2FCW - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF A COMPLEX BETWEEN THE PAIR OF THE LDL RECEPTOR LIGAND-BINDING MODULES 3-4 AND THE RECEPTOR ASSOCIATED PROTEIN (RAP).

Authors :   N. Beglova, C. Fisher, S. C. Blacklow

Date :   12 Dec 05 (Deposition) - 16 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.26

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)

Keywords :   Protein-Protein Complex, Rap, Ldlr, Escort Protein, Calcium- Binding, Lipid Transport/Endocytosis/Chaperone Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Fisher, N. Beglova, S. C. Blacklow
Structure Of An Ldlr-Rap Complex Reveals A General Mode For Ligand Recognition By Lipoprotein Receptors
Mol. Cell V. 22 277 2006
PubMed-ID: 16630895 | Reference-DOI: 10.1016/J.MOLCEL.2006.02.021
(for further references see the PDB file header)

Molecule 1 - ALPHA-2-MACROGLOBULIN RECEPTOR-ASSOCIATED PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PDEST15
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	DOMAIN THREE
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ALPHA-2- MRAP, LOW DENSITY LIPOPROTEIN RECEPTOR- RELATED PROTEIN-ASSOCIATED PROTEIN 1, RAP

Molecule 2 - LOW-DENSITY LIPOPROTEIN RECEPTOR
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PMM
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	A PAIR OF LIGAND-BINDING MODULES 3 AND 4
	Gene	:	LDLR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LDL RECEPTOR

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	MPD	5	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	NA	4	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	5	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 10)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	10	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE B:105 , ASP B:108 , ASP B:110 , ASP B:112 , ASP B:118 , GLU B:119	BINDING SITE FOR RESIDUE CA B 3001
02	AC2	SOFTWARE	TRP B:144 , ASP B:147 , ASP B:149 , ASP B:151 , ASP B:157 , GLU B:158	BINDING SITE FOR RESIDUE CA B 3002
03	AC3	SOFTWARE	HOH A:61 , HOH A:73 , GLU A:265 , GLU A:269 , HOH B:5023	BINDING SITE FOR RESIDUE NA A 5001
04	AC4	SOFTWARE	LYS B:86 , GLY B:98 , HOH B:5003 , HOH B:5004 , HOH B:5012	BINDING SITE FOR RESIDUE NA B 5002
05	AC5	SOFTWARE	HOH A:68 , HOH A:110 , ASP A:228 , SER A:232	BINDING SITE FOR RESIDUE NA A 5003
06	AC6	SOFTWARE	HOH A:56 , HOH A:91 , HOH A:121 , LEU A:240 , HOH B:5014	BINDING SITE FOR RESIDUE NA A 5004
07	AC7	SOFTWARE	HIS A:259 , ASP B:151 , GLU B:153	BINDING SITE FOR RESIDUE MPD A 4001
08	AC8	SOFTWARE	HOH A:145 , GLU A:217 , PHE A:218 , ARG A:244 , LYS A:248 , LYS A:298	BINDING SITE FOR RESIDUE MPD A 4002
09	AC9	SOFTWARE	GLN B:133	BINDING SITE FOR RESIDUE MPD B 4003
10	BC1	SOFTWARE	PRO B:129 , ASN B:135 , SER B:137 , GLN B:142	BINDING SITE FOR RESIDUE MPD B 4004
11	BC2	SOFTWARE	ARG A:222 , GLY A:313 , SER A:316 , THR B:87 , CYS B:88 , SER B:89 , GLN B:90	BINDING SITE FOR RESIDUE MPD B 4005

Asymmetric Unit

No.	Residues
1	B:88	-	B:100
2	B:95	-	B:113
3	B:107	-	B:122
4	B:127	-	B:139
5	B:134	-	B:152
6	B:146	-	B:163

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

Asymmetric Unit (25, 25)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_005316	C	109	R	LDLR_HUMAN	Polymorphism	140807148	B	C	88	R
02	UniProt	VAR_005317	C	116	R	LDLR_HUMAN	Disease (FH)	879254482	B	C	95	R
03	UniProt	VAR_062371	C	134	F	LDLR_HUMAN	Disease (FH)	879254514	B	C	113	F
04	UniProt	VAR_062372	C	134	W	LDLR_HUMAN	Disease (FH)	879254515	B	C	113	W
05	UniProt	VAR_065780	D	139	H	LDLR_HUMAN	Polymorphism	879254517	B	D	118	H
06	UniProt	VAR_005318	E	140	K	LDLR_HUMAN	Disease (FH)	748944640	B	E	119	K
07	UniProt	VAR_072828	C	143	R	LDLR_HUMAN	Disease (FH)	875989901	B	C	122	R
08	UniProt	VAR_072829	C	148	Y	LDLR_HUMAN	Disease (FH)	879254526	B	C	127	Y
09	UniProt	VAR_005319	C	155	G	LDLR_HUMAN	Polymorphism	879254535	B	C	134	G
10	UniProt	VAR_072830	C	155	Y	LDLR_HUMAN	Disease (FH)	879254536	B	C	134	Y
11	UniProt	VAR_005320	C	160	Y	LDLR_HUMAN	Unclassified (FH)	879254541	B	C	139	Y
12	UniProt	VAR_072831	D	168	A	LDLR_HUMAN	Unclassified (FH)	---	B	D	147	A
13	UniProt	VAR_005321	D	168	H	LDLR_HUMAN	Disease (FH)	200727689	B	D	147	H
14	UniProt	VAR_005322	D	168	N	LDLR_HUMAN	Disease (FH)	200727689	B	D	147	N
15	UniProt	VAR_005323	D	168	Y	LDLR_HUMAN	Disease (FH)	200727689	B	D	147	Y
16	UniProt	VAR_013950	D	172	H	LDLR_HUMAN	Polymorphism	879254554	B	D	151	H
17	UniProt	VAR_072832	D	172	N	LDLR_HUMAN	Disease (FH)	879254554	B	D	151	N
18	UniProt	VAR_005324	C	173	R	LDLR_HUMAN	Polymorphism	879254558	B	C	152	R
19	UniProt	VAR_005325	C	173	W	LDLR_HUMAN	Disease (FH)	769318035	B	C	152	W
20	UniProt	VAR_005326	D	175	N	LDLR_HUMAN	Disease (FH)	121908033	B	D	154	N
21	UniProt	VAR_007981	D	175	Y	LDLR_HUMAN	Disease (FH)	121908033	B	D	154	Y
22	UniProt	VAR_005327	S	177	L	LDLR_HUMAN	Disease (FH)	121908026	B	S	156	L
23	UniProt	VAR_072833	C	184	W	LDLR_HUMAN	Disease (FH)	879254571	B	C	163	W
24	UniProt	VAR_013951	C	184	Y	LDLR_HUMAN	Disease (FH)	121908039	B	C	163	Y
25	UniProt	VAR_011821	V	311	M	AMRP_HUMAN	Polymorphism	1800493	A	V	277	M

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

Biological Unit 1 (25, 25)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_005316	C	109	R	LDLR_HUMAN	Polymorphism	140807148	B	C	88	R
02	UniProt	VAR_005317	C	116	R	LDLR_HUMAN	Disease (FH)	879254482	B	C	95	R
03	UniProt	VAR_062371	C	134	F	LDLR_HUMAN	Disease (FH)	879254514	B	C	113	F
04	UniProt	VAR_062372	C	134	W	LDLR_HUMAN	Disease (FH)	879254515	B	C	113	W
05	UniProt	VAR_065780	D	139	H	LDLR_HUMAN	Polymorphism	879254517	B	D	118	H
06	UniProt	VAR_005318	E	140	K	LDLR_HUMAN	Disease (FH)	748944640	B	E	119	K
07	UniProt	VAR_072828	C	143	R	LDLR_HUMAN	Disease (FH)	875989901	B	C	122	R
08	UniProt	VAR_072829	C	148	Y	LDLR_HUMAN	Disease (FH)	879254526	B	C	127	Y
09	UniProt	VAR_005319	C	155	G	LDLR_HUMAN	Polymorphism	879254535	B	C	134	G
10	UniProt	VAR_072830	C	155	Y	LDLR_HUMAN	Disease (FH)	879254536	B	C	134	Y
11	UniProt	VAR_005320	C	160	Y	LDLR_HUMAN	Unclassified (FH)	879254541	B	C	139	Y
12	UniProt	VAR_072831	D	168	A	LDLR_HUMAN	Unclassified (FH)	---	B	D	147	A
13	UniProt	VAR_005321	D	168	H	LDLR_HUMAN	Disease (FH)	200727689	B	D	147	H
14	UniProt	VAR_005322	D	168	N	LDLR_HUMAN	Disease (FH)	200727689	B	D	147	N
15	UniProt	VAR_005323	D	168	Y	LDLR_HUMAN	Disease (FH)	200727689	B	D	147	Y
16	UniProt	VAR_013950	D	172	H	LDLR_HUMAN	Polymorphism	879254554	B	D	151	H
17	UniProt	VAR_072832	D	172	N	LDLR_HUMAN	Disease (FH)	879254554	B	D	151	N
18	UniProt	VAR_005324	C	173	R	LDLR_HUMAN	Polymorphism	879254558	B	C	152	R
19	UniProt	VAR_005325	C	173	W	LDLR_HUMAN	Disease (FH)	769318035	B	C	152	W
20	UniProt	VAR_005326	D	175	N	LDLR_HUMAN	Disease (FH)	121908033	B	D	154	N
21	UniProt	VAR_007981	D	175	Y	LDLR_HUMAN	Disease (FH)	121908033	B	D	154	Y
22	UniProt	VAR_005327	S	177	L	LDLR_HUMAN	Disease (FH)	121908026	B	S	156	L
23	UniProt	VAR_072833	C	184	W	LDLR_HUMAN	Disease (FH)	879254571	B	C	163	W
24	UniProt	VAR_013951	C	184	Y	LDLR_HUMAN	Disease (FH)	121908039	B	C	163	Y
25	UniProt	VAR_011821	V	311	M	AMRP_HUMAN	Polymorphism	1800493	A	V	277	M

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

Biological Unit 2 (25, 50)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_005316	C	109	R	LDLR_HUMAN	Polymorphism	140807148	B	C	88	R
02	UniProt	VAR_005317	C	116	R	LDLR_HUMAN	Disease (FH)	879254482	B	C	95	R
03	UniProt	VAR_062371	C	134	F	LDLR_HUMAN	Disease (FH)	879254514	B	C	113	F
04	UniProt	VAR_062372	C	134	W	LDLR_HUMAN	Disease (FH)	879254515	B	C	113	W
05	UniProt	VAR_065780	D	139	H	LDLR_HUMAN	Polymorphism	879254517	B	D	118	H
06	UniProt	VAR_005318	E	140	K	LDLR_HUMAN	Disease (FH)	748944640	B	E	119	K
07	UniProt	VAR_072828	C	143	R	LDLR_HUMAN	Disease (FH)	875989901	B	C	122	R
08	UniProt	VAR_072829	C	148	Y	LDLR_HUMAN	Disease (FH)	879254526	B	C	127	Y
09	UniProt	VAR_005319	C	155	G	LDLR_HUMAN	Polymorphism	879254535	B	C	134	G
10	UniProt	VAR_072830	C	155	Y	LDLR_HUMAN	Disease (FH)	879254536	B	C	134	Y
11	UniProt	VAR_005320	C	160	Y	LDLR_HUMAN	Unclassified (FH)	879254541	B	C	139	Y
12	UniProt	VAR_072831	D	168	A	LDLR_HUMAN	Unclassified (FH)	---	B	D	147	A
13	UniProt	VAR_005321	D	168	H	LDLR_HUMAN	Disease (FH)	200727689	B	D	147	H
14	UniProt	VAR_005322	D	168	N	LDLR_HUMAN	Disease (FH)	200727689	B	D	147	N
15	UniProt	VAR_005323	D	168	Y	LDLR_HUMAN	Disease (FH)	200727689	B	D	147	Y
16	UniProt	VAR_013950	D	172	H	LDLR_HUMAN	Polymorphism	879254554	B	D	151	H
17	UniProt	VAR_072832	D	172	N	LDLR_HUMAN	Disease (FH)	879254554	B	D	151	N
18	UniProt	VAR_005324	C	173	R	LDLR_HUMAN	Polymorphism	879254558	B	C	152	R
19	UniProt	VAR_005325	C	173	W	LDLR_HUMAN	Disease (FH)	769318035	B	C	152	W
20	UniProt	VAR_005326	D	175	N	LDLR_HUMAN	Disease (FH)	121908033	B	D	154	N
21	UniProt	VAR_007981	D	175	Y	LDLR_HUMAN	Disease (FH)	121908033	B	D	154	Y
22	UniProt	VAR_005327	S	177	L	LDLR_HUMAN	Disease (FH)	121908026	B	S	156	L
23	UniProt	VAR_072833	C	184	W	LDLR_HUMAN	Disease (FH)	879254571	B	C	163	W
24	UniProt	VAR_013951	C	184	Y	LDLR_HUMAN	Disease (FH)	121908039	B	C	163	Y
25	UniProt	VAR_011821	V	311	M	AMRP_HUMAN	Polymorphism	1800493	A	V	277	M

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

Asymmetric Unit (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LDLRA_2	PS50068	LDL-receptor class A (LDLRA) domain profile.	LDLR_HUMAN	26-64 67-105 108-144 147-185 196-232 235-271 275-314	2	- - B:87-123 B:126-163 - - -
2	LDLRA_1	PS01209	LDL-receptor class A (LDLRA) domain signature.	LDLR_HUMAN	39-63 82-104 121-143 160-184 209-231 248-270 289-313	2	- - B:100-122 B:139-163 - - -
3	ER_TARGET	PS00014	Endoplasmic reticulum targeting sequence.	AMRP_HUMAN	354-357	1	A:320-320

Biological Unit 1 (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LDLRA_2	PS50068	LDL-receptor class A (LDLRA) domain profile.	LDLR_HUMAN	26-64 67-105 108-144 147-185 196-232 235-271 275-314	2	- - B:87-123 B:126-163 - - -
2	LDLRA_1	PS01209	LDL-receptor class A (LDLRA) domain signature.	LDLR_HUMAN	39-63 82-104 121-143 160-184 209-231 248-270 289-313	2	- - B:100-122 B:139-163 - - -
3	ER_TARGET	PS00014	Endoplasmic reticulum targeting sequence.	AMRP_HUMAN	354-357	1	A:320-320

Biological Unit 2 (3, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LDLRA_2	PS50068	LDL-receptor class A (LDLRA) domain profile.	LDLR_HUMAN	26-64 67-105 108-144 147-185 196-232 235-271 275-314	4	- - B:87-123 B:126-163 - - -
2	LDLRA_1	PS01209	LDL-receptor class A (LDLRA) domain signature.	LDLR_HUMAN	39-63 82-104 121-143 160-184 209-231 248-270 289-313	4	- - B:100-122 B:139-163 - - -
3	ER_TARGET	PS00014	Endoplasmic reticulum targeting sequence.	AMRP_HUMAN	354-357	2	A:320-320

(no "Exon" information available for 2FCW)

Asymmetric 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:106
 aligned with AMRP_HUMAN | P30533 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:106
                                   258       268       278       288       298       308       318       328       338       348      
           AMRP_HUMAN   249 EAEFEEPRVIDLWDLAQSANLTDKELEAFREELKHFEAKIEKHNHYQKQLEIAHEKLRHAESVGDGERVSRSREKHALLEGRTKELGYTVKKHLQDLSGRISRARH 354
               SCOP domains -d2fcwa1 A:216-320 alpha-2-Macroglobulin receptor associated protein (RAP)                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------M------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------E PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2fcw A 215 GAEFEEPRVIDLWDLAQSANLTDKELEAFREELKHFEAKIEKHNHYQKQLEIAHEKLRHAESVGDGERVSRSREKHALLEGRTKELGYTVKKHLQDLSGRISRARH 320
                                   224       234       244       254       264       274       284       294       304       314

Chain B from PDB  Type:PROTEIN  Length:78
 aligned with LDLR_HUMAN | P01130 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:78
                                   116       126       136       146       156       166       176        
           LDLR_HUMAN   107 KTCSQDEFRCHDGKCISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTCIPQLWACDNDPDCEDGSDEWPQRC 184
               SCOP domains d2fcwb1 B:86-124                       d2fcwb2 B:125-163                       SCOP domains
               CATH domains 2fcwB01 B:86-121                    2fcwB02 B:122-163                          CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee.....eee.hhh..............hhhhhhh...eee.....eee.hhh.........hhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --R------R-----------------F----HK--R----Y------G----Y-------A---HR-N-L------W SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------W--------------------Y------------H---NW-Y--------Y SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------------------------------N---------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) -------------------------------------------------------------Y---------------- SAPs(SNPs) (4)
                PROSITE (1) -LDLRA_2  PDB: B:87-123               --LDLRA_2  PDB: B:126-163                PROSITE (1)
                PROSITE (2) --------------LDLRA_1  PDB: B:100-122----------------LDLRA_1  PDB: B:139-163   PROSITE (2)
                 Transcript ------------------------------------------------------------------------------ Transcript
                 2fcw B  86 KTCSQAEFRCHDGKCISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTCIPQLWACDNDPDCEDGSDEWPQRC 163
                                    95       105       115       125       135       145       155

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Low-density Lipoprotein Receptor (15)

Homologous Superfamily: Low-density Lipoprotein Receptor (15)

Human (Homo sapiens) (12)

1a	2fcwB02	B:122-163
1b	2fcwB01	B:86-121

(no "Pfam Domain" information available for 2FCW)

Asymmetric Unit(hide GO term definitions)

Chain A (AMRP_HUMAN | P30533)

molecular function
	GO:0004873	asialoglycoprotein receptor activity	Receiving an asialoglycoprotein, and delivering the asialoglycoprotein into the cell via endocytosis. An asialoglycoprotein is a plasma glycoproteins from which the terminal sialic acid residue on their complex carbohydrate groups has been removed. The asialoglycoprotein receptor recognizes the terminal galactose and N-acetylgalactosamine units of the asialoglycoprotein, the receptor-ligand complex is internalized and transported to a sorting organelle where disassociation occurs before the receptor is recycled to the cell membrane.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0035473	lipase binding	Interacting selectively and non-covalently with any lipase.
	GO:0050750	low-density lipoprotein particle receptor binding	Interacting selectively and non-covalently with a low-density lipoprotein receptor.
	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:0048019	receptor antagonist activity	Interacts with receptors to reduce the action of another ligand, the agonist.
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
	GO:0070326	very-low-density lipoprotein particle receptor binding	Interacting selectively and non-covalently with a very-low-density lipoprotein receptor.
biological process
	GO:1900116	extracellular negative regulation of signal transduction	Any negative regulation of signal transduction that takes place in extracellular region.
	GO:1900222	negative regulation of amyloid-beta clearance	Any process that stops, prevents or reduces the frequency, rate or extent of amyloid-beta clearance.
	GO:0032091	negative regulation of protein binding	Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
	GO:0010916	negative regulation of very-low-density lipoprotein particle clearance	Any process that decreases the rate, frequency or extent of very-low-density lipoprotein particle clearance. Very-low-density lipoprotein particle clearance is the process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
	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: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: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: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: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: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: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:0048237	rough endoplasmic reticulum lumen	The volume enclosed by the membranes of the rough endoplasmic reticulum.
	GO:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

Chain B (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.

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Description

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SS Bonds (6, 6)

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