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- PDB-3c4m: Structure of human parathyroid hormone in complex with the extrac... -

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Basic information

Entry
Database: PDB / ID: 3c4m
TitleStructure of human parathyroid hormone in complex with the extracellular domain of its G-protein-coupled receptor (PTH1R)
Components
  • Fusion protein of Maltose-binding periplasmic protein and Parathyroid hormone/parathyroid hormone-related peptide receptor
  • Parathyroid hormone
KeywordsMEMBRANE PROTEIN / parathyroid hormone / G-protein-coupled receptor / Sugar transport / Transport / Cleavage on pair of basic residues / Disease mutation / Secreted / Dwarfism / Glycoprotein / Membrane / Receptor / Transducer / Transmembrane
Function / homology
Function and homology information


type 1 parathyroid hormone receptor binding / parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / hormone-mediated apoptotic signaling pathway / response to parathyroid hormone / parathyroid hormone receptor activity / positive regulation of cell proliferation in bone marrow / magnesium ion homeostasis ...type 1 parathyroid hormone receptor binding / parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / hormone-mediated apoptotic signaling pathway / response to parathyroid hormone / parathyroid hormone receptor activity / positive regulation of cell proliferation in bone marrow / magnesium ion homeostasis / positive regulation of signal transduction / macromolecule biosynthetic process / response to fibroblast growth factor / phosphate ion homeostasis / cAMP metabolic process / response to vitamin D / G protein-coupled peptide receptor activity / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / peptide hormone receptor binding / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / bone mineralization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / peptide hormone binding / Rho protein signal transduction / activation of phospholipase C activity / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / positive regulation of glycogen biosynthetic process / chondrocyte differentiation / positive regulation of bone mineralization / response to cadmium ion / homeostasis of number of cells within a tissue / cell maturation / bone resorption / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / skeletal system development / positive regulation of glucose import / response to lead ion / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / intracellular calcium ion homeostasis / : / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / outer membrane-bounded periplasmic space / G alpha (s) signalling events / regulation of gene expression / basolateral plasma membrane / response to ethanol / cell population proliferation / in utero embryonic development / transcription by RNA polymerase II / receptor ligand activity / periplasmic space / cell surface receptor signaling pathway / receptor complex / response to xenobiotic stimulus / apical plasma membrane / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / negative regulation of gene expression / DNA damage response / positive regulation of cell population proliferation / positive regulation of gene expression / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
GPCR, family 2, extracellular hormone receptor domain / Parathyroid hormone / Hormone receptor fold / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain ...GPCR, family 2, extracellular hormone receptor domain / Parathyroid hormone / Hormone receptor fold / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / 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 / Parathyroid hormone / Maltose/maltodextrin-binding periplasmic 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 / Resolution: 1.95 Å
AuthorsPioszak, A.A. / Xu, H.E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Molecular recognition of parathyroid hormone by its G protein-coupled receptor.
Authors: Pioszak, A.A. / Xu, H.E.
History
DepositionJan 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: 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 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.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion protein of Maltose-binding periplasmic protein and Parathyroid hormone/parathyroid hormone-related peptide receptor
B: Fusion protein of Maltose-binding periplasmic protein and Parathyroid hormone/parathyroid hormone-related peptide receptor
C: Parathyroid hormone
D: Parathyroid hormone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3726
Polymers125,6884
Non-polymers6852
Water10,449580
1
A: Fusion protein of Maltose-binding periplasmic protein and Parathyroid hormone/parathyroid hormone-related peptide receptor
C: Parathyroid hormone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1863
Polymers62,8442
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
MethodPISA
2
B: Fusion protein of Maltose-binding periplasmic protein and Parathyroid hormone/parathyroid hormone-related peptide receptor
D: Parathyroid hormone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1863
Polymers62,8442
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.919, 116.791, 78.416
Angle α, β, γ (deg.)90.000, 108.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fusion protein of Maltose-binding periplasmic protein and Parathyroid hormone/parathyroid hormone-related peptide receptor / / Maltodextrin-binding protein / MMBP / PTH/PTHr receptor / PTH/PTHrP type I receptor


Mass: 60297.941 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Genus: Escherichia, Homo / Species: , / Strain: , / Gene: malE, PTHR1, PTHR / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q03431
#2: Protein/peptide Parathyroid hormone / / Parathyrin / PTH / Parathormone


Mass: 2545.959 Da / Num. of mol.: 2 / Fragment: residues 15-34 / Source method: obtained synthetically / References: UniProt: P01270
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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 / Water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PPG P400, 0.1 M NaCacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97869 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 76526 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 31.18 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.13
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.15 / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ANF

1anf


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.261 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3848 5 %RANDOM
Rwork0.186 ---
obs0.188 76488 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.311 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å2-0.34 Å2
2--1.8 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7723 0 46 580 8349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227977
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.95910833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3685972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01825.189370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.481151323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2991528
X-RAY DIFFRACTIONr_chiral_restr0.0840.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026092
X-RAY DIFFRACTIONr_nbd_refined0.1940.23802
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2597
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.225
X-RAY DIFFRACTIONr_mcbond_it0.6091.55038
X-RAY DIFFRACTIONr_mcangle_it0.94327814
X-RAY DIFFRACTIONr_scbond_it1.63633450
X-RAY DIFFRACTIONr_scangle_it2.5124.53019
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 274 -
Rwork0.254 5005 -
all-5279 -
obs--92.03 %
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)
12.25620.25670.62751.63990.23051.54090.09150.05860.012-0.0139-0.1170.00780.04280.25050.0254-0.20280.0090.0274-0.24970.0036-0.2225.207932.72936.2521
22.33510.5794-0.32361.2583-0.27372.90660.0529-0.5278-0.11550.118-0.0692-0.08590.14360.40330.0163-0.0769-0.025-0.01770.1060.0518-0.1919-20.09736.505172.905
34.93810.517-0.15782.6225-0.71455.90680.1922-1.26320.69640.4168-0.2123-0.1726-0.54820.26430.02-0.01-0.1959-0.02850.1173-0.25660.1313.822462.537864.8645
43.03580.30320.46584.50921.22685.5790.20870.01410.1139-0.1275-0.0798-0.0061-0.1042-0.1237-0.1289-0.1677-0.00810.0158-0.36090.0316-0.05-20.71558.84838.6312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-344 - 282 - 374
2X-RAY DIFFRACTION1AE194
3X-RAY DIFFRACTION2BB-340 - 286 - 374
4X-RAY DIFFRACTION2BF194
5X-RAY DIFFRACTION3AA29 - 174375 - 520
6X-RAY DIFFRACTION3CC15 - 351
7X-RAY DIFFRACTION4BB29 - 175375 - 521
8X-RAY DIFFRACTION4DD15 - 351

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