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

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Basic information

Entry
Database: PDB / ID: 4mqw
TitleStructure of follicle-stimulating hormone in complex with the entire ectodomain of its receptor (P31)
Components
  • Follicle-stimulating hormone receptor
  • Follitropin subunit beta
  • Glycoprotein hormones, alpha polypeptide
KeywordsSIGNALING PROTEIN / cystine-knot / leucine-rich repeats / Glycoprotein hormone / GPCR / Sulfation
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 phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / 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 / Ribbon / G-protein coupled receptors family 1 signature. / 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
Chem-JEF / 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: 2.9 Å
AuthorsJiang, X. / Liu, H. / Chen, X. / He, X.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Evidence for Follicle-stimulating Hormone Receptor as a Functional Trimer.
Authors: Jiang, X. / Fischer, D. / Chen, X. / McKenna, S.D. / Liu, H. / Sriraman, V. / Yu, H.N. / Goutopoulos, A. / Arkinstall, S. / He, X.
History
DepositionSep 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Jan 10, 2024Group: Derived calculations / Category: struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein hormones, alpha polypeptide
B: Follitropin subunit beta
X: Follicle-stimulating hormone receptor
D: Glycoprotein hormones, alpha polypeptide
E: Follitropin subunit beta
Y: Follicle-stimulating hormone receptor
G: Glycoprotein hormones, alpha polypeptide
H: Follitropin subunit beta
Z: Follicle-stimulating hormone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,81730
Polymers195,5919
Non-polymers4,22621
Water2,792155
1
A: Glycoprotein hormones, alpha polypeptide
B: Follitropin subunit beta
X: Follicle-stimulating hormone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,55112
Polymers65,1973
Non-polymers1,3549
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-6 kcal/mol
Surface area22070 Å2
MethodPISA
2
D: Glycoprotein hormones, alpha polypeptide
E: Follitropin subunit beta
Y: Follicle-stimulating hormone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3659
Polymers65,1973
Non-polymers1,1686
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-11 kcal/mol
Surface area21460 Å2
MethodPISA
3
G: Glycoprotein hormones, alpha polypeptide
H: Follitropin subunit beta
Z: Follicle-stimulating hormone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9019
Polymers65,1973
Non-polymers1,7046
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-12 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.900, 95.900, 204.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21Y
31Z
12A
22D
32G
13B
23E
33H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115X15 - 279
2115Y15 - 279
3115Z15 - 279
1125A1 - 200
2125D1 - 200
3125G1 - 200
1135B1 - 200
2135E1 - 200
3135H1 - 200

NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 9 molecules ADGBEHXYZ

#1: Protein Glycoprotein hormones, alpha polypeptide


Mass: 11364.014 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGA / 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) / Gene: FSHB / 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: 41332.734 Da / Num. of mol.: 3 / Mutation: C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FSHR, LGR1 / Plasmid: PVLAD6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P23945

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Sugars , 1 types, 15 molecules

#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


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

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Non-polymers , 3 types, 161 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: The FSH-FSHRED complex was concentrated by ultrafiltration to about 10 mg/ml in HBS. 0.1M imidazole and 20% Jeffamine M-600, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 5, 2011
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 46705 / Num. obs: 43220 / % possible obs: 95.5 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 65.88 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.9
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.9-2.95170
2.95-3178.1
3-3.06184
3.06-3.12190.1
3.12-3.19194
3.19-3.27197.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
REFMAC5.5.0066refinement
HKL-3000data reduction
HKL-3000data scaling
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4ay9

4ay9


Resolution: 2.9→24.93 Å / Cor.coef. Fo:Fc: 0.9573 / Cor.coef. Fo:Fc free: 0.9172 / SU B: 45.932 / SU ML: 0.379 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 2233 5.02 %RANDOM
Rwork0.1737 ---
obs0.1769 42207 95.56 %-
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: 86.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.0752 Å20 Å20 Å2
2--2.0752 Å20 Å2
3----4.1503 Å2
Refine analyzeLuzzati coordinate error obs: 0.471 Å
Refinement stepCycle: LAST / Resolution: 2.9→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11405 0 238 155 11798
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911928HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2116216HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4160SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes299HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1706HARMONIC5
X-RAY DIFFRACTIONt_it11928HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2908 150 6.04 %
Rwork0.2551 2334 -
all0.2573 2484 -
obs--95.56 %
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)
12.60240.8088-0.883710.83-3.07484.4039-0.1121-0.0709-0.42980.16650.2038-0.14530.32370.5462-0.0917-0.1911-0.00550.042-0.2429-0.07810.12946.3708-28.9422.105
23.27862.7635-2.62696.451-2.80265.7953-0.04520.2148-0.1757-0.6550.2754-0.6243-0.31240.4667-0.2302-0.1349-0.13290.1736-0.1164-0.10980.039812.865-13.1166-9.1951
38.2629-4.0027-2.18375.31381.79914.24190.033-0.05980.0618-0.1254-0.13420.53560.1969-0.56540.1012-0.3161-0.0599-0.0344-0.0936-0.01730.1097-45.240112.66261.7338
44.2468-3.4376-1.46686.9413.80253.97690.23410.6239-0.3709-0.1891-0.16690.40680.61-0.1499-0.0672-0.14930.002-0.1129-0.0866-0.1007-0.0032-34.5929-0.4749-9.6245
510.73892.53113.41453.48090.29144.7432-0.04040.24380.16160.12550.0732-0.349-0.77140.2023-0.0328-0.0884-0.14010.131-0.19170.06640.183116.717136.68882.1053
68.6414-0.05594.68632.025-0.32084.2521-0.22770.53810.3493-0.0650.20870.163-0.4346-0.32120.019-0.1904-0.07370.1308-0.03850.16880.0407-0.11934.4334-9.2475
73.41511.4235-0.40455.2-0.17483.4431-0.13760.33280.3116-0.06350.39041.13620.204-0.4976-0.2528-0.29-0.11480.0323-0.21230.18350.3554-8.4068-18.31413.0263
84.6995-2.32710.14235.49610.56153.98590.22380.11180.9236-0.45710.0979-0.7236-0.4697-0.0381-0.3216-0.3012-0.02130.1421-0.362-0.02740.1978-28.397420.35432.3733
95.8657-0.21820.04282.2584-0.53674.40830.22770.4575-1.2214-0.15370.1624-0.06150.21780.531-0.3901-0.42230.01080.0013-0.309-0.12260.448214.902418.57593.1734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|92 A|201 - A|202 }A5 - 92
2X-RAY DIFFRACTION1{ A|5 - A|92 A|201 - A|202 }A201 - 202
3X-RAY DIFFRACTION2{ Z|401 - Z|401 B|1 - B|109 B|201 - B|202 }Z401
4X-RAY DIFFRACTION2{ Z|401 - Z|401 B|1 - B|109 B|201 - B|202 }B1 - 109
5X-RAY DIFFRACTION2{ Z|401 - Z|401 B|1 - B|109 B|201 - B|202 }B201 - 202
6X-RAY DIFFRACTION3{ D|4 - D|92 D|201 - D|202 }D4 - 92
7X-RAY DIFFRACTION3{ D|4 - D|92 D|201 - D|202 }D201 - 202
8X-RAY DIFFRACTION4{ E|1 - E|108 E|201 - E|202 }E1 - 108
9X-RAY DIFFRACTION4{ E|1 - E|108 E|201 - E|202 }E201 - 202
10X-RAY DIFFRACTION5{ G|5 - G|92 G|201 - G|202 }G5 - 92
11X-RAY DIFFRACTION5{ G|5 - G|92 G|201 - G|202 }G201 - 202
12X-RAY DIFFRACTION6{ H|1 - H|108 H|201 - H|202 }H1 - 108
13X-RAY DIFFRACTION6{ H|1 - H|108 H|201 - H|202 }H201 - 202
14X-RAY DIFFRACTION7{ X|18 - X|356 X|403 - X|403 }X18 - 356
15X-RAY DIFFRACTION7{ X|18 - X|356 X|403 - X|403 }X403
16X-RAY DIFFRACTION8{ Y|18 - Y|357 Y|402 - Y|402 }Y18 - 357
17X-RAY DIFFRACTION8{ Y|18 - Y|357 Y|402 - Y|402 }Y402
18X-RAY DIFFRACTION9{ Z|18 - Z|356 Z|402 - Z|402 }Z18 - 356
19X-RAY DIFFRACTION9{ Z|18 - Z|356 Z|402 - Z|402 }Z402

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