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- PDB-4ay9: Structure of follicle-stimulating hormone in complex with the ent... -

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Basic information

Entry
Database: PDB / ID: 4ay9
TitleStructure of follicle-stimulating hormone in complex with the entire ectodomain of its receptor
Components
  • FOLLICLE-STIMULATING HORMONE RECEPTOR
  • FOLLITROPIN SUBUNIT BETA
  • GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDEGonadotropin
KeywordsHORMONE/RECEPTOR / HORMONE-RECEPTOR COMPLEX / LEUCINE-RICH REPEATS / LRR / GPCR
Function / homology
Function and homology information


follicle-stimulating hormone receptor activity / progesterone biosynthetic process / follicle-stimulating hormone activity / follicle-stimulating hormone complex / pituitary gonadotropin complex / luteinizing hormone secretion / follicle-stimulating hormone secretion / positive regulation of steroid biosynthetic process / Thyroxine biosynthesis / Mineralocorticoid biosynthesis ...follicle-stimulating hormone receptor activity / progesterone biosynthetic process / follicle-stimulating hormone activity / follicle-stimulating hormone complex / pituitary gonadotropin complex / luteinizing hormone secretion / follicle-stimulating hormone secretion / positive regulation of steroid biosynthetic process / Thyroxine biosynthesis / Mineralocorticoid biosynthesis / Hormone ligand-binding receptors / Glycoprotein hormones / Reactions specific to the complex N-glycan synthesis pathway / Androgen biosynthesis / follicle-stimulating hormone signaling pathway / female gamete generation / Sertoli cell proliferation / gonad development / negative regulation of organ growth / cellular response to follicle-stimulating hormone stimulus / regulation of osteoclast differentiation / regulation of protein kinase A signaling / thyroid hormone generation / G protein-coupled peptide receptor activity / regulation of signaling receptor activity / organ growth / female gonad development / thyroid gland development / positive regulation of bone resorption / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / hormone-mediated signaling pathway / transforming growth factor beta receptor signaling pathway / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / Golgi lumen / male gonad development / G alpha (s) signalling events / spermatogenesis / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Follicle stimulating hormone receptor / Gonadotropin hormone receptor, transmembrane domain / Gonadotropin hormone receptor transmembrane region / Gonadotropin, beta subunit, conserved site / Glycoprotein hormones beta chain signature 1. / Glycoprotein hormones beta chain signature 2. / Glycoprotein hormone beta chain homologues. / Glycoprotein hormone alpha chain / Glycoprotein hormone / Glycoprotein hormones alpha chain signature 1. ...Follicle stimulating hormone receptor / Gonadotropin hormone receptor, transmembrane domain / Gonadotropin hormone receptor transmembrane region / Gonadotropin, beta subunit, conserved site / Glycoprotein hormones beta chain signature 1. / Glycoprotein hormones beta chain signature 2. / Glycoprotein hormone beta chain homologues. / Glycoprotein hormone alpha chain / Glycoprotein hormone / Glycoprotein hormones alpha chain signature 1. / Glycoprotein hormones alpha chain signature 2. / Glycoprotein hormones alpha chain family profile. / Glycoprotein hormone alpha chain homologues. / Gonadotropin, beta subunit / Glycoprotein hormone subunit beta / Cystine-knot domain / Glycoprotein hormone receptor family / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Cystine-knot cytokine / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / G-protein coupled receptors family 1 signature. / Ribbon / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycoprotein hormones alpha chain / Follitropin subunit beta / Follicle-stimulating hormone receptor / Glycoprotein hormones alpha chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJiang, X. / Liu, H. / Chen, X. / He, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of Follicle-Stimulating Hormone in Complex with the Entire Ectodomain of its Receptor.
Authors: Jiang, X. / Liu, H. / Chen, X. / Chen, P. / Fischer, D. / Sriraman, V. / Yu, H.N. / Arkinstall, S. / He, X.
History
DepositionJun 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 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: GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE
B: FOLLITROPIN SUBUNIT BETA
D: GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE
E: FOLLITROPIN SUBUNIT BETA
G: GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE
H: FOLLITROPIN SUBUNIT BETA
X: FOLLICLE-STIMULATING HORMONE RECEPTOR
Y: FOLLICLE-STIMULATING HORMONE RECEPTOR
Z: FOLLICLE-STIMULATING HORMONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,56624
Polymers188,2489
Non-polymers3,31815
Water4,017223
1
D: GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE
E: FOLLITROPIN SUBUNIT BETA
Y: FOLLICLE-STIMULATING HORMONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8558
Polymers62,7493
Non-polymers1,1065
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-17 kcal/mol
Surface area23970 Å2
MethodPISA
2
G: GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE
H: FOLLITROPIN SUBUNIT BETA
Z: FOLLICLE-STIMULATING HORMONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8558
Polymers62,7493
Non-polymers1,1065
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-9.4 kcal/mol
Surface area23720 Å2
MethodPISA
3
A: GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE
B: FOLLITROPIN SUBUNIT BETA
X: FOLLICLE-STIMULATING HORMONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8558
Polymers62,7493
Non-polymers1,1065
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-12.6 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.716, 95.478, 95.675
Angle α, β, γ (deg.)60.30, 80.02, 75.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE / Gonadotropin


Mass: 10183.753 Da / Num. of mol.: 3 / Fragment: RESIDUES 25-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: BACMAN SYSTEM / Plasmid: PVLAD6 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q96QJ4, UniProt: P01215*PLUS
#2: Protein FOLLITROPIN SUBUNIT BETA / FOLLICLE-STIMULATING HORMONE BETA SUBUNIT / FSH-B / FSH-BETA / FOLLITROPIN BETA CHAIN


Mass: 12500.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: BACMAN SYSTEM / Plasmid: PVLAD6 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P01225
#3: Protein FOLLICLE-STIMULATING HORMONE RECEPTOR / / FSH-R / FOLLITROPIN RECEPTOR


Mass: 40065.406 Da / Num. of mol.: 3 / Fragment: RESIDUES 17-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: BACMAN SYSTEM / Plasmid: PVLAD6 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P23945
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.88 Å3/Da / Density % sol: 57.33 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5, 10% (V/V) ISOPROPANOL AND 20% (W/V) POLYETHYLENE GLYCOL 4000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979
DetectorType: MARRESEARCH MX-300 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 70869 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
HKL-3000data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XWD

1xwd


Resolution: 2.5→47.9 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.9 / SU B: 31.462 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26901 3599 5.1 %RANDOM
Rwork0.23508 ---
obs0.23683 67270 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.853 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å2-2.36 Å2-1.13 Å2
2---1.29 Å22.14 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11911 0 210 223 12344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212418
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210929
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.97616879
X-RAY DIFFRACTIONr_angle_other_deg0.669325553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49551495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07524.652561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.929152110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6731563
X-RAY DIFFRACTIONr_chiral_restr0.0740.21937
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022332
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1031.57541
X-RAY DIFFRACTIONr_mcbond_other0.0791.53014
X-RAY DIFFRACTIONr_mcangle_it2.013212285
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.92734877
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1734.54594
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 241 -
Rwork0.4 4885 -
obs--100 %
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)
13.33030.96811.87531.16231.14742.6544-0.07450.02-0.1921-0.11020.1202-0.01810.1580.0185-0.04580.2101-0.00640.04460.02330.01440.07111.4525.9870.28
24.78622.03132.07921.40060.76212.2520.1823-0.3376-0.37910.20430.0349-0.10990.21290.0208-0.21720.23540.0250.00530.13320.01160.072125.54313.00113.038
31.0235-0.1229-0.27350.83720.64160.9176-0.10040.24960.0204-0.10550.07650.0729-0.09830.15510.02380.2403-0.0401-0.01230.12730.00520.009115.89321.991-8.22
42.71751.6691-2.77581.0267-1.70612.84190.19110.18910.31290.10840.14560.2007-0.1284-0.1946-0.33670.4755-0.1357-0.08510.6296-0.45130.6906-14.28515.1252.579
52.7149-0.0585-1.46086.2349-5.56576.78310.07270.00620.46890.92820.93790.925-0.9098-0.809-1.01050.3916-0.00250.05380.4372-0.00620.4884-7.47631.12611.874
61.6194-0.6232-0.07963.6032-0.60040.67520.02660.2029-0.02410.0849-0.0923-0.1032-0.17370.14340.06570.1615-0.01560.01390.13020.0030.017625.75765.217-23.257
71.6107-1.74850.5253.971-0.80530.28750.01430.1771-0.1098-0.1729-0.0651-0.18680.02490.01850.05080.13360.00660.05720.056-0.01370.125232.54846.435-21.59
81.92080.3766-0.19131.3639-0.50060.7371-0.046-0.09110.07840.4169-0.06-0.0835-0.25130.14640.1060.2122-0.0582-0.01530.04350.00120.04428.35563.983-4.474
96.0617-5.61663.73245.2405-3.47622.3780.56150.8365-0.2093-0.2819-0.53520.31370.45970.2187-0.02631.275-0.49920.44171.25680.22580.411-0.54671.591-17.321
107.45560.5368-1.39284.2359-2.93532.2012-0.22070.03531.45460.06291.04410.7629-0.0177-0.7914-0.82350.162-0.18660.13560.757-0.0040.8174-2.95454.282-8.15
112.6435-0.1535-1.2080.6089-0.48442.25870.0055-0.10640.16360.1234-0.0564-0.08510.028-0.11230.05090.1501-0.0374-0.03140.0616-0.03490.083626.12754.57242.373
122.9477-0.0066-2.22130.0527-0.27753.8411-0.03220.06870.31620.0177-0.0652-0.0355-0.16930.25480.09740.1570.0094-0.01020.08350.04710.097338.27658.67526.046
131.4691-0.1147-0.02130.5385-0.64780.7969-0.1155-0.0891-0.2009-0.16630.04-0.04380.2167-0.03980.07550.189-0.00480.0150.00750.00850.037623.51239.05732.072
142.2353-1.4161-2.29670.89861.45432.36060.3953-0.04940.4297-0.21620.0226-0.2853-0.40930.0507-0.41790.5967-0.2118-0.17440.66130.15220.2054-2.19358.14640.581
154.89373.5638-1.26232.7525-1.39237.22-0.77340.6227-0.6229-0.25110.3877-0.6116-1.0336-1.60910.38560.6527-0.0729-0.12790.6506-0.17410.4677-0.08158.61521.172
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 92
2X-RAY DIFFRACTION2B1 - 111
3X-RAY DIFFRACTION3X17 - 278
4X-RAY DIFFRACTION4X279 - 341
5X-RAY DIFFRACTION5X342 - 366
6X-RAY DIFFRACTION6D1 - 92
7X-RAY DIFFRACTION7E1 - 111
8X-RAY DIFFRACTION8Y17 - 278
9X-RAY DIFFRACTION9Y279 - 341
10X-RAY DIFFRACTION10Y342 - 366
11X-RAY DIFFRACTION11G1 - 92
12X-RAY DIFFRACTION12H1 - 111
13X-RAY DIFFRACTION13Z17 - 278
14X-RAY DIFFRACTION14Z279 - 341
15X-RAY DIFFRACTION15Z342 - 366

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