2A6V - JenaLib

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Title :   CRYSTAL STRUCTURE OF EMP46P CARBOHYDRATE RECOGNITION DOMAIN (CRD), POTASSIUM-BOUND FORM

Authors :   T. Satoh, K. Sato, A. Kanoh, K. Yamashita, R. Kato, A. Nakano, S. Wakatsuki

Date :   04 Jul 05 (Deposition) - 31 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.52

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

Keywords :   Beta Sandwich, Carbohydrate Binding Protein, Cargo Receptor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Satoh, K. Sato, A. Kanoh, K. Yamashita, Y. Yamada, N. Igarashi, R. Kato, A. Nakano, S. Wakatsuki
Structures Of The Carbohydrate Recognition Domain Of Ca2+-Independent Cargo Receptors Emp46P And Emp47P.
J. Biol. Chem. V. 281 10410 2006
PubMed-ID: 16439369 | Reference-DOI: 10.1074/JBC.M512258200
(for further references see the PDB file header)

Molecule 1 - EMP46P
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T-1
	Expression System Strain	:	BL21(DE3), DL41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 6-229
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	K	2	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:131 , ILE A:141 , GLU A:142 , SER A:144 , HOH A:241 , HOH A:262	BINDING SITE FOR RESIDUE K A 1
2	AC2	SOFTWARE	LEU A:29 , TRP A:32 , HOH A:452 , ASP B:67 , HOH B:248	BINDING SITE FOR RESIDUE K A 2
3	AC3	SOFTWARE	LEU A:151 , MET A:179 , ARG A:182 , VAL A:183 , CYS A:184	BINDING SITE FOR RESIDUE EDO A 3
4	AC4	SOFTWARE	ASN B:112 , GLY B:113 , ASN B:133 , LYS B:191 , HOH B:297	BINDING SITE FOR RESIDUE EDO B 230
5	AC5	SOFTWARE	SER B:83 , THR B:84 , HOH B:288 , HOH B:357	BINDING SITE FOR RESIDUE EDO B 231

Asymmetric Unit

No.	Residues
1	A:150	-	A:184
2	B:150	-	B:184

(no "Cis Peptide Bond" information available for 2A6V)

(no "SAP(SNP)/Variant" information available for 2A6V)

(no "PROSITE Motif" information available for 2A6V)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLR080W	1	YLR080W.1	XII:287917-289251	1335	EMP46_YEAST	1-444	444	2	A:9-226 B:9-225	218 217

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:218
 aligned with EMP46_YEAST | Q12396 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:218
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264        
          EMP46_YEAST    55 KWNKGYSLPNLLEVTDQQKELSQWTLGDKVKLEEGRFVLTPGKNTKGSLWLKPEYSIKDAMTIEWTFRSFGFRGSTKGGLAFWLKQGNEGDSTELFGGSSKKFNGLMILLRLDDKLGESVTAYLNDGTKDLDIESSPYFASCLFQYQDSMVPSTLRLTYNPLDNHLLKLQMDNRVCFQTRKVKFMGSSPFRIGTSAINDASKESFEILKMKLYDGVIE 272
               SCOP domains d2a6va1 A:9-226 Emp46p N-terminal domain                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.........hhhhh..eeeee..eee..eee.......eeeeee.........eeeeeeeeee........eeeeeeee.................eeeeeeeeee....eeeeeeeee.............eeee.........eeeeeeee.....eeeeee..eeeeee..........eeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:9-226 UniProt: 1-444 [INCOMPLETE]                                                                                                                                                                         Transcript 1
                 2a6v A   9 KWNKGYSLPNLLEVTDQQKELSQWTLGDKVKLEEGRFVLTPGKNTKGSLWLKPEYSIKDAMTIEWTFRSFGFRGSTKGGLAFWLKQGNEGDSTELFGGSSKKFNGLMILLRLDDKLGESVTAYLNDGTKDLDIESSPYFASCLFQYQDSMVPSTLRLTYNPLDNHLLKLQMDNRVCFQTRKVKFMGSSPFRIGTSAINDASKESFEILKMKLYDGVIE 226
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with EMP46_YEAST | Q12396 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:217
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       
          EMP46_YEAST    55 KWNKGYSLPNLLEVTDQQKELSQWTLGDKVKLEEGRFVLTPGKNTKGSLWLKPEYSIKDAMTIEWTFRSFGFRGSTKGGLAFWLKQGNEGDSTELFGGSSKKFNGLMILLRLDDKLGESVTAYLNDGTKDLDIESSPYFASCLFQYQDSMVPSTLRLTYNPLDNHLLKLQMDNRVCFQTRKVKFMGSSPFRIGTSAINDASKESFEILKMKLYDGVI 271
               SCOP domains d2a6vb_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.........hhhhh..eeeee..eee..eee.......eeeeee.........eeeeeeeeee........eeeeeeee.................eeeeeeeeee....eeeeeeeee.............eeee.........eeeeeeee.....eeeeee..eeeeee..........eeeeeeee......eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:9-225 UniProt: 1-444 [INCOMPLETE]                                                                                                                                                                        Transcript 1
                 2a6v B   9 KWNKGYSLPNLLEVTDQQKELSQWTLGDKVKLEEGRFVLTPGKNTKGSLWLKPEYSIKDAMTIEWTFRSFGFRGSTKGGLAFWLKQGNEGDSTELFGGSSKKFNGLMILLRLDDKLGESVTAYLNDGTKDLDIESSPYFASCLFQYQDSMVPSTLRLTYNPLDNHLLKLQMDNRVCFQTRKVKFMGSSPFRIGTSAINDASKESFEILKMKLYDGVI 225
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "CATH Domain" information available for 2A6V)

(no "Pfam Domain" information available for 2A6V)

Asymmetric Unit(hide GO term definitions)

Chain A,B (EMP46_YEAST | Q12396)

molecular function
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0030134	COPII-coated ER to Golgi transport vesicle	A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	2a6v
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	EMP46_YEAST \| Q12396	:	2a6w 2a6x

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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Exons (1, 2)

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