1A8X - JenaLib

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Theoretical Model (Jmol Viewer)

Title :   HUMAN MAC-1 BETA-PROPELLER, THEORETICAL MODEL

Authors :   C. Oxvig, T. A. Springer

Date :   30 Mar 98 (Deposition) - 17 Jun 98 (Release) - 17 Jun 98 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,_^#
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Integrin, Cell Adhesion Protein, Extracellular (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Oxvig, T. A. Springer
Experimental Support For A Beta-Propeller Domain In Integrin Alpha-Subunits And A Calcium Binding Site On Its Lower Surface.
Proc. Natl. Acad. Sci. Usa V. 95 4870 1998
PubMed: search
(for further references see the PDB file header)

Molecule 1 - INTEGRIN MAC-1
	Cellular Location	:	EXTRACELLULAR
	Chains	:	A
	Fragment	:	PUTATIVE BETA-PROPELLER DOMAIN OF ALPHA SUBUNIT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS


Theoretical Model	:

( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

Theoretical Model (1, 3)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION

(no "Site" information available for 1A8X)

Theoretical Model

No.	Residues
1	A:50	-	A:57
2	A:89	-	A:107
3	A:478	-	A:489

Theoretical Model

No.	Residues
1	Ser A:82	-	Pro A:83
2	Gly A:574	-	Gln A:575

Theoretical Model (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_043870	R	77	H	ITAM_HUMAN	Polymorphism	1143679	A	R	61	H
2	UniProt	VAR_043871	M	441	T	ITAM_HUMAN	Polymorphism	11861251	A	M	425	T

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

Theoretical Model (1, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FG_GAP	PS51470	FG-GAP repeat profile.	ITAM_HUMAN	18-75 76-135 339-390 443-503 391-442 506-564 569-629	7	A:2-59 A:60-119 A:330-374 A:427-487 A:375-426 A:490-548 A:553-600

Theoretical Model (12, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000287497	1	ENSE00001716458	chr16:31271288-31271413	126	ITAM_HUMAN	1-10	10	0	-	-
1.2	ENST00000287497	2	ENSE00001304825	chr16:31273013-31273118	106	ITAM_HUMAN	10-45	36	1	A:1-29	29
1.3	ENST00000287497	3	ENSE00001802514	chr16:31276716-31276819	104	ITAM_HUMAN	45-80	36	1	A:29-64	36
1.4	ENST00000287497	4	ENSE00001675692	chr16:31277132-31277202	71	ITAM_HUMAN	80-103	24	1	A:64-87	24
1.5	ENST00000287497	5	ENSE00001028855	chr16:31277351-31277468	118	ITAM_HUMAN	104-143	40	1	A:88-127	40
1.6	ENST00000287497	6	ENSE00001028857	chr16:31282275-31282405	131	ITAM_HUMAN	143-186	44	1	A:127-130	4
1.7	ENST00000287497	7	ENSE00001191919	chr16:31283168-31283313	146	ITAM_HUMAN	187-235	49	0	-	-
1.8	ENST00000287497	8	ENSE00001028975	chr16:31284686-31284839	154	ITAM_HUMAN	235-286	52	0	-	-
1.9	ENST00000287497	9	ENSE00001028959	chr16:31286870-31287020	151	ITAM_HUMAN	287-337	51	0	-	-
1.10	ENST00000287497	10	ENSE00001028953	chr16:31287992-31288065	74	ITAM_HUMAN	337-361	25	1	A:330-345	16
1.11	ENST00000287497	11	ENSE00001028971	chr16:31288241-31288370	130	ITAM_HUMAN	362-405	44	1	A:346-389	44
1.12	ENST00000287497	12	ENSE00001191904	chr16:31289288-31289430	143	ITAM_HUMAN	405-452	48	1	A:389-436	48
1.13	ENST00000287497	13	ENSE00001691688	chr16:31308835-31308975	141	ITAM_HUMAN	453-499	47	1	A:437-483	47
1.14	ENST00000287497	14	ENSE00001709132	chr16:31309066-31309275	210	ITAM_HUMAN	500-569	70	1	A:484-553	70
1.15	ENST00000287497	15	ENSE00001028860	chr16:31332562-31332692	131	ITAM_HUMAN	570-613	44	1	A:554-597	44
1.16	ENST00000287497	16	ENSE00001191889	chr16:31332785-31332948	164	ITAM_HUMAN	613-668	56	1	A:597-600	4
1.17	ENST00000287497	17	ENSE00001191883	chr16:31335720-31335874	155	ITAM_HUMAN	668-719	52	0	-	-
1.18	ENST00000287497	18	ENSE00001028868	chr16:31335972-31336103	132	ITAM_HUMAN	720-763	44	0	-	-
1.19	ENST00000287497	19	ENSE00001028854	chr16:31336279-31336352	74	ITAM_HUMAN	764-788	25	0	-	-
1.20	ENST00000287497	20	ENSE00001028859	chr16:31336584-31336725	142	ITAM_HUMAN	788-835	48	0	-	-
1.21	ENST00000287497	21	ENSE00001028853	chr16:31336821-31336943	123	ITAM_HUMAN	836-876	41	0	-	-
1.22	ENST00000287497	22	ENSE00001242102	chr16:31338177-31338256	80	ITAM_HUMAN	877-903	27	0	-	-
1.23	ENST00000287497	23	ENSE00001191849	chr16:31339468-31339551	84	ITAM_HUMAN	903-931	29	0	-	-
1.24	ENST00000287497	24	ENSE00001242085	chr16:31340549-31340624	76	ITAM_HUMAN	931-956	26	0	-	-
1.25	ENST00000287497	25	ENSE00001242076	chr16:31341119-31341226	108	ITAM_HUMAN	957-992	36	0	-	-
1.26	ENST00000287497	26	ENSE00001191843	chr16:31341402-31341485	84	ITAM_HUMAN	993-1020	28	0	-	-
1.27	ENST00000287497	27	ENSE00001191837	chr16:31341629-31341742	114	ITAM_HUMAN	1021-1058	38	0	-	-
1.28	ENST00000287497	28	ENSE00001191835	chr16:31341825-31341926	102	ITAM_HUMAN	1059-1092	34	0	-	-
1.29	ENST00000287497	29	ENSE00001191829	chr16:31342486-31342596	111	ITAM_HUMAN	1093-1129	37	0	-	-
1.30	ENST00000287497	30	ENSE00001330465	chr16:31342957-31344213	1257	ITAM_HUMAN	1130-1152	23	0	-	-

Theoretical Model

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:401
 aligned with ITAM_HUMAN | P11215 from UniProtKB/Swiss-Prot  Length:1152

    Alignment length:600
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616
           ITAM_HUMAN    17 FNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAPQEIVAANQRGSLYQCDYSTGSCEPIRLQVPVEAVNMSLGLSLAATTSPPQLLACGPTVHQTCSENTYVKGLCFLFGSNLRQQPQKFPEALRGCPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFAIEGTQTGSSSSFEHEMSQEGFSAAITSNGPLLSTVGSYDWAGGVFLYTSKEKSTFINMTRVDSDMNDAYLGYAAAIILRNRVQSLVLGAPRYQHIGLVAMFRQNTGMWESNANVKGTQIGAYFGASLCSVDVDSNGSTDLVLIGAPHYYEQTRGGQVSVCPLPRGRARWQCDAVLYGEQGQPWGRFGAALTVLGDVNGDKLTDVAIGAPGEEDNRGAVYLFHGTSGSGISPSHSQRIAGSKLSPRLQYFGQSLSGGQDLTMDGLVDLTVGAQGHVLLLRSQP 616
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee.........ee.....eeeee.............eeeeehhh.eeeee.................eeee...eeee...................eeeehhhh.eeee..........-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------...........eee....eeee.........eeeeee....eeeeeee..............eee........eeee.........eeee........eeeee......eee..eeee...........eeeeeeee.......eeeeee........eeeeeee..............ee.........eeeeee.........eeeeeee........eeeeeee..............eee...........eeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------H---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -FG_GAP  PDB: A:2-59 UniProt: 18-75                        FG_GAP  PDB: A:60-119 UniProt: 76-135                       -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FG_GAP  PDB: A:330-374 UniProt: 339-390             FG_GAP  PDB: A:375-426 UniProt: 391-442             FG_GAP  PDB: A:427-487 UniProt: 443-503                      --FG_GAP  PDB: A:490-548 UniProt: 506-564                    ----FG_GAP  PDB: A:553-600 UniProt: 569-629          PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:1-29        ----------------------------------Exon 1.4  PDB: A:64-87  Exon 1.5  PDB: A:88-127 UniProt: 104-143-------------------------------------------Exon 1.7  PDB: - UniProt: 187-235                -----------------------------------------------------------------------------------------------------Exon 1.10  PDB: A:330-345Exon 1.11  PDB: A:346-389 UniProt: 362-405  -----------------------------------------------Exon 1.13  PDB: A:437-483 UniProt: 453-499     Exon 1.14  PDB: A:484-553 UniProt: 500-569                            Exon 1.15  PDB: A:554-597 UniProt: 570-613  --- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.3  PDB: A:29-64              --------------------------------------------------------------Exon 1.6  PDB: A:127-130 UniProt: 143-186   ------------------------------------------------Exon 1.8  PDB: - UniProt: 235-286                   Exon 1.9  PDB: - UniProt: 287-337                  -------------------------------------------------------------------Exon 1.12  PDB: A:389-436 UniProt: 405-452      ----------------------------------------------------------------------------------------------------------------------------------------------------------------1.16 Transcript 1 (2)
                 1a8x A   1 FNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAPQEIVAANQRGSLYQCDYSTGSCEPIRLQVPVEAVNMSLGLSLAATTSPPQLLACGPTVHQTCSENTYVKGLCFLFGSNLRQQPQKFPEALRGCPQ-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FEHEMSQEGFSAAITSNGPLLSTVGSYDWAGGVFLYTSKEKSTFINMTRVDSDMNDAYLGYAAAIILRNRVQSLVLGAPRYQHIGLVAMFRQNTGMWESNANVKGTQIGAYFGASLCSVDVDSNGSTDLVLIGAPHYYEQTRGGQVSVCPLPRGRARWQCDAVLYGEQGQPWGRFGAALTVLGDVNGDKLTDVAIGAPGEEDNRGAVYLFHGTSGSGISPSHSQRIAGSKLSPRLQYFGQSLSGGQDLTMDGLVDLTVGAQGHVLLLRSQP 600
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600
                                                                                                                                                           130                                                                                                                                                                                                     330

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 1A8X)

(no "CATH Domain" information available for 1A8X)

(no "Pfam Domain" information available for 1A8X)

Theoretical Model(hide GO term definitions)

Chain A (ITAM_HUMAN | P11215)

molecular function
	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).
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:0010668	ectodermal cell differentiation	The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an ectodermal cell. Differentiation includes the processes involved in commitment of a cell to a specific fate.
	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: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:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	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: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.

Theoretical Model
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	Sites
(no "Sites" information available for 1a8x)

	Cis Peptide Bonds
		Gly A:574 - Gln A:575	[ RasMol ]
		Ser A:82 - Pro A:83	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1A8X)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (0, 0)

SS Bonds (3, 3)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (1, 7)

Exons (12, 12)

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Gene Ontology (15, 15)

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