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- PDB-7l0j: Structure of AMH bound to AMHR2-ECD -

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Basic information

Entry
Database: PDB / ID: 7l0j
TitleStructure of AMH bound to AMHR2-ECD
Components
  • Anti-Muellerian hormone type-2 receptor
  • Muellerian-inhibiting factor
KeywordsSIGNALING PROTEIN / Transforming Growth Factor Beta / Complex / Mullerian Duct Regression
Function / homology
Function and homology information


preantral ovarian follicle growth / anti-Mullerian hormone receptor signaling pathway / anti-Mullerian hormone receptor activity / negative regulation of ovarian follicle development / gonadal mesoderm development / Mullerian duct regression / transforming growth factor beta receptor activity, type II / activin receptor activity / urogenital system development / sex determination ...preantral ovarian follicle growth / anti-Mullerian hormone receptor signaling pathway / anti-Mullerian hormone receptor activity / negative regulation of ovarian follicle development / gonadal mesoderm development / Mullerian duct regression / transforming growth factor beta receptor activity, type II / activin receptor activity / urogenital system development / sex determination / Transcriptional regulation of testis differentiation / : / response to xenobiotic stimulus => GO:0009410 / sex differentiation / activin receptor complex / hormone binding / transforming growth factor beta receptor binding / receptor protein serine/threonine kinase / Signaling by BMP / activin binding / activin receptor signaling pathway / female gonad development / BMP signaling pathway / transforming growth factor beta receptor signaling pathway / growth factor activity / response to organic cyclic compound / hormone activity / cellular response to growth factor stimulus / male gonad development / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / receptor complex / protein phosphorylation / signaling receptor binding / protein serine/threonine kinase activity / positive regulation of gene expression / extracellular space / extracellular region / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Anti-Mullerian hormone, N-terminal / Anti-muellerian hormone receptor, type II / Muellerian-inhibiting factor / Anti-Mullerian hormone, N terminal region / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta (TGF-beta) family / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta, C-terminal ...Anti-Mullerian hormone, N-terminal / Anti-muellerian hormone receptor, type II / Muellerian-inhibiting factor / Anti-Mullerian hormone, N terminal region / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta (TGF-beta) family / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Muellerian-inhibiting factor / Anti-Muellerian hormone type-2 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHart, K.N. / Thompson, T.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)5T32ES007250-30 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structure of AMH bound to AMHR2 provides insight into a unique signaling pair in the TGF-beta family.
Authors: Hart, K.N. / Stocker, W.A. / Nagykery, N.G. / Walton, K.L. / Harrison, C.A. / Donahoe, P.K. / Pepin, D. / Thompson, T.B.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muellerian-inhibiting factor
B: Anti-Muellerian hormone type-2 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1694
Polymers23,8522
Non-polymers3172
Water00
1
A: Muellerian-inhibiting factor
B: Anti-Muellerian hormone type-2 receptor
hetero molecules

A: Muellerian-inhibiting factor
B: Anti-Muellerian hormone type-2 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3398
Polymers47,7044
Non-polymers6354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7550 Å2
ΔGint-44 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.376, 66.376, 125.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Muellerian-inhibiting factor / Anti-Muellerian hormone / AMH / Muellerian-inhibiting substance / MIS


Mass: 11659.373 Da / Num. of mol.: 1 / Fragment: UNP residues 459-560 / Mutation: V515A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMH, MIF / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P03971
#2: Protein Anti-Muellerian hormone type-2 receptor / Anti-Muellerian hormone type II receptor / AMH type II receptor / MIS type II receptor / MRII


Mass: 12192.711 Da / Num. of mol.: 1 / Fragment: UNP residues 18-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMHR2, AMHR, MISR2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q16671, receptor protein serine/threonine kinase
#3: 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.: 1 / Source method: obtained synthetically / 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 6.5, 0.2 M lithium sulfate, 17.5% PEG3350, 5% 1-butyl-3-methylimidazolium trifluoroacetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2020
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→45.68 Å / Num. obs: 9187 / % possible obs: 99.83 % / Redundancy: 6.2 % / Biso Wilson estimate: 64.5 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.12
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 899 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1WAQ & 6MAC

1waq

6mac


Resolution: 2.6→45.68 Å / SU ML: 0.3851 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1444
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 444 4.83 %
Rwork0.2407 8741 -
obs0.2426 9185 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 19 0 1628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271664
X-RAY DIFFRACTIONf_angle_d0.55792262
X-RAY DIFFRACTIONf_chiral_restr0.0413248
X-RAY DIFFRACTIONf_plane_restr0.0049303
X-RAY DIFFRACTIONf_dihedral_angle_d17.5667625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.33991330.31862843X-RAY DIFFRACTION99.97
2.98-3.750.35651450.26372873X-RAY DIFFRACTION99.8
3.75-45.680.22661660.21683025X-RAY DIFFRACTION99.78

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