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- PDB-3h3g: Crystal structure of the extracellular domain of the human parath... -

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Basic information

Entry
Database: PDB / ID: 3h3g
TitleCrystal structure of the extracellular domain of the human parathyroid hormone receptor (PTH1R) in complex with parathyroid hormone-related protein (PTHrP)
Components
  • Fusion protein of Maltose-binding periplasmic domain and human parathyroid hormone receptor extracellular domain
  • Parathyroid hormone-related protein
KeywordsMEMBRANE PROTEIN / GPCR / extracellular domain / PTHrP / PTH / PTHR1 / Sugar transport / Transport / Hormone
Function / homology
Function and homology information


negative regulation of chondrocyte development / regulation of chondrocyte differentiation / adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway / parathyroid hormone receptor activity / cAMP metabolic process / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / negative regulation of chondrocyte differentiation / osteoblast development / peptide hormone receptor binding ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway / parathyroid hormone receptor activity / cAMP metabolic process / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / negative regulation of chondrocyte differentiation / osteoblast development / peptide hormone receptor binding / bone mineralization / detection of maltose stimulus / maltose transport complex / positive regulation of inositol phosphate biosynthetic process / carbohydrate transport / peptide hormone binding / epidermis development / chondrocyte differentiation / carbohydrate transmembrane transporter activity / bone resorption / maltose binding / maltose transport / maltodextrin transmembrane transport / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cell maturation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / skeletal system development / female pregnancy / hormone activity / G protein-coupled receptor activity / intracellular calcium ion homeostasis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cell-cell signaling / outer membrane-bounded periplasmic space / adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of gene expression / G alpha (s) signalling events / in utero embryonic development / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / periplasmic space / cell surface receptor signaling pathway / signaling receptor complex / cell population proliferation / apical plasma membrane / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / DNA damage response / nucleolus / Golgi apparatus / protein homodimerization activity / : / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / : ...Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsPioszak, A.A. / Xu, H.E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural basis for parathyroid hormone-related protein binding to the parathyroid hormone receptor and design of conformation-selective peptides.
Authors: Pioszak, A.A. / Parker, N.R. / Gardella, T.J. / Xu, H.E.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion protein of Maltose-binding periplasmic domain and human parathyroid hormone receptor extracellular domain
B: Parathyroid hormone-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4043
Polymers63,0622
Non-polymers3421
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-13 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.041, 84.041, 164.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Fusion protein of Maltose-binding periplasmic domain and human parathyroid hormone receptor extracellular domain / Maltodextrin-binding protein / MMBP / PTH/PTHr receptor / PTH/PTHrP type I receptor


Mass: 60297.941 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: b4034, JW3994, malE, PTHR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q03431
#2: Protein/peptide Parathyroid hormone-related protein / PTH-rP / PTHrP / PLP / Osteostatin


Mass: 2764.239 Da / Num. of mol.: 1 / Fragment: residues 12-34 / Source method: obtained synthetically / References: UniProt: P12272
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 7.5% PEG 2000, 13% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 40884 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 17 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 29.66
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.25 / % possible all: 55

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3C4M

3c4m


Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.784 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2065 5.1 %RANDOM
Rwork0.193 ---
obs0.195 40693 91.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.37 Å2 / Biso mean: 44.976 Å2 / Biso min: 28.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2--1.48 Å20 Å2
3----2.95 Å2
Refinement stepCycle: LAST / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 23 237 4149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224016
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9595452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6645489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8724.728184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0615663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8281517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023059
X-RAY DIFFRACTIONr_nbd_refined0.1980.21805
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.213
X-RAY DIFFRACTIONr_mcbond_it0.7131.52529
X-RAY DIFFRACTIONr_mcangle_it1.09723934
X-RAY DIFFRACTIONr_scbond_it1.85531731
X-RAY DIFFRACTIONr_scangle_it2.8584.51518
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 87 -
Rwork0.262 1654 -
all-1741 -
obs--54.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.61210.5824-1.0511.5924-1.16572.4972-0.02360.0930.01490.09010.029-0.0224-0.1442-0.1058-0.0055-0.16220.0221-0.0591-0.1217-0.0155-0.213632.8866-1.8562-20.4937
26.57691.14653.8692.8771-0.36099.09590.3881-0.6622-0.55370.1994-0.3967-0.3820.2073-0.05230.0085-0.1159-0.0965-0.0253-0.02530.1466-0.006339.0258-27.7314-58.2677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-344 - 26
2X-RAY DIFFRACTION1A194
3X-RAY DIFFRACTION2A31 - 175
4X-RAY DIFFRACTION2B13 - 35

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