3P5B | pdb_00003p5b

The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation

PDB DOI: https://doi.org/10.2210/pdb3P5B/pdb

Classification: HYDROLASE/LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2010-10-08 Released: 2011-10-26
Deposition Author(s): Lo Surdo, P., Bottomley, M.J., Calzetta, A., Settembre, E.C., Cirillo, A., Pandit, S., Ni, Y., Hubbard, B., Sitlani, A., Carfi, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.298 (Depositor), 0.268 (DCC)
R-Value Work:
0.271 (Depositor), 0.274 (DCC)
R-Value Observed:
0.275 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH.

Lo Surdo, P., Bottomley, M.J., Calzetta, A., Settembre, E.C., Cirillo, A., Pandit, S., Ni, Y.G., Hubbard, B., Sitlani, A., Carfi, A.

(2011) EMBO Rep 12: 1300-1305

PubMed: 22081141 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/embor.2011.205
Primary Citation Related Structures:
3P5B, 3P5C

PubMed Abstract:
The protein PCSK9 (proprotein convertase subtilisin/kexin type 9) is a key regulator of low-density lipoprotein receptor (LDLR) levels and cardiovascular health. We have determined the crystal structure of LDLR bound to PCSK9 at neutral pH. The structure shows LDLR in a new extended conformation. The PCSK9 C-terminal domain is solvent exposed, enabling cofactor binding, whereas the catalytic domain and prodomain interact with LDLR epidermal growth factor(A) and β-propeller domains, respectively. Thus, PCSK9 seems to hold LDLR in an extended conformation and to interfere with conformational rearrangements required for LDLR recycling.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, IRBM P. Angeletti, Via Pontina Km 30.600, Pomezia, Rome I-00040, Italy.

Macromolecule Content

Total Structure Weight: 112.74 kDa
Atom Count: 7,464
Modeled Residue Count: 979
Deposited Residue Count: 1,032
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proprotein convertase subtilisin/kexin type 9	A [auth P]	92	Homo sapiens	Mutation(s): 0 Gene Names: NARC1, PCSK9, PSEC0052 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens) Explore Q8NBP7 Go to UniProtKB: Q8NBP7
PHAROS: Q8NBP7 GTEx: ENSG00000169174
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NBP7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proprotein convertase subtilisin/kexin type 9	B [auth A]	540	Homo sapiens	Mutation(s): 0 Gene Names: LDLR, NARC1, PCSK9, PSEC0052 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens) Explore Q8NBP7 Go to UniProtKB: Q8NBP7
PHAROS: Q8NBP7 GTEx: ENSG00000169174
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NBP7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Low density lipoprotein receptor variant	C [auth L]	400	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01130 (Homo sapiens) Explore P01130 Go to UniProtKB: P01130
PHAROS: P01130 GTEx: ENSG00000130164
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01130
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain E [auth L] SDF format, chain D [auth A] MOL2 format, chain F [auth L] MOL2 format, chain E [auth L] MOL2 format, chain D [auth A] mmCIF format, chain F [auth L] mmCIF format, chain E [auth L] mmCIF format, chain D [auth A]	D [auth A], E [auth L], F [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth L] Focus chain F [auth L] Interactions & Density Focus chain D [auth A] Focus chain E [auth L] Focus chain F [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.298 (Depositor), 0.268 (DCC)
R-Value Work: 0.271 (Depositor), 0.274 (DCC)
R-Value Observed: 0.275 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77	α = 90
b = 109.701	β = 90
c = 178.456	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 1.1: 2015-05-27
Changes: Database references
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary