1I0U - JenaLib

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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR

Authors :   N. D. Kurniawan, K. Aliabadizadeh, I. M. Brereton, P. A. Kroon, R. Smith

Date :   29 Jan 01 (Deposition) - 15 Aug 01 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A

Keywords :   Anti-Parallel Beta Strands, Calcium Binding Sites, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. D. Kurniawan, K. Aliabadizadeh, I. M. Brereton, P. A. Kroon, R. Smith
Nmr Structure And Backbone Dynamics Of A Concatemer Of Epidermal Growth Factor Homology Modules Of The Human Low-Density Lipoprotein Receptor.
J. Mol. Biol. V. 311 341 2001
PubMed-ID: 11478865 | Reference-DOI: 10.1006/JMBI.2001.4867
(for further references see the PDB file header)

Molecule 1 - LOW DENSITY LIPOPROTEIN RECEPTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T; PET-30A+
	Expression System Strain	:	DH5-ALPHA; BL21-DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EGF-AB CONCATEMER(RESIDUES 314-395)
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LDL RECEPTOR
	Tissue	:	LIVER


NMR Structure	:

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	THR A:2 , ASN A:3 , GLU A:4 , ASP A:18	BINDING SITE FOR RESIDUE CA A 83
2	AC2	SOFTWARE	ASP A:41 , ILE A:42 , GLU A:44 , ASN A:57 , LEU A:58 , GLY A:60	BINDING SITE FOR RESIDUE CA A 84

NMR Structure

No.	Residues
1	A:5	-	A:16
2	A:12	-	A:25
3	A:27	-	A:39
4	A:45	-	A:55
5	A:51	-	A:64
6	A:66	-	A:79

(no "Cis Peptide Bond" information available for 1I0U)

NMR Structure (30, 30)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_072841	G	314	R	LDLR_HUMAN	Unclassified (FH)	72658858	A	G	1	R
02	UniProt	VAR_005360	C	318	F	LDLR_HUMAN	Disease (FH)	879254739	A	C	5	F
03	UniProt	VAR_062376	C	318	R	LDLR_HUMAN	Disease (FH)	879254738	A	C	5	R
04	UniProt	VAR_005359	C	318	Y	LDLR_HUMAN	Polymorphism	879254739	A	C	5	Y
05	UniProt	VAR_072842	S	326	C	LDLR_HUMAN	Unclassified (FH)	879254747	A	S	13	C
06	UniProt	VAR_005361	H	327	Y	LDLR_HUMAN	Disease (FH)	747507019	A	H	14	Y
07	UniProt	VAR_067196	C	329	F	LDLR_HUMAN	Disease (FH)	---	A	C	16	F
08	UniProt	VAR_005362	C	329	Y	LDLR_HUMAN	Disease (FH)	761954844	A	C	16	Y
09	UniProt	VAR_005363	G	335	S	LDLR_HUMAN	Polymorphism	544453230	A	G	22	S
10	UniProt	VAR_005364	C	338	S	LDLR_HUMAN	Disease (FH)	879254753	A	C	25	S
11	UniProt	VAR_005365	D	342	E	LDLR_HUMAN	Unclassified	---	A	D	29	E
12	UniProt	VAR_005366	D	342	N	LDLR_HUMAN	Unclassified (FH)	139361635	A	D	29	N
13	UniProt	VAR_005367	G	343	S	LDLR_HUMAN	Unclassified (FH)	730882096	A	G	30	S
14	UniProt	VAR_005368	R	350	P	LDLR_HUMAN	Disease (FH)	875989914	A	R	37	P
15	UniProt	VAR_072843	C	352	R	LDLR_HUMAN	Unclassified (FH)	879254769	A	C	39	R
16	UniProt	VAR_005369	C	352	Y	LDLR_HUMAN	Polymorphism	193922566	A	C	39	Y
17	UniProt	VAR_005370	D	354	G	LDLR_HUMAN	Polymorphism	755449669	A	D	41	G
18	UniProt	VAR_005371	D	354	V	LDLR_HUMAN	Unclassified	---	A	D	41	V
19	UniProt	VAR_007984	D	356	Y	LDLR_HUMAN	Disease (FH)	---	A	D	43	Y
20	UniProt	VAR_005372	E	357	K	LDLR_HUMAN	Polymorphism	879254781	A	E	44	K
21	UniProt	VAR_062377	C	358	Y	LDLR_HUMAN	Disease (FH)	875989915	A	C	45	Y
22	UniProt	VAR_005373	C	364	R	LDLR_HUMAN	Polymorphism	879254787	A	C	51	R
23	UniProt	VAR_007985	Q	366	R	LDLR_HUMAN	Disease (FH)	746982741	A	Q	53	R
24	UniProt	VAR_005374	C	368	R	LDLR_HUMAN	Disease (FH)	---	A	C	55	R
25	UniProt	VAR_072844	C	368	Y	LDLR_HUMAN	Unclassified (FH)	768430352	A	C	55	Y
26	UniProt	VAR_062378	N	370	T	LDLR_HUMAN	Disease (FH)	879254792	A	N	57	T
27	UniProt	VAR_072845	G	373	D	LDLR_HUMAN	Unclassified (FH)	879254797	A	G	60	D
28	UniProt	VAR_005375	C	379	R	LDLR_HUMAN	Polymorphism	879254803	A	C	66	R
29	UniProt	VAR_007986	C	379	Y	LDLR_HUMAN	Disease (FH)	879254804	A	C	66	Y
30	UniProt	VAR_024519	A	391	T	LDLR_HUMAN	Polymorphism	11669576	A	A	78	T

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

NMR Structure (4, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_3	PS50026	EGF-like domain profile.	LDLR_HUMAN	314-353 354-393	2	A:1-40 A:41-80
2	ASX_HYDROXYL	PS00010	Aspartic acid and asparagine hydroxylation site.	LDLR_HUMAN	329-340 368-379	2	A:16-27 A:55-66
3	EGF_2	PS01186	EGF-like domain signature 2.	LDLR_HUMAN	338-352 377-392	2	A:25-39 A:64-79
4	EGF_CA	PS01187	Calcium-binding EGF-like domain signature.	LDLR_HUMAN	354-377	1	A:41-64

(no "Exon" information available for 1I0U)

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
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Chain A from PDB  Type:PROTEIN  Length:82
 aligned with LDLR_HUMAN | P01130 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:82
                                   323       333       343       353       363       373       383       393  
           LDLR_HUMAN   314 GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAV 395
               SCOP domains d1i0ua1 A:1-41                           d1i0ua2 A:42-82                           SCOP domains
               CATH domains 1i0uA02 A:1-41 Laminin                   1i0uA01 A:42-82 Laminin                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..eee......eee.....eeee..eee..............ee......ee.....eee......eee. Sec.struct. author
             SAPs(SNPs) (1) R---F-------CY-F-----S--S---ES------P-R-G-YKY-----R-R-R-T--D-----R-----------T---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----R----------Y------------N---------Y-V-------------Y----------Y---------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----Y----------------------------------------------------------------------------- SAPs(SNPs) (3)
                PROSITE (1) EGF_3  PDB: A:1-40 UniProt: 314-353     EGF_3  PDB: A:41-80 UniProt: 354-393    -- PROSITE (1)
                PROSITE (2) ---------------ASX_HYDROXYL---------------------------ASX_HYDROXYL---------------- PROSITE (2)
                PROSITE (3) ------------------------EGF_2          ------------------------EGF_2           --- PROSITE (3)
                PROSITE (4) ----------------------------------------EGF_CA  PDB: A:41-64    ------------------ PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1i0u A   1 GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAV  82
                                    10        20        30        40        50        60        70        80

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

NMR Structure

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Knottins (small inhibitors, toxins, lectins) (761)

Superfamily: EGF/Laminin (347)

Family: EGF-type module (304)

Protein domain: Low density lipoprotein (LDL) receptor, different EGF domains (7)

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

1a	d1i0ua1	A:1-41
1b	d1i0ua2	A:42-82

NMR Structure

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Laminin (270)

Homologous Superfamily: Laminin (263)

Human (Homo sapiens) (195)

1a	1i0uA01	A:42-82
1b	1i0uA02	A:1-41

(no "Pfam Domain" information available for 1I0U)

NMR Structure(hide GO term definitions)

Chain A (LDLR_HUMAN | P01130)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0032050	clathrin heavy chain binding	Interacting selectively and non-covalently with a clathrin heavy chain.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0030169	low-density lipoprotein particle binding	Interacting selectively and non-covalently with a low-density lipoprotein particle, a lipoprotein particle that is rich in cholesterol esters and low in triglycerides, is typically composed of APOB100 and APOE, and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm.
	GO:0005041	low-density lipoprotein receptor activity	Combining with a low-density lipoprotein particle and delivering the low-density lipoprotein into the cell via endocytosis.
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	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:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0030229	very-low-density lipoprotein particle receptor activity	Combining with a very-low-density lipoprotein particle and delivering the very-low-density lipoprotein into the cell via endocytosis.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
biological process
	GO:0042632	cholesterol homeostasis	Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
	GO:0070508	cholesterol import	The directed movement of cholesterol into a cell or organelle.
	GO:0008203	cholesterol metabolic process	The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
	GO:0030301	cholesterol transport	The directed movement of cholesterol, cholest-5-en-3-beta-ol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0030299	intestinal cholesterol absorption	Uptake of cholesterol into the blood by absorption from the small intestine.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0006869	lipid transport	The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0042159	lipoprotein catabolic process	The chemical reactions and pathways resulting in the breakdown of any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
	GO:0042157	lipoprotein metabolic process	The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
	GO:0034383	low-density lipoprotein particle clearance	The process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
	GO:0015914	phospholipid transport	The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Phospholipids are any lipids containing phosphoric acid as a mono- or diester.
	GO:0010867	positive regulation of triglyceride biosynthetic process	Any process that increases the rate, frequency, or extent of triglyceride biosynthesis. Triglyceride biosynthesis is the collection of chemical reactions and pathways resulting in the formation of triglyceride, any triester of glycerol.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	GO:2000188	regulation of cholesterol homeostasis	Any process that modulates the frequency, rate or extent of cholesterol homeostasis.
	GO:0010899	regulation of phosphatidylcholine catabolic process	Any process that modulates the rate, frequency or extent of phosphatidylcholine catabolism. Phosphatidylcholine catabolic processes are the chemical reactions and pathways resulting in the breakdown of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	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:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	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:1990666	PCSK9-LDLR complex	A protein complex consisting of the serine protease PCSK9 (Proprotein convertase subtilisin/kexin-9) and a low-density lipoprotein receptor (LDLR). Interaction typically occurs through the epidermal growth factor-like repeat A (EGF-A) domain of the LDLR, and complex formation promotes degradation of the LDLR through the endosome/lysosome pathway.
	GO:0045177	apical part of cell	The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
	GO:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0005905	clathrin-coated pit	A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0012505	endomembrane system	A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0034362	low-density lipoprotein particle	A lipoprotein particle, rich in cholesterol esters and low in triglycerides that is typically composed of APOB100 and APOE and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm. LDL particles are formed from VLDL particles (via IDL) by the loss of triglyceride and gain of cholesterol ester. They transport endogenous cholesterol (and to some extent triglycerides) from peripheral tissues back to the liver.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	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.
	GO:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

NMR Structure
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1f5y	1F5Y CONTAINS LIGAND BINDING MODULES (LB1-2) OF THE HUMAN LDL RECEPTOR
1hz8	1HZ8 IS THE ENSEMBLE OF 30 STRUCTURES
1lrx	1LRX CONTAINS YWTD MODULES OF THE HUMAN LDL RECEPTOR

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (30, 30)

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