LDL receptor-mediated endocytic uptake — apoB-100 ligand, LDLR internalization and recycling, PCSK9 degradation control

Low-density lipoprotein (LDL) carries most plasma cholesterol and is cleared mainly by hepatocyte LDL receptors. Each LDL particle contains one apolipoprotein B-100 molecule, whose receptor-binding region is the ligand for the cysteine-rich ligand-binding repeats of the LDL receptor (LDLR) at the cell surface. LDLR-LDL complexes cluster in clathrin-coated pits through the LDLR cytoplasmic NPxY motif (with the adaptor LDLRAP1/ARH in liver) and are internalized by receptor-mediated endocytosis. In the acidic early endosome the receptor releases LDL, which proceeds to lysosomes where cholesteryl esters are hydrolysed and free cholesterol is delivered to the cell; the empty receptor recycles to the plasma membrane for further rounds. Secreted PCSK9 binds the LDLR EGF-A repeat and, after co-internalization, prevents the receptor's acid-induced conformational change so that it is routed to lysosomes and degraded instead of recycling, lowering receptor number and LDL clearance (IDOL/MYLIP provides an intracellular, ubiquitin-dependent degradation route). Loss of LDLR, of the apoB-100 receptor-binding region, or of LDLRAP1, or gain of function of PCSK9, causes familial hypercholesterolaemia; PCSK9 loss of function lowers LDL cholesterol and is the target of PCSK9-inhibitor therapy.

MODULE:ldl_receptor_mediated_endocytosisDRAFTTransport Stepmodules/ldl_receptor_mediated_endocytosis.yaml
receptor-mediated endocytosis involved in cholesterol transportGO:0090118 low-density lipoprotein particle clearanceGO:0034383
GO:0034383
low-density lipoprotein particle clearance
The module is the cellular LDLR route of low-density lipoprotein particle clearance.
Reactome:R-HSA-171122
LDL + LDLR => LDL:LDLR complex
Ligand binding follows human Reactome reaction R-HSA-171122.
Reactome:R-HSA-171141
LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-independent)
Internalization follows human Reactome reaction R-HSA-171141.
Reactome:R-HSA-171106
LDLR:LDL complex => LDLR + LDL
Endosomal ligand release follows human Reactome reaction R-HSA-171106.
Reactome:R-HSA-171087
LDLR [endosome membrane] => LDLR [plasma membrane]
Receptor recycling follows human Reactome reaction R-HSA-171087.
file:human/APOB/APOB-ai-review.yaml
APOB gene review (human)
The ligand step (UniProtKB:P04114, GO:0050750 low-density lipoprotein particle receptor binding) matches the completed human APOB review.
file:human/LDLR/LDLR-ai-review.yaml
LDLR gene review (human)
The receptor step (UniProtKB:P01130, GO:0005041, GO:0090118, clathrin-coated pit / early endosome) matches the completed human LDLR review.
file:human/PCSK9/PCSK9-ai-review.yaml
PCSK9 gene review (human)
The regulatory step (UniProtKB:Q8NBP7, GO:0050750, GO:0032805) matches the completed human PCSK9 review.
Reactome:R-HSA-8865667
LIPA hydrolyses sterol esters to sterols and fatty acids
Lysosomal cholesteryl-ester hydrolysis follows human Reactome reaction R-HSA-8865667.
file:human/LIPA/LIPA-ai-review.yaml
LIPA gene review (human)
The lysosomal hydrolysis step (UniProtKB:P38571, GO:0004771 sterol ester esterase activity, GO:0090122, lysosomal lumen) matches the completed human LIPA review.
5Nodes
4Parts
0Variant Sets
0Variants
4Annotons
3Connections

Executable models all models

Agent-based derived from this module
Agent-based LDL particle clearance and PCSK9 receptor-degradation model
✓ Maximal PCSK9-independent hepatic LDL clearance (complete lysosomal cholesteryl-ester hydrolysis)
✓ PCSK9 gain-of-function / familial hypercholesterolaemia (LDLR degraded; extracellular LDL retention)
✓ LDLR loss-of-function familial hypercholesterolaemia (receptor uptake blocked)
✓ LIPA loss-of-function (Wolman disease / CESD; endolysosomal cholesteryl-ester accumulation)
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Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:ldl_receptor_mediated_endocytosis deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

4 gene-function check(s) reflected in core functions · 0 conflict(s) · 4 evidence or coverage gap(s) (8 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
apob_ldlr_binding APOB (human)
UniProtKB:P04114
Family Representative
low-density lipoprotein particle receptor binding
GO:0050750
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ldlr_receptor LDLR (human)
UniProtKB:P01130
Family Representative
low-density lipoprotein particle receptor activity
GO:0005041
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
pcsk9_ldlr_binding PCSK9 (human)
UniProtKB:Q8NBP7
Family Representative
low-density lipoprotein particle receptor binding
GO:0050750
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
lipa_sterol_esterase LIPA (human)
UniProtKB:P38571
Family Representative
sterol ester esterase activity
GO:0004771
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
apob_ldlr_binding Apolipoprotein B-100
PANTHER:PTHR13769:SF1
Family
low-density lipoprotein particle receptor binding
GO:0050750
Family Review Missing
No supported structured family review is available for PANTHER:PTHR13769:SF1.
ldlr_receptor Low-density lipoprotein receptor
PANTHER:PTHR22722:SF15
Family
low-density lipoprotein particle receptor activity
GO:0005041
Family Review Missing
No supported structured family review is available for PANTHER:PTHR22722:SF15.
pcsk9_ldlr_binding Proprotein convertase subtilisin/kexin type 9
PANTHER:PTHR43806:SF60
Family
low-density lipoprotein particle receptor binding
GO:0050750
Family Review Missing
No supported structured family review is available for PANTHER:PTHR43806:SF60.
lipa_sterol_esterase Lysosomal acid lipase/cholesteryl ester hydrolase
PANTHER:PTHR11005:SF26
Family
sterol ester esterase activity
GO:0004771
Family Review Missing
No supported structured family review is available for PANTHER:PTHR11005:SF26.

Feedback loops (advisory, prose-driven: a regulator counts as "feedback" when its own description says so)

✓ every negative regulator described as feedback has an upstream edge closing the loop.

  • pcsk9_degradation ⊣ ldlr_endocytosis [input]
    pcsk9_degradation is a negative regulator with no upstream edge (not described as feedback)

Gene-review completeness (4/4 grounded genes reviewed)

1 complete review(s) · 2 with deep research · 0 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
APOB P04114 ✓ 126/158 ✗
LDLR P01130 ✓ 180/181 ✓
LIPA P38571 ✓ ✓ ✗
PCSK9 Q8NBP7 ✓ 103/105 ✓

Details

LDL receptor-mediated endocytic uptakeTransport Stepldl_receptor_mediated_endocytosis
receptor-mediated endocytosis involved in cholesterol transportGO:0090118 low-density lipoprotein particle clearanceGO:0034383

Grounded to the completed human reviews of APOB (UniProtKB:P04114), LDLR (P01130) and PCSK9 (Q8NBP7); GO terms are taken from their core_functions. PANTHER subfamily ids are those in each representative's UniProt cross-references, with labels copied from interpro/panther/panther.obo (the PTHR22722:SF15 official name is "LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED"). Reactome reaction ids/titles were checked against the local reactome cache. Members not modelled as parts because no AIGR gene review exists yet: LDLRAP1 (ARH clathrin adaptor required for hepatic LDLR internalization; loss causes autosomal recessive hypercholesterolaemia) and MYLIP (IDOL, LXR-induced E3 ligase that ubiquitinates LDLR for degradation). Part 4 adds the first downstream lysosomal step, cholesteryl-ester hydrolysis by LIPA (completed human LIPA review, P38571; PANTHER PTHR11005:SF26 from the PANTHER human classification), as in Reactome R-HSA-8865667. NPC2/NPC1 export of the released cholesterol from lysosomes is not modelled because neither has a gene review; SREBP2-dependent transcriptional control of LDLR and PCSK9 is upstream regulation, not modelled. ApoE-mediated remnant uptake by LDLR is noted in the LDLR review but kept out of this LDL-specific module.

Connections

apob_ligand -> ldlr_endocytosis Provides Input For
ApoB-100-containing LDL is the ligand bound and internalized by LDLR.
pcsk9_degradation -> ldlr_endocytosis Negatively Regulates
PCSK9 binding prevents LDLR recycling and sends the receptor to lysosomes, reducing LDL uptake.
ldlr_endocytosis -> lipa_ce_hydrolysis Provides Input For
LDL released from the receptor in endosomes reaches lysosomes, where its cholesteryl esters are the substrate of lysosomal acid lipase.
Part 1: receptor ligand on the LDL particle
apoB-100 presents the LDLR-binding surface of LDLMolecular Functionapob_ligand

Annotons

APOB (apoB-100): LDL receptor ligand
apob_ldlr_binding
Participant: Family: Apolipoprotein B-100
Family:
Apolipoprotein B-100PANTHER:PTHR13769:SF1
Representative Members: APOB (human)UniProtKB:P04114

Function

low-density lipoprotein particle receptor bindingGO:0050750

Locations

extracellular regionGO:0005576

The single apoB-100 per LDL particle is the LDLR ligand; receptor-binding-region variants (e.g. R3527Q) cause familial defective apoB-100.

Part 2: receptor binding, internalization, release and recycling
LDLR binds LDL and internalizes it via clathrin-coated pits, then recyclesTransport Stepldlr_endocytosis

Annotons

LDLR: low-density lipoprotein receptor
ldlr_receptor
Participant: Family: Low-density lipoprotein receptor
Family:
Low-density lipoprotein receptorPANTHER:PTHR22722:SF15
Representative Members: LDLR (human)UniProtKB:P01130

Function

low-density lipoprotein particle receptor activityGO:0005041
Substrates: LDL particle (apoB-100)

Processes

receptor-mediated endocytosis involved in cholesterol transportGO:0090118

Locations

clathrin-coated pitGO:0005905 early endosomeGO:0005769

Ligand-binding repeats capture LDL; the NPxY cytoplasmic motif engages clathrin adaptors (LDLRAP1 in hepatocytes); acid-dependent ligand release in endosomes allows receptor recycling. Loss of function = familial hypercholesterolaemia.

Part 3: control of receptor number by lysosomal degradation
PCSK9 binds LDLR EGF-A and diverts it to lysosomal degradationRegulatory Steppcsk9_degradation

Annotons

PCSK9: secreted LDLR-degradation chaperone
pcsk9_ldlr_binding
Participant: Family: Proprotein convertase subtilisin/kexin type 9
Family:
Proprotein convertase subtilisin/kexin type 9PANTHER:PTHR43806:SF60
Representative Members: PCSK9 (human)UniProtKB:Q8NBP7

Function

low-density lipoprotein particle receptor bindingGO:0050750

Processes

positive regulation of low-density lipoprotein particle receptor catabolic processGO:0032805

Locations

endosomeGO:0005768

Acts as a non-catalytic chaperone for LDLR degradation (its protease activity is needed only for autoprocessing). Gain of function = familial hypercholesterolaemia; loss of function = low LDL cholesterol; therapeutic target.

Part 4: lysosomal hydrolysis of LDL cholesteryl esters
Lysosomal acid lipase hydrolyses LDL-derived cholesteryl esters to free cholesterolMolecular Functionlipa_ce_hydrolysis

Annotons

LIPA (lysosomal acid lipase): cholesteryl ester hydrolase
lipa_sterol_esterase
Participant: Family: Lysosomal acid lipase/cholesteryl ester hydrolase
Family:
Lysosomal acid lipase/cholesteryl ester hydrolasePANTHER:PTHR11005:SF26
Representative Members: LIPA (human)UniProtKB:P38571

Function

sterol ester esterase activityGO:0004771
Substrates: cholesteryl esters of endocytosed LDL

Processes

cholesterol ester hydrolysis involved in cholesterol transportGO:0090122

Locations

lysosomal lumenGO:0043202

Acid-pH hydrolase that releases free cholesterol (and fatty acid) from the cholesteryl esters of LDL delivered to lysosomes, the step that makes LDL cholesterol available to the cell; it also hydrolyses LDL triacylglycerol. Complete loss = Wolman disease; residual activity = cholesteryl ester storage disease. Export of the released cholesterol by NPC2/NPC1 is downstream and not modelled (no gene reviews).