2QTW - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE CRYSTAL STRUCTURE OF PCSK9 AT 1.9 ANGSTROMS RESOLUTION REVEALS STRUCTURAL HOMOLOGY TO RESISTIN WITHIN THE C-TERMINAL DOMAIN

Authors :   E. N. Hampton, M. W. Knuth, J. Li, J. L. Harris, S. A. Lesley, G. Spraggon

Date :   02 Aug 07 (Deposition) - 18 Sep 07 (Release) - 18 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Pro-Protein Convertase, Coronary Heart Disease, Hypercholesterolemia, Low Density Lipoprotein Receptor, Autocatalytic Cleavage, Cholesterol Metabolism, Disease Mutation, Glycoprotein, Hydrolase, Lipid Metabolism, Phosphorylation, Protease, Secreted, Serine Protease, Steroid Metabolism, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. N. Hampton, M. W. Knuth, J. Li, J. L. Harris, S. A. Lesley, G. Spraggon
The Self-Inhibited Structure Of Full-Length Pcsk9 At 1. 9 A Reveals Structural Homology With Resistin Within The C-Terminal Domain.
Proc. Natl. Acad. Sci. Usa V. 104 14604 2007
PubMed-ID: 17804797 | Reference-DOI: 10.1073/PNAS.0703402104

Molecule 1 - PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 PROPEPTIDE
	Chains	:	A
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	MAMMALIAN KIDNEY CELLS HEK293
	Fragment	:	UNP RESIDUES 29-152
	Gene	:	PCSK9, NARC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	FREESTYLE 293
	Synonym	:	PROPROTEIN CONVERTASE PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9, NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1

Molecule 2 - PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
	Chains	:	B
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	MAMMALIAN KIDNEY CELLS HEK293
	Fragment	:	UNP RESIDUES 153-692
	Gene	:	PCSK9, NARC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	FREESTYLE 293
	Synonym	:	PROPROTEIN CONVERTASE PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9, NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:531 , ASN B:533 , HIS B:602 , PRO B:604 , HOH B:1229	BINDING SITE FOR RESIDUE NAG B 1001
2	AC2	SOFTWARE	ALA B:328 , ALA B:330 , VAL B:333 , THR B:335 , CYS B:358 , ASP B:360 , HOH B:1231	BINDING SITE FOR RESIDUE CA B 1

Asymmetric/Biological Unit

No.	Residues
1	B:223	-	B:255
2	B:323	-	B:358
3	B:375	-	B:378
4	B:457	-	B:527
5	B:477	-	B:526
6	B:486	-	B:509
7	B:534	-	B:601
8	B:552	-	B:600
9	B:562	-	B:588
10	B:608	-	B:679
11	B:626	-	B:678
12	B:635	-	B:654

Asymmetric/Biological Unit

No.	Residues
1	Ser B:326	-	Pro B:327

Asymmetric/Biological Unit (30, 30)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_058520	T	77	I	PCSK9_HUMAN	Polymorphism	756060557	A	T	77	I
02	UniProt	VAR_058521	R	93	C	PCSK9_HUMAN	Polymorphism	151193009	A	R	93	C
03	UniProt	VAR_058522	G	106	R	PCSK9_HUMAN	Polymorphism	---	A	G	106	R
04	UniProt	VAR_058523	V	114	A	PCSK9_HUMAN	Polymorphism	775988212	A	V	114	A
05	UniProt	VAR_017199	S	127	R	PCSK9_HUMAN	Disease (HCHOLA3)	28942111	A	S	127	R
06	UniProt	VAR_058524	D	129	G	PCSK9_HUMAN	Disease (HCHOLA3)	---	A	D	129	G
07	UniProt	VAR_058525	N	157	K	PCSK9_HUMAN	Polymorphism	143117125	B	N	157	K
08	UniProt	VAR_025452	R	237	W	PCSK9_HUMAN	Polymorphism	148195424	B	R	237	W
09	UniProt	VAR_058529	A	239	D	PCSK9_HUMAN	Polymorphism	---	B	A	239	D
10	UniProt	VAR_025453	L	253	F	PCSK9_HUMAN	Polymorphism	28362270	B	L	253	F
11	UniProt	VAR_058530	R	357	H	PCSK9_HUMAN	Disease (HCHOLA3)	370507566	B	R	357	H
12	UniProt	VAR_058531	D	374	H	PCSK9_HUMAN	Disease (HCHOLA3)	---	B	D	374	H
13	UniProt	VAR_058532	D	374	Y	PCSK9_HUMAN	Disease (HCHOLA3)	137852912	B	D	374	Y
14	UniProt	VAR_025454	H	391	N	PCSK9_HUMAN	Polymorphism	146471967	B	H	391	N
15	UniProt	VAR_067282	G	394	S	PCSK9_HUMAN	Unclassified	368257906	B	G	394	S
16	UniProt	VAR_025455	H	417	Q	PCSK9_HUMAN	Polymorphism	143275858	B	H	417	Q
17	UniProt	VAR_021337	N	425	S	PCSK9_HUMAN	Polymorphism	28362261	B	N	425	S
18	UniProt	VAR_021338	A	443	T	PCSK9_HUMAN	Polymorphism	28362263	B	A	443	T
19	UniProt	VAR_058533	G	452	D	PCSK9_HUMAN	Polymorphism	---	B	G	452	D
20	UniProt	VAR_025456	R	469	W	PCSK9_HUMAN	Polymorphism	141502002	B	R	469	W
21	UniProt	VAR_021339	V	474	I	PCSK9_HUMAN	Polymorphism	562556	B	I	474	I
22	UniProt	VAR_025457	E	482	G	PCSK9_HUMAN	Polymorphism	141995194	B	E	482	G
23	UniProt	VAR_073657	E	482	Q	PCSK9_HUMAN	Unclassified	---	B	E	482	Q
24	UniProt	VAR_058534	R	496	W	PCSK9_HUMAN	Disease (HCHOLA3)	374603772	B	R	496	W
25	UniProt	VAR_025458	F	515	L	PCSK9_HUMAN	Polymorphism	---	B	F	515	L
26	UniProt	VAR_058535	A	522	T	PCSK9_HUMAN	Polymorphism	777300852	B	A	522	T
27	UniProt	VAR_021340	H	553	R	PCSK9_HUMAN	Polymorphism	28362270	B	H	553	R
28	UniProt	VAR_025459	Q	554	E	PCSK9_HUMAN	Polymorphism	149311926	B	Q	554	E
29	UniProt	VAR_058536	P	616	L	PCSK9_HUMAN	Polymorphism	755750316	B	P	616	L
30	UniProt	VAR_021341	Q	619	P	PCSK9_HUMAN	Polymorphism	28362277	B	Q	619	P

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

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

Asymmetric/Biological Unit (12, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000302118	1b	ENSE00001884398	chr1:55505221-55505717	497	PCSK9_HUMAN	1-69	69	1	A:61-69 -	9 -
1.2	ENST00000302118	2	ENSE00001279167	chr1:55509516-55509707	192	PCSK9_HUMAN	70-133	64	1	A:70-133 -	64 -
1.3	ENST00000302118	3	ENSE00001279161	chr1:55512196-55512319	124	PCSK9_HUMAN	134-175	42	2	A:134-152 B:153-167	19 15
1.4c	ENST00000302118	4c	ENSE00001279157	chr1:55517951-55518084	134	PCSK9_HUMAN	175-219	45	1	- B:176-212	- 37
1.5	ENST00000302118	5	ENSE00001279150	chr1:55518323-55518464	142	PCSK9_HUMAN	220-267	48	1	- B:220-267	- 48
1.6	ENST00000302118	6	ENSE00001279145	chr1:55521666-55521862	197	PCSK9_HUMAN	267-332	66	1	- B:267-332	- 66
1.7a	ENST00000302118	7a	ENSE00001156685	chr1:55523004-55523187	184	PCSK9_HUMAN	333-394	62	1	- B:333-394	- 62
1.8	ENST00000302118	8	ENSE00001139624	chr1:55523709-55523882	174	PCSK9_HUMAN	394-452	59	1	- B:394-452 (gaps)	- 59
1.9	ENST00000302118	9	ENSE00001279131	chr1:55524172-55524320	149	PCSK9_HUMAN	452-501	50	1	- B:452-501	- 50
1.10	ENST00000302118	10	ENSE00001338737	chr1:55525159-55525336	178	PCSK9_HUMAN	502-561	60	1	- B:502-561	- 60
1.11	ENST00000302118	11	ENSE00001338722	chr1:55527048-55527229	182	PCSK9_HUMAN	561-621	61	1	- B:561-621 (gaps)	- 61
1.12b	ENST00000302118	12b	ENSE00001922690	chr1:55529042-55530525	1484	PCSK9_HUMAN	622-692	71	1	- B:622-682 (gaps)	- 61

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:92
 aligned with PCSK9_HUMAN | Q8NBP7 from UniProtKB/Swiss-Prot  Length:692

    Alignment length:92
                                    70        80        90       100       110       120       130       140       150  
          PCSK9_HUMAN    61 TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ 152
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------Inhibitor_I9-2qtwA01 A:77-152                                                Pfam domains
         Sec.struct. author ..eee...hhh.eeeeeeeeee....hhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee.hhhhhhhhhh...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------I---------------C------------R-------A------------R-G----------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1bExon 1.2  PDB: A:70-133 UniProt: 70-133                         Exon 1.3            Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2qtw A  61 TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ 152
                                    70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:486
 aligned with PCSK9_HUMAN | Q8NBP7 from UniProtKB/Swiss-Prot  Length:692

    Alignment length:530
                                   162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682
          PCSK9_HUMAN   153 SIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAVARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEGAVTAVAICCRSR 682
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------        -----Peptidase_S8-2qtwB01 B:181-443                                                                                                                                                                                                                                         ------  ------------------------------------------------------------------------------------------------------------------------            ---------------------------------  ---------------------  ------------------           ------------ Pfam domains
         Sec.struct. author ..hhhhhhh......--------.....eeeeee.............eeeeeee......-------....hhhhhhhhhhhhh.........eeeeee......eeehhhhhhhhhhhhhhhhhh....eeeee.eeee.hhhhhhhhhhhhhh..eeeee......hhh.ee.......eeeeee.......ee..ee........eeee...eeee.......eeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee...hhhhhhhhhh.....ee........--....eeeeee..........eeee......eeeeeeee.....eeeeeeeee..eeeeeeee.......eeeeeeee....eeeeeee........eeee......eeeeeeee......------------...eeee....eeeeeeee...eeeeeeeeee.--..eeeee.....eeeeeee..--..eeeeeee..eeeeee.-----------.eeeeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) ----K-------------------------------------------------------------------------------W-D-------------F-------------------------------------------------------------------------------------------------------H----------------H----------------N--S----------------------Q-------S-----------------T--------D----------------W----I-------G-------------W------------------L------T------------------------------RE-------------------------------------------------------------L--P--------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-----------------------------------------------------------------------------------------------------------Q-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:153-16--------------------------------------------Exon 1.5  PDB: B:220-267 UniProt: 220-267       -----------------------------------------------------------------Exon 1.7a  PDB: B:333-394 UniProt: 333-394                    ---------------------------------------------------------Exon 1.9  PDB: B:452-501 UniProt: 452-501         Exon 1.10  PDB: B:502-561 UniProt: 502-561                  ------------------------------------------------------------Exon 1.12b  PDB: B:622-682 (gaps) UniProt: 622-692            Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.4c  PDB: B:176-212 UniProt: 175-219   -----------------------------------------------Exon 1.6  PDB: B:267-332 UniProt: 267-332                         -------------------------------------------------------------Exon 1.8  PDB: B:394-452 (gaps) UniProt: 394-452           ------------------------------------------------------------------------------------------------------------Exon 1.11  PDB: B:561-621 (gaps) UniProt: 561-621            ------------------------------------------------------------- Transcript 1 (2)
                 2qtw B 153 SIPWNLERITPPRYR--------GGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEED-------ASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTH--GWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDL------------QPNQCVGHREASIHASCCHAPGLECKVKEHGIP--QEQVTVACEEGWTLTGCSALP--SHVLGAYAVDNTCVVRSR-----------AVTAVAICCRSR 682
                                   162    |    -   |   182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442      |452       462       472       482       492       502       512       522       532       542       552       562        |-         - |     592       602       612   |  |622       632      |642       652      |  -       672       682
                                        167      176                                 212     220                                                                                                                                                                                                                                  449  |                                                                                                                    571          584                             616  |                 639  |              659         671           
                                                                                                                                                                                                                                                                                                                                     452                                                                                                                                                                    619                    642

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 2QTW)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Inhibitor_I9] (12)

Family: Inhibitor_I9 (12)

Homo sapiens (Human) (10)

Inhibitor_I9-2qtwA01

A:77-152

Clan: no clan defined [family: Peptidase_S8] (104)

Family: Peptidase_S8 (104)

Homo sapiens (Human) (10)

Peptidase_S8-2qtwB01

B:181-443

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PCSK9_HUMAN | Q8NBP7)

molecular function
	GO:0034185	apolipoprotein binding	Interacting selectively and non-covalently with an apolipoprotein, the protein component of a lipoprotein complex.
	GO:0034190	apolipoprotein receptor binding	Interacting selectively and non-covalently with an apolipoprotein receptor.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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:0050750	low-density lipoprotein particle receptor binding	Interacting selectively and non-covalently with a low-density lipoprotein receptor.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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:0043621	protein self-association	Interacting selectively and non-covalently with a domain within the same polypeptide.
	GO:0030547	receptor inhibitor activity	The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is decreased.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0019871	sodium channel inhibitor activity	Stops, prevents, or reduces the activity of a sodium channel.
	GO:0034189	very-low-density lipoprotein particle binding	Interacting selectively and non-covalently with a very-low-density lipoprotein particle, a triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm.
	GO:0070326	very-low-density lipoprotein particle receptor binding	Interacting selectively and non-covalently with a very-low-density lipoprotein receptor.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0032869	cellular response to insulin 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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0009267	cellular response to starvation	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 deprivation of nourishment.
	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:0001822	kidney development	The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
	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: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:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0032802	low-density lipoprotein particle receptor catabolic process	The chemical reactions and pathways resulting in the breakdown of a low-density lipoprotein particle receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0032799	low-density lipoprotein receptor particle metabolic process	The chemical reactions and pathways involving low-density lipoprotein receptors.
	GO:0007041	lysosomal transport	The directed movement of substances into, out of or within a lysosome.
	GO:0010989	negative regulation of low-density lipoprotein particle clearance	Any process that decreases the rate, frequency or extent of low-density lipoprotein particle clearance. Low-density lipoprotein particle clearance is the process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
	GO:2000272	negative regulation of receptor activity	Any process that stops, prevents or reduces the frequency, rate or extent of receptor activity.
	GO:0001920	negative regulation of receptor recycling	Any process that stops, prevents, or reduces the rate of receptor recycling.
	GO:2000650	negative regulation of sodium ion transmembrane transporter activity	Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transporter activity.
	GO:0022008	neurogenesis	Generation of cells within the nervous system.
	GO:0030182	neuron differentiation	The process in which a relatively unspecialized cell acquires specialized features of a neuron.
	GO:0006644	phospholipid metabolic process	The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.
	GO:0032805	positive regulation of low-density lipoprotein particle receptor catabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of low-density lipoprotein particle receptors.
	GO:0043525	positive regulation of neuron apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
	GO:0002092	positive regulation of receptor internalization	Any process that activates or increases the frequency, rate or extent of receptor internalization.
	GO:0016540	protein autoprocessing	Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0032803	regulation of low-density lipoprotein particle receptor catabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of low-density lipoprotein particle receptors.
	GO:0043523	regulation of neuron apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons.
	GO:0010469	regulation of receptor activity	Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	GO:0006641	triglyceride metabolic process	The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
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:1990667	PCSK9-AnxA2 complex	A protein complex consisting of the serine protease PCSK9 (Proprotein convertase subtilisin/kexin-9) and Annexin A2 (AnxA2).
	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:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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: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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0031232	extrinsic component of external side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its external surface, but not integrated into the hydrophobic region.
	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: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: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:0005791	rough endoplasmic reticulum	The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.

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	2qtw
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(no "Related Entries Specified in the PDB File" available for 2QTW)

Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (12, 12)

Cis Peptide Bonds (1, 1)

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Exons (12, 13)

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