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- PDB-2xdg: Crystal structure of the extracellular domain of human growth hor... -

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Basic information

Entry
Database: PDB / ID: 2xdg
TitleCrystal structure of the extracellular domain of human growth hormone releasing hormone receptor.
ComponentsGROWTH HORMONE-RELEASING HORMONE RECEPTORGrowth-hormone-releasing hormone receptor
KeywordsSIGNALING PROTEIN / RECEPTOR / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of intracellular steroid hormone receptor signaling pathway / somatotropin secreting cell development / growth hormone-releasing hormone receptor activity / growth hormone secretion / positive regulation of growth hormone secretion / regulation of protein metabolic process / positive regulation of multicellular organism growth / multicellular organismal reproductive process / G protein-coupled peptide receptor activity / hormone metabolic process ...regulation of intracellular steroid hormone receptor signaling pathway / somatotropin secreting cell development / growth hormone-releasing hormone receptor activity / growth hormone secretion / positive regulation of growth hormone secretion / regulation of protein metabolic process / positive regulation of multicellular organism growth / multicellular organismal reproductive process / G protein-coupled peptide receptor activity / hormone metabolic process / nuclear outer membrane / positive regulation of insulin-like growth factor receptor signaling pathway / nuclear inner membrane / growth factor binding / peptide hormone binding / cAMP-mediated signaling / cell maturation / response to glucocorticoid / lactation / secretory granule / G protein-coupled receptor activity / establishment of localization in cell / determination of adult lifespan / response to insulin / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / nuclear matrix / response to estrogen / cellular response to insulin stimulus / G alpha (s) signalling events / cell surface receptor signaling pathway / positive regulation of cell population proliferation / cell surface / membrane / plasma membrane / cytoplasm
Similarity search - Function
GPCR, family 2, growth hormone-releasing hormone receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / 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, growth hormone-releasing hormone receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Growth hormone-releasing hormone receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPike, A.C.W. / Quigley, A. / Barr, A.J. / Burgess Brown, N. / Shrestha, L. / Yang, J. / Chaikuad, A. / Vollmar, M. / Muniz, J.R.C. / von Delft, F. ...Pike, A.C.W. / Quigley, A. / Barr, A.J. / Burgess Brown, N. / Shrestha, L. / Yang, J. / Chaikuad, A. / Vollmar, M. / Muniz, J.R.C. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Carpenter, E.P.
CitationJournal: To be Published
Title: Crystal Structure of the Extracellular Domain of Human Growth Hormone Releasing Hormone Receptor.
Authors: Pike, A.C.W. / Quigley, A. / Barr, A.J. / Burgess Brown, N. / Shrestha, L. / Yang, J. / Chaikuad, A. / Vollmar, M. / Muniz, J.R.C. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, ...Authors: Pike, A.C.W. / Quigley, A. / Barr, A.J. / Burgess Brown, N. / Shrestha, L. / Yang, J. / Chaikuad, A. / Vollmar, M. / Muniz, J.R.C. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Carpenter, E.P.
History
DepositionApr 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GROWTH HORMONE-RELEASING HORMONE RECEPTOR
B: GROWTH HORMONE-RELEASING HORMONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2497
Polymers20,0522
Non-polymers1975
Water1,49583
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-19.6 kcal/mol
Surface area11170 Å2
MethodPISA
2
A: GROWTH HORMONE-RELEASING HORMONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1133
Polymers10,0261
Non-polymers862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: GROWTH HORMONE-RELEASING HORMONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1374
Polymers10,0261
Non-polymers1113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.648, 31.648, 287.138
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein GROWTH HORMONE-RELEASING HORMONE RECEPTOR / Growth-hormone-releasing hormone receptor / GHRH RECEPTOR / GROWTH HORMONE-RELEASING FACTOR GRF RECEPTOR / GRFR


Mass: 10026.190 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 34-123 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-SEC-NH / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q02643
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 50 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASN 50 TO GLN
Sequence detailsSYNTHETIC CONSTRUCT WITH GLYCOSYLATION SITE ASN50 MUTATED TO GLUTAMINE (N50Q)

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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: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 7
Details: 20% PEG6000, 0.15M MGCL2, 10% ETHYLENE GLYCOL, 0.1M TRIS PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9779
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.491
11h+k,-k,-l20.509
ReflectionResolution: 1.95→28.71 Å / Num. obs: 11887 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.6 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0066refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X57

2x57


Resolution: 1.95→27.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.459 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.22288 609 5.2 %RANDOM
Rwork0.16451 ---
obs0.16742 11160 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.414 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å20 Å20 Å2
2--3.07 Å20 Å2
3----6.13 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 11 83 1410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221379
X-RAY DIFFRACTIONr_bond_other_d0.0010.02907
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.971902
X-RAY DIFFRACTIONr_angle_other_deg1.5043.0112216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1145176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0392548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55715174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.967152
X-RAY DIFFRACTIONr_chiral_restr0.080.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
X-RAY DIFFRACTIONr_nbd_refined0.2210.2290
X-RAY DIFFRACTIONr_nbd_other0.1950.2863
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2677
X-RAY DIFFRACTIONr_nbtor_other0.0940.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1320.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.949→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 52 -
Rwork0.197 798 -
obs--97.93 %
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)
16.25631.2656-0.61826.0473-4.5546.82280.15170.1164-0.1621-0.1348-0.0596-0.0810.38040.3789-0.09210.18020.09290.04050.1786-0.0640.116620.3954-7.1955-9.9755
22.8358-0.9376-1.73264.52280.27113.62850.0229-0.0688-0.0507-0.0197-0.012-0.11590.110.132-0.01090.0519-0.0247-0.00540.0614-0.00670.008411.2668-1.5742-4.8077
31.91541.2031-2.17355.0447-7.041214.021-0.00060.190.0928-0.1081-0.0142-0.0892-0.3693-0.06560.01480.1483-0.00330.02680.0958-0.01770.02616.78924.8724-11.6596
41.5269-0.98153.00381.3932-3.81311.13280.25840.3391-0.0779-0.15840.05490.15310.18880.0771-0.31330.23320.0175-0.03790.18180.0310.04670.72570.7677-14.7419
53.6082-0.89862.07777.48371.40034.1228-0.1888-0.0527-0.07560.03490.13090.1649-0.3393-0.14460.0580.13870.04440.03590.27690.01710.1332-16.257114.10019.6288
64.8599-0.2303-0.35170.18910.36518.4431-0.249-0.3264-0.23340.0091-0.13290.0931-0.16-0.44810.38190.1409-0.00430.00730.1531-0.05710.0545-10.01618.85195.8665
74.39181.81064.2622.88993.807111.00820.0709-0.1313-0.04090.18650.0005-0.0922-0.12690.245-0.07140.0997-0.00180.00850.06660.01180.00890.1268.56358.5858
82.1227-0.30864.24090.49840.672412.33510.1809-0.389-0.28130.0970.26210.08760.513-0.1121-0.4430.2516-0.04920.00210.21150.06540.04320.28651.063614.3754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 52
2X-RAY DIFFRACTION2A53 - 79
3X-RAY DIFFRACTION3A80 - 98
4X-RAY DIFFRACTION4A99 - 121
5X-RAY DIFFRACTION5B0 - 52
6X-RAY DIFFRACTION6B53 - 69
7X-RAY DIFFRACTION7B70 - 98
8X-RAY DIFFRACTION8B99 - 121

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