6FJ3 | pdb_00006fj3

High resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist.

PDB DOI: https://doi.org/10.2210/pdb6FJ3/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Pyrococcus abyssi GE5, Equus caballus
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2018-01-19 Released: 2018-11-21
Deposition Author(s): Ehrenmann, J., Schoppe, J., Klenk, C., Rappas, M., Kummer, L., Dore, A.S., Pluckthun, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.248 (Depositor), 0.252 (DCC)
R-Value Work:
0.209 (Depositor), 0.212 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

High-resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist.

Ehrenmann, J., Schoppe, J., Klenk, C., Rappas, M., Kummer, L., Dore, A.S., Pluckthun, A.

(2018) Nat Struct Mol Biol 25: 1086-1092

PubMed: 30455434 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-018-0151-4
Primary Citation Related Structures:
6FJ3

PubMed Abstract:
Parathyroid hormone 1 receptor (PTH1R) is a class B multidomain G-protein-coupled receptor (GPCR) that controls calcium homeostasis. Two endogenous peptide ligands, parathyroid hormone (PTH) and parathyroid hormone-related protein (PTHrP), activate the receptor, and their analogs teriparatide and abaloparatide are used in the clinic to increase bone formation as an effective yet costly treatment for osteoporosis. Activation of PTH1R involves binding of the peptide ligand to the receptor extracellular domain (ECD) and transmembrane domain (TMD), a hallmark of class B GPCRs. Here, we present the crystal structure of human PTH1R in complex with a peptide agonist at 2.5-Å resolution, allowing us to delineate the agonist binding mode for this receptor and revealing molecular details within conserved structural motifs that are critical for class B receptor function. Thus, this study provides structural insight into the function of PTH1R and extends our understanding of this therapeutically important class of GPCRs.

Organizational Affiliation

Department of Biochemistry, University of Zürich, Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 78.58 kDa
Atom Count: 5,352
Modeled Residue Count: 597
Deposited Residue Count: 637
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathyroid hormone/parathyroid hormone-related peptide receptor,Parathyroid hormone/parathyroid hormone-related peptide receptor,GlgA glycogen synthase,Parathyroid hormone/parathyroid hormone-related peptide receptor	A	602	Homo sapiens, Pyrococcus abyssi GE5	Mutation(s): 10 Gene Names: PTH1R, PTHR, PTHR1, PAB2292 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q03431 (Homo sapiens) Explore Q03431 Go to UniProtKB: Q03431
PHAROS: Q03431 GTEx: ENSG00000160801
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2J8 Go to UniProtKB: Q9V2J8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q9V2J8 Q03431
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: Q03431-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathyroid hormone	B	35	Equus caballus	Mutation(s): 5 Gene Names: PTH Membrane Entity: Yes
UniProt
Find proteins for Q27IM2 (Equus caballus) Explore Q27IM2 Go to UniProtKB: Q27IM2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q27IM2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLA Query on OLA Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A] mmCIF format, chain S [auth A]	S [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A] mmCIF format, chain T [auth A]	T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]

Modified Residues 4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM Query on YCM	A	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃ S		CYS
AC5 Query on AC5	B	PEPTIDE LINKING	C₆ H₁₁ N O₂		--
AIB Query on AIB	B	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
HRG Query on HRG	B	L-PEPTIDE LINKING	C₇ H₁₆ N₄ O₂		ARG
NLE Query on NLE	B	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.248 (Depositor), 0.252 (DCC)
R-Value Work: 0.209 (Depositor), 0.212 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.115	α = 80.63
b = 52.864	β = 83.76
c = 111.874	γ = 79.16

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2018-11-28
Changes: Data collection, Database references
Version 1.2: 2018-12-19
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary