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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   STRUCTURE OF HUMAN MCFD2

Authors :   J. E. Guy, E. Wigren, M. Svard, T. Hard, Y. Lindqvist

Date :   04 Apr 08 (Deposition) - 15 Jul 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Er-Golgi Transport, Glycoprotein Sorting, Disease Mutation, Secretory Pathway, Protein Transport, Er, Ef-Hand, Calcium, Transport, Golgi Apparatus, Endoplasmic Reticulum, Coagulation Factor Deficiency (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Guy, E. Wigren, M. Svard, T. Hard, Y. Lindqvist
New Insights Into Multiple Coagulation Factor Deficiency From The Solution Structure Of Human Mcfd2.
J. Mol. Biol. V. 381 941 2008
PubMed-ID: 18590741 | Reference-DOI: 10.1016/J.JMB.2008.06.042

Molecule 1 - MULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NEURAL STEM CELL-DERIVED NEURONAL SURVIVAL PROTEIN, MCFD2


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:81 , ASP A:83 , ASN A:85 , LEU A:87 , GLU A:92	BINDING SITE FOR RESIDUE CA A1147
2	AC2	SOFTWARE	ASP A:129 , ASN A:131 , ASP A:133 , TYR A:135 , GLU A:140	BINDING SITE FOR RESIDUE CA A1148

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

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

NMR Structure (4, 4)

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

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

NMR Structure (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	MCFD2_HUMAN	68-103 116-146	2	A:68-103 A:116-146
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	MCFD2_HUMAN	81-93 129-141	2	A:81-93 A:129-141

(no "Exon" information available for 2VRG)

NMR Structure

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:80
 aligned with MCFD2_HUMAN | Q8NI22 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:80
                                    76        86        96       106       116       126       136       146
          MCFD2_HUMAN    67 MSPQELQLHYFKMHDYDGNNLLDGLELSTAITHVHKEEGSEQAPLMSEDELINIIDGVLRDDDKNNDGYIDYAEFAKSLQ 146
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains EF_hand_5-2vrgA01 A:67-145                                                     - Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhh.........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------H-----------------------------------------------E-----NT---------- SAPs(SNPs)
                PROSITE (1) -EF_HAND_2  PDB: A:68-103            ------------EF_HAND_2  PDB: A:116-146       PROSITE (1)
                PROSITE (2) --------------EF_HAND_1    -----------------------------------EF_HAND_1    ----- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------- Transcript
                 2vrg A  67 MSPQELQLHYFKMHDYDGNNLLDGLELSTAITHVHKEEGSEQAPLMSEDELINIIDGVLRDDDKNNDGYIDYAEFAKSLQ 146
                                    76        86        96       106       116       126       136       146

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 2VRG)

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

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: EF_hand_5 (126)

Homo sapiens (Human) (31)

EF_hand_5-2vrgA01

A:67-145

NMR Structure(hide GO term definitions)

Chain A (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.

NMR Structure
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	2vrg
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	MCFD2_HUMAN \| Q8NI22	:	3a4u 3lcp 3wht 3whu 3wnx 4ygb 4ygc 4ygd 4yge

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Description

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Ligands, Modified Residues, Ions (1, 2)

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