2W94 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   NATIVE STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM AT 1.8 ANGSTROM RESOLUTION

Authors :   K. Saboia Aragao, A. Imberty, A. Varrot

Date :   21 Jan 09 (Deposition) - 31 Mar 10 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Cell Adhesion, H Type Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Mathieu, K. Saboia Aragao, A. Imberty, A. Varrot
Discoidin I From Dictyostelium Discoideum And Interactions With Oligosaccharides: Specificity, Affinity, Crystal Structures And Comparison With Discoidin Ii.
J. Mol. Biol. V. 400 540 2010
PubMed-ID: 20580724 | Reference-DOI: 10.1016/J.JMB.2010.05.042

Molecule 1 - DISCOIDIN-1 SUBUNIT A
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEXHTB
	Expression System Strain	:	ROSETTA2(DE3)PLYSS
	Expression System Taxid	:	562
	Organism Common	:	SLIME MOLD
	Organism Scientific	:	DICTYOSTELIUM DISCOIDEUM
	Organism Taxid	:	366501
	Strain	:	AX2
	Synonym	:	DISCOIDIN I, DISCOIDIN-1 SUBUNIT ALPHA, DISCOIDIN I CHAIN A

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 13)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
4	NI	1	Ligand/Ion	NICKEL (II) ION
5	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:62 , ARG A:92 , TRP A:100 , HOH A:2345 , HOH A:2346 , ASN C:12	BINDING SITE FOR RESIDUE MPD A1254
02	AC2	SOFTWARE	ARG A:79 , GLN A:84 , HIS A:142 , HOH A:2047 , THR B:41 , HOH B:2075	BINDING SITE FOR RESIDUE MPD A1255
03	AC3	SOFTWARE	ARG A:104 , VAL A:109 , THR A:110 , HIS A:121 , HOH A:2347	BINDING SITE FOR RESIDUE SO4 A1256
04	AC4	SOFTWARE	ASP A:164 , ASP A:203 , ASP A:246 , GLN B:219 , HOH B:2281 , HOH B:2282	BINDING SITE FOR RESIDUE CA A1257
05	AC5	SOFTWARE	HIS A:16 , HIS B:16 , HIS C:16 , HOH C:2035	BINDING SITE FOR RESIDUE NI A1258
06	AC6	SOFTWARE	SER A:157 , VAL A:158 , THR A:159 , SER B:157 , THR B:159 , SER C:157 , THR C:159	BINDING SITE FOR RESIDUE SO4 A1259
07	AC7	SOFTWARE	THR A:41 , TYR B:23 , ARG B:79 , GLN B:84 , HIS B:142 , HOH B:2042	BINDING SITE FOR RESIDUE MPD B1254
08	AC8	SOFTWARE	ARG B:104 , VAL B:109 , THR B:110 , HIS B:121	BINDING SITE FOR RESIDUE SO4 B1255
09	AC9	SOFTWARE	ASP B:164 , ASP B:203 , ASP B:246 , GLN C:219 , HOH C:2263 , HOH C:2264	BINDING SITE FOR RESIDUE CA B1256
10	BC1	SOFTWARE	ARG C:18 , VAL C:62 , ARG C:92 , TRP C:100 , HIS C:135 , HOH C:2305	BINDING SITE FOR RESIDUE MRD C1254
11	BC2	SOFTWARE	THR C:41 , ASN C:42 , ARG C:79 , GLN C:84 , HIS C:142 , HOH C:2075	BINDING SITE FOR RESIDUE MRD C1255
12	BC3	SOFTWARE	ARG C:104 , VAL C:109 , THR C:110 , HIS C:121 , HOH C:2165 , HOH C:2306	BINDING SITE FOR RESIDUE SO4 C1256
13	BC4	SOFTWARE	GLN A:219 , HOH A:2288 , HOH A:2289 , ASP C:164 , ASP C:203 , ASP C:246	BINDING SITE FOR RESIDUE CA C1257

(no "SS Bond" information available for 2W94)

(no "Cis Peptide Bond" information available for 2W94)

(no "SAP(SNP)/Variant" information available for 2W94)

Asymmetric/Biological Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FA58C_3	PS50022	Coagulation factors 5/8 type C domain (FA58C) profile.	DIS1A_DICDI	1-152	3	A:1-152 B:1-152 C:1-152
2	FA58C_1	PS01285	Coagulation factors 5/8 type C domain (FA58C) signature 1.	DIS1A_DICDI	49-78	3	A:49-78 B:49-78 C:49-78

(no "Exon" information available for 2W94)

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:254
 aligned with DIS1A_DICDI | P02886 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:254
                             1                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
          DIS1A_DICDI     - -MSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhh...eeee.........................................eeeee...eeeeeeeee.......eeeeeeeeee.....eeee.....eee.......eeee....eeeeeeeeeeeeee...eeeeeeee.....eeeeeeeeee.............eeeeeeee.........eeeeeeeeeeee........eeeee.....eeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -FA58C_3  PDB: A:1-152 UniProt: 1-152                                                                                                                    ----------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------FA58C_1  PDB: A:49-78         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w94 A   0 AMSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with DIS1A_DICDI | P02886 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
          DIS1A_DICDI     1 MSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhh...eeee.........................................eeeee...eeeeeeeee.......eeeeeeeeee.....eeee.....eee.......eeee....eeeeeeeeeeeeee...eeeeeeee.....eeeeeeeeee.............eeeeeeee.........eeeeeeeeeeee........eeeee.....eeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) FA58C_3  PDB: B:1-152 UniProt: 1-152                                                                                                                    ----------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------FA58C_1  PDB: B:49-78         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w94 B   1 MSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain C from PDB  Type:PROTEIN  Length:253
 aligned with DIS1A_DICDI | P02886 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
          DIS1A_DICDI     1 MSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------F5_F8_type_C-2w94C01 C:16-149                                                                                                         ------------------------------H_lectin-2w94C04 C:180-252                                               - Pfam domains (1)
           Pfam domains (2) ---------------F5_F8_type_C-2w94C02 C:16-149                                                                                                         ------------------------------H_lectin-2w94C05 C:180-252                                               - Pfam domains (2)
           Pfam domains (3) ---------------F5_F8_type_C-2w94C03 C:16-149                                                                                                         ------------------------------H_lectin-2w94C06 C:180-252                                               - Pfam domains (3)
         Sec.struct. author ........hhhh...eeee.........................................eeeee...eeeeeeeee.......eeeeeeeeee.....eeee.....eee.......eeee....eeeeeeeeeeeeee...eeeeeeee.....eeeeeeeeee.............eeeeeeee.........eeeeeeeeeeee........eeeee.....eeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) FA58C_3  PDB: C:1-152 UniProt: 1-152                                                                                                                    ----------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------FA58C_1  PDB: C:49-78         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w94 C   1 MSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

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 2W94)

(no "CATH Domain" information available for 2W94)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GBD (153)

Family: F5_F8_type_C (45)

Dictyostelium discoideum (Slime mold) (8)

1a	F5_F8_type_C-2w94C01	C:16-149
1b	F5_F8_type_C-2w94C02	C:16-149
1c	F5_F8_type_C-2w94C03	C:16-149

Clan: no clan defined [family: H_lectin] (8)

Family: H_lectin (8)

Dictyostelium discoideum (Slime mold) (8)

2a	H_lectin-2w94C04	C:180-252
2b	H_lectin-2w94C05	C:180-252
2c	H_lectin-2w94C06	C:180-252

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (DIS1A_DICDI | P02886)

molecular function
	GO:0046871	N-acetylgalactosamine binding	Interacting selectively and non-covalently with N-acetylgalactosamine, 2-acetamido-2-deoxygalactopyranose, the n-acetyl derivative of galactosamine.
	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:0070492	oligosaccharide binding	Interacting selectively and non-covalently with any oligosaccharide, a molecule with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
	GO:0030247	polysaccharide binding	Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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:0098609	cell-cell adhesion	The attachment of one cell to another cell via adhesion molecules.
	GO:0007010	cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	GO:0044351	macropinocytosis	An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size.
	GO:0051262	protein tetramerization	The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
	GO:0009617	response to bacterium	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 a stimulus from a bacterium.
	GO:1902168	response to catechin	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 a catechin stimulus.
	GO:1904643	response to curcumin	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 a curcumin stimulus.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0045335	phagocytic vesicle	A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
	GO:0098636	protein complex involved in cell adhesion	Any protein complex that is capable of carrying out some part of the process of cell adhesion to the cell matrix or to another cell.

Asymmetric/Biological Unit
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	2w94
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	DIS1A_DICDI \| P02886	:	2w95 2wn2 2wn3

2w95	STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN COMPLEX WITH GALNAC AT 1.75 ANGSTROM RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (0, 0)

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Gene Ontology (16, 16)

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