adhesion molecules.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0002523	leukocyte migration involved in inflammatory response	The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response.
	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:0030593	neutrophil chemotaxis	The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0045429	positive regulation of nitric oxide biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
	GO:0043113	receptor clustering	The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
	GO:0031623	receptor internalization	A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	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:0050730	regulation of peptidyl-tyrosine phosphorylation	Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	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.
	GO:0034142	toll-like receptor 4 signaling pathway	Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.
cellular component
	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:1903561	extracellular vesicle	Any vesicle that is part of the extracellular region.
	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:0034687	integrin alphaL-beta2 complex	An integrin complex that comprises one alphaL subunit and one beta2 subunit.
	GO:0008305	integrin complex	A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands.
	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.
	GO:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0030141	secretory granule	A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asn A:366 - Gly A:367	[ RasMol ]
		Gln A:1 - Glu A:2	[ RasMol ]
		Gly A:71 - Gly A:72	[ RasMol ]
		Leu A:341 - Ser A:342	[ RasMol ]
		Pro A:503 - Gly A:504	[ RasMol ]
		Ser A:77 - Pro A:78	[ RasMol ]

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	2p26
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Description

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Ligands, Modified Residues, Ions (1, 3)

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SS Bonds (13, 13)

Cis Peptide Bonds (6, 6)

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