3GKH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   NPC1(NTD)

Authors :   H. J. Kwon

Date :   10 Mar 09 (Deposition) - 14 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

Chains :   Asym./Biol. Unit : A

Keywords :   Cholesterol, Cholesterol Transfer, Disease Mutation, Endosome, Glycoprotein, Lysosome, Membrane, Transmembrane, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. J. Kwon, L. Abi-Mosleh, M. L. Wang, J. Deisenhofer, J. L. Goldstein, M. S. Brown, R. E. Infante
Structure Of N-Terminal Domain Of Npc1 Reveals Distinct Subdomains For Binding And Transfer Of Cholesterol.
Cell(Cambridge, Mass. ) V. 137 1213 2009
PubMed-ID: 19563754 | Reference-DOI: 10.1016/J.CELL.2009.03.049

Molecule 1 - NIEMANN-PICK C1 PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Taxid	:	7111
	Gene	:	NPC1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	NAG A:2 , HOH A:11 , GLY A:65 , ASN A:106 , CYS A:109 , GLU A:110 , ASN A:222 , HOH A:267 , HOH A:307	BINDING SITE FOR RESIDUE NAG A 1
2	AC2	SOFTWARE	NAG A:1 , GLY A:65 , PHE A:68 , HOH A:307	BINDING SITE FOR RESIDUE NAG A 2
3	AC3	SOFTWARE	HOH A:6 , ASN A:158 , ASP A:162 , ASP A:182 , CYS A:227 , ILE A:245 , HOH A:279 , HOH A:322	BINDING SITE FOR RESIDUE NAG A 3
4	AC4	SOFTWARE	ASN A:86 , PHE A:108 , MET A:193 , GOL A:254 , HOH A:315	BINDING SITE FOR RESIDUE GOL A 253
5	AC5	SOFTWARE	ASN A:41 , ASN A:86 , PHE A:203 , GOL A:253 , HOH A:284	BINDING SITE FOR RESIDUE GOL A 254

Asymmetric/Biological Unit

No.	Residues
1	A:25	-	A:74
2	A:31	-	A:42
3	A:63	-	A:109
4	A:75	-	A:113
5	A:97	-	A:238
6	A:100	-	A:160
7	A:177	-	A:184
8	A:227	-	A:243
9	A:240	-	A:247

(no "Cis Peptide Bond" information available for 3GKH)

Asymmetric/Biological Unit (16, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_043172	C	63	R	NPC1_HUMAN	Disease (NPC1)	747049347	A	C	63	R
02	UniProt	VAR_043173	C	74	Y	NPC1_HUMAN	Disease (NPC1)	---	A	C	74	Y
03	UniProt	VAR_043174	Q	92	R	NPC1_HUMAN	Disease (NPC1)	---	A	Q	92	R
04	UniProt	VAR_043175	C	113	R	NPC1_HUMAN	Disease (NPC1)	120074136	A	C	113	R
05	UniProt	VAR_043176	T	137	M	NPC1_HUMAN	Disease (NPC1)	372947142	A	T	137	M
06	UniProt	VAR_043177	S	151	G	NPC1_HUMAN	Polymorphism	17855819	A	S	151	G
07	UniProt	VAR_043178	P	166	S	NPC1_HUMAN	Disease (NPC1)	866966704	A	P	166	S
08	UniProt	VAR_008815	C	177	G	NPC1_HUMAN	Disease (NPC1)	---	A	C	177	G
09	UniProt	VAR_015561	C	177	Y	NPC1_HUMAN	Disease (NPC1)	80358252	A	C	177	Y
10	UniProt	VAR_008816	H	215	R	NPC1_HUMAN	Polymorphism	1805081	A	H	215	R
11	UniProt	VAR_043179	N	222	S	NPC1_HUMAN	Disease (NPC1)	55680026	A	N	222	S
12	UniProt	VAR_043180	V	231	G	NPC1_HUMAN	Disease (NPC1)	---	A	V	231	G
13	UniProt	VAR_008817	P	237	S	NPC1_HUMAN	Disease (NPC1)	80358251	A	P	237	S
14	UniProt	VAR_043181	D	242	H	NPC1_HUMAN	Disease (NPC1)	---	A	D	242	H
15	UniProt	VAR_043182	D	242	N	NPC1_HUMAN	Disease (NPC1)	---	A	D	242	N
16	UniProt	VAR_043183	C	247	Y	NPC1_HUMAN	Disease (NPC1)	---	A	C	247	Y

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

(no "PROSITE Motif" information available for 3GKH)

(no "Exon" information available for 3GKH)

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:225
 aligned with NPC1_HUMAN | O15118 from UniProtKB/Swiss-Prot  Length:1278

    Alignment length:225
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
           NPC1_HUMAN    23 QSCVWYGECGIAYGDKRYNCEYSGPPKPLPKDGYDLVQELCPGFFFGNVSLCCDVRQLQTLKDNLQLPLQFLSRCPSCFYNLLNLFCELTCSPRQSQFLNVTATEDYVDPVTNQTKTNVKELQYYVGQSFANAMYNACRDVEAPSSNDKALGLLCGKDADACNATNWIEYMFNKDNGQAPFTITPVFSDFPVHGMEPMNNATKGCDESVDEVTAPCSCQDCSIVC 247
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..eeeeee.....ee.hhhhhhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhh.eeeeeeeeee......eeeeeeeeeeeehhhhhhhhhhhhh..........hhhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeee.............................hhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------R----------Y-----------------R--------------------R-----------------------M-------------G--------------S----------G-------------------------------------R------S--------G-----S----H----Y SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------Y----------------------------------------------------------------N----- SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gkh A  23 QSCVWYGECGIAYGDKRYNCEYSGPPKPLPKDGYDLVQELCPGFFFGQVSLCCDVRQLQTLKDNLQLPLQFLSRCPSCFYNLLNLFCELTCSPRQSQFLQVTATEDYVDPVTNQTKTNVKELQYYVGQSFANAMYNACRDVEAPSSNDKALGLLCGKDADACQATNWIEYMFNKDNGQAPFTITPVFSDFPVHGMEPMNNATKGCDESVDEVTAPCSCQDCSIVC 247
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

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 3GKH)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NPC1_HUMAN | O15118)

molecular function
	GO:0015485	cholesterol binding	Interacting selectively and non-covalently with cholesterol (cholest-5-en-3-beta-ol); the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
	GO:0005319	lipid transporter activity	Enables the directed movement of lipids into, out of or within a cell, or between cells.
	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:0015248	sterol transporter activity	Enables the directed movement of sterols into, out of or within a cell, or between cells. Sterol are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
biological process
	GO:0007628	adult walking behavior	The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0008206	bile acid metabolic process	The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
	GO:0071404	cellular response to low-density lipoprotein particle stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a low-density lipoprotein particle stimulus.
	GO:0071383	cellular response to steroid hormone stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.
	GO:0033344	cholesterol efflux	The directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
	GO:0042632	cholesterol homeostasis	Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
	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:0090150	establishment of protein localization to membrane	The directed movement of a protein to a specific location in a membrane.
	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:0007041	lysosomal transport	The directed movement of substances into, out of or within a lysosome.
	GO:0031579	membrane raft organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of membrane rafts, small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes.
	GO:0060548	negative regulation of cell death	Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
	GO:0016242	negative regulation of macroautophagy	Any process that stops, prevents, or reduces the frequency, rate or extent of macroautophagy.
	GO:2000189	positive regulation of cholesterol homeostasis	Any process that activates or increases the frequency, rate or extent of cholesterol homeostasis.
	GO:0006486	protein glycosylation	A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
	GO:0046686	response to cadmium ion	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 cadmium (Cd) ion stimulus.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	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: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:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	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:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

Asymmetric/Biological Unit
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	NPC1_HUMAN \| O15118	:	3gki 3gkj 3jd8 5f18 5f1b 5hns 5i31 5jnx 5kwy

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (9, 9)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (16, 16)

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