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Title :   CRYSTAL STRUCTURE OF ERGIC-53/MCFD2, CALCIUM/MAN3-BOUND FORM

Authors :   T. Satoh, K. Suzuki, T. Yamaguchi, K. Kato

Date :   18 Dec 13 (Deposition) - 15 Jan 14 (Release) - 19 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   Beta-Sandwich, Ef-Hand, Cargo Receptor, Calcium Binding, Er, Ergic, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Satoh, K. Suzuki, T. Yamaguchi, K. Kato
Structural Basis For Disparate Sugar-Binding Specificities In The Homologous Cargo Receptors Ergic-53 And Vip36
Plos One V. 9 87963 2014
PubMed-ID: 24498414 | Reference-DOI: 10.1371/JOURNAL.PONE.0087963

Molecule 1 - PROTEIN ERGIC-53
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCOLD-III
	Expression System Strain	:	BL21-CODONPLUS(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CARBOHYDRATE RECOGNITION DOMAIN (UNP RESIDUES 31-269)
	Gene	:	ERGIC53
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ER-GOLGI INTERMEDIATE COMPARTMENT 53 KDA PROTEIN, GP58, INTRACELLULAR MANNOSE-SPECIFIC LECTIN MR60, LECTIN MANNOSE-BINDING 1

Molecule 2 - MULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-16B
	Expression System Strain	:	BL21-CODONPLUS(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 67-146
	Gene	:	MCFD2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MCFD2, NEURAL STEM CELL-DERIVED NEURONAL SURVIVAL PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:152 , PHE A:154 , ASN A:156 , ASP A:181	BINDING SITE FOR RESIDUE CA A 501
2	AC2	SOFTWARE	ASP A:155 , ASN A:156 , ASP A:157 , ASN A:161 , ASN A:162 , ASP A:181	BINDING SITE FOR RESIDUE CA A 502
3	AC3	SOFTWARE	ASP B:81 , ASP B:83 , ASN B:85 , LEU B:87 , GLU B:92	BINDING SITE FOR RESIDUE CA B 501
4	AC4	SOFTWARE	ASP B:129 , ASN B:131 , ASP B:133 , TYR B:135 , GLU B:140	BINDING SITE FOR RESIDUE CA B 502
5	AC5	SOFTWARE	SER A:88 , ALA A:120 , ASP A:121 , PHE A:154 , ASN A:156 , GLY A:251 , GLY A:252 , LEU A:253	BINDING SITE FOR DI-SACCHARIDE MAN A 503 AND MAN A 504

Asymmetric/Biological Unit

No.	Residues
1	A:190	-	A:230

Asymmetric/Biological Unit

No.	Residues
1	Gly A:54	-	Pro A:55
2	Ala A:120	-	Asp A:121
3	Asn A:162	-	Pro A:163

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_071969	W	67	S	LMAN1_HUMAN	Disease (F5F8D1)	---	A	W	67	S
2	UniProt	VAR_072245	D	81	H	MCFD2_HUMAN	Disease (F5F8D2)	78289603	B	D	81	H
3	UniProt	VAR_019076	D	129	E	MCFD2_HUMAN	Disease (F5F8D2)	28942113	B	D	129	E
4	UniProt	VAR_072246	Y	135	N	MCFD2_HUMAN	Disease (F5F8D2)	748641905	B	Y	135	N
5	UniProt	VAR_019077	I	136	T	MCFD2_HUMAN	Disease (F5F8D2)	28942114	B	I	136	T

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

Asymmetric/Biological Unit (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LECTIN_LIKE	PS51328	L-type lectin-like (leguminous) domain profile.	LMAN1_HUMAN	44-267	1	A:44-267
2	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	MCFD2_HUMAN	68-103 116-146	1	- B:116-142
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	MCFD2_HUMAN	81-93 129-141	2	B:81-93 B:129-141

(no "Exon" information available for 3WNX)

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:226
 aligned with LMAN1_HUMAN | P49257 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:226
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261      
          LMAN1_HUMAN    42 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAFENWEVEVTFRVTGRGRIGADGLAIWYAENQGLEGPVFGSADLWNGVGIFFDSFDNDGKKNNPAIVIIGNNGQIHYDHQNDGASQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQL 267
               SCOP domains d3wnxa_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhee.............eeeee..ee....eeee......eeeeee........eeeeeeeeee........eeeeeee................eeeeeeee...........eeeeeeee..............eeeee..........eeeeeee...eeeeeee..........eeeeeee........eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --L_LECTIN_LIKE  PDB: A:44-267 UniProt: 44-267                                                                                                                                                                                     PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wnx A  42 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAFENWEVEVTFRVTGRGRIGADGLAIWYAENQGLEGPVFGSADLWNGVGIFFDSFDNDGKKNNPAIVIIGNNGQIHYDHQNDGASQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQL 267
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with MCFD2_HUMAN | Q8NI22 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:70
                                    82        92       102       112       122       132       142
          MCFD2_HUMAN    73 QLHYFKMHDYDGNNLLDGLELSTAITHVHKEEGSEQAPLMSEDELINIIDGVLRDDDKNNDGYIDYAEFA 142
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.........hhhhhhhhh.-------------.hhhhhhhhhhhhhhhhh.......hhhhhh Sec.struct. author
                 SAPs(SNPs) --------H-----------------------------------------------E-----NT------ SAPs(SNPs)
                PROSITE (2) EF_HAND_2  PDB: -              ------------EF_HAND_2  PDB: B:116-142   PROSITE (2)
                PROSITE (3) --------EF_HAND_1    -----------------------------------EF_HAND_1    - PROSITE (3)
                 Transcript ---------------------------------------------------------------------- Transcript
                 3wnx B  73 QLHYFKMHDYDGNNLLDGLELSTAIT-------------MSEDELINIIDGVLRDDDKNNDGYIDYAEFA 142
                                    82        92     |   -       112       122       132       142
                                                    98           112

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Lectin leg-like (18)

Protein domain: automated matches (10)

Human (Homo sapiens) [TaxId: 9606] (7)

d3wnxa_

(no "CATH Domain" information available for 3WNX)

(no "Pfam Domain" information available for 3WNX)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LMAN1_HUMAN | P49257)

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:0005537	mannose binding	Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
	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:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	GO:0048208	COPII vesicle coating	The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
	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:0007030	Golgi organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0034498	early endosome to Golgi transport	The directed movement of substances from early endosomes to the Golgi.
	GO:0007029	endoplasmic reticulum organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum.
	GO:0010638	positive regulation of organelle organization	Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
	GO:0018279	protein N-linked glycosylation via asparagine	The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.
	GO:0032527	protein exit from endoplasmic reticulum	The directed movement of proteins from the endoplasmic reticulum.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	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.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
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:0012507	ER to Golgi transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
	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:0005793	endoplasmic reticulum-Golgi intermediate compartment	A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
	GO:0033116	endoplasmic reticulum-Golgi intermediate compartment membrane	The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
	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:0044220	host cell perinuclear region of cytoplasm	The host cell cytoplasm situated near, or occurring around, the host nucleus.
	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.
	GO:0030017	sarcomere	The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.

Chain B (MCFD2_HUMAN | Q8NI22)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0048208	COPII vesicle coating	The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
	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:0018279	protein N-linked glycosylation via asparagine	The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.
	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.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0012507	ER to Golgi transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
	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:0005793	endoplasmic reticulum-Golgi intermediate compartment	A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
	GO:0033116	endoplasmic reticulum-Golgi intermediate compartment membrane	The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:120 - Asp A:121	[ RasMol ]
		Asn A:162 - Pro A:163	[ RasMol ]
		Gly A:54 - Pro A:55	[ RasMol ]

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	3wnx
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (5, 5)

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

PROSITE Motifs (3, 4)

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