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- PDB-5jhw: Crystal Structure of the GDF11:Follistatin 288 complex -

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Basic information

Entry
Database: PDB / ID: 5jhw
TitleCrystal Structure of the GDF11:Follistatin 288 complex
Components
  • Follistatin
  • Growth/differentiation factor 11
KeywordsCYTOKINE/Signaling Protein / GDF11 / follistatin / TGFbeta / Ligand / CYTOKINE-Signaling Protein complex
Function / homology
Function and homology information


spinal cord anterior/posterior patterning / type B pancreatic cell maturation / negative regulation of amacrine cell differentiation / activin receptor antagonist activity / Antagonism of Activin by Follistatin / amacrine cell differentiation / ameloblast differentiation / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation ...spinal cord anterior/posterior patterning / type B pancreatic cell maturation / negative regulation of amacrine cell differentiation / activin receptor antagonist activity / Antagonism of Activin by Follistatin / amacrine cell differentiation / ameloblast differentiation / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation / camera-type eye morphogenesis / activin binding / pattern specification process / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / metanephros development / heparan sulfate proteoglycan binding / ureteric bud development / hair follicle morphogenesis / female gonad development / negative regulation of epithelial cell differentiation / odontogenesis of dentin-containing tooth / mesoderm development / roof of mouth development / positive regulation of SMAD protein signal transduction / keratinocyte proliferation / BMP signaling pathway / hematopoietic progenitor cell differentiation / cytokine activity / skeletal system development / growth factor activity / nervous system development / cell differentiation / cell population proliferation / negative regulation of cell population proliferation / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / : / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. / Follistatin-like, N-terminal ...Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / : / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Kazal domain superfamily / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Cystine-knot cytokine / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / PHOSPHATE ION / Growth/differentiation factor 11 / Follistatin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWalker, R.G. / Thompson, T.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM114640 United States
Muscular Dystrophy Association240087 United States
American Heart Association12PRE11790027 United States
CitationJournal: BMC Biol. / Year: 2017
Title: Structural basis for potency differences between GDF8 and GDF11.
Authors: Walker, R.G. / Czepnik, M. / Goebel, E.J. / McCoy, J.C. / Vujic, A. / Cho, M. / Oh, J. / Aykul, S. / Walton, K.L. / Schang, G. / Bernard, D.J. / Hinck, A.P. / Harrison, C.A. / Martinez- ...Authors: Walker, R.G. / Czepnik, M. / Goebel, E.J. / McCoy, J.C. / Vujic, A. / Cho, M. / Oh, J. / Aykul, S. / Walton, K.L. / Schang, G. / Bernard, D.J. / Hinck, A.P. / Harrison, C.A. / Martinez-Hackert, E. / Wagers, A.J. / Lee, R.T. / Thompson, T.B.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 11
B: Growth/differentiation factor 11
C: Follistatin
D: Follistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,73614
Polymers88,1274
Non-polymers1,60910
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-76 kcal/mol
Surface area39860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.960, 59.080, 288.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNSERSERchain AAA1 - 1091 - 109
21ASNASNSERSERchain BBB1 - 1091 - 109
12GLYGLYASNASNchain CCC1 - 2881 - 288
22GLYGLYASNASNchain DDD1 - 2881 - 288

NCS ensembles :
ID
1
2

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Components

#1: Protein Growth/differentiation factor 11 / GDF-11 / Bone morphogenetic protein 11 / BMP-11


Mass: 12471.309 Da / Num. of mol.: 2 / Fragment: UNP residues 299-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF11, BMP11 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O95390
#2: Protein Follistatin / FS / Activin-binding protein


Mass: 31592.205 Da / Num. of mol.: 2 / Fragment: UNP residues 30-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FST / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19883
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 100mM Phosphate/Citrate pH 4.2, 14% EtOH, 1% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03321 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.2→72.11 Å / Num. obs: 49861 / % possible obs: 100 % / Redundancy: 3.7 % / CC1/2: 0.74 / Rmerge(I) obs: 0.076 / Net I/σ(I): 10
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.519 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HH2

3hh2


Resolution: 2.35→41.276 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.04
RfactorNum. reflection% reflection
Rfree0.2468 2120 5.17 %
Rwork0.2024 --
obs0.2047 40978 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.58 Å2 / Biso mean: 60.65 Å2 / Biso min: 25.32 Å2
Refinement stepCycle: final / Resolution: 2.35→41.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6011 0 106 170 6287
Biso mean--89.64 50.84 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056309
X-RAY DIFFRACTIONf_angle_d0.968456
X-RAY DIFFRACTIONf_chiral_restr0.038878
X-RAY DIFFRACTIONf_plane_restr0.0061114
X-RAY DIFFRACTIONf_dihedral_angle_d14.2872368
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1044X-RAY DIFFRACTION5.9TORSIONAL
12B1044X-RAY DIFFRACTION5.9TORSIONAL
21C2522X-RAY DIFFRACTION5.9TORSIONAL
22D2522X-RAY DIFFRACTION5.9TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.40470.36351080.270125582666100
2.4047-2.46480.28591540.257225652719100
2.4648-2.53140.29011240.255225412665100
2.5314-2.60590.31281340.241925302664100
2.6059-2.690.29341270.236826012728100
2.69-2.78610.30061290.231525602689100
2.7861-2.89770.27811450.229225442689100
2.8977-3.02950.29951410.234425622703100
3.0295-3.18920.27621580.221925462704100
3.1892-3.38890.271600.218225702730100
3.3889-3.65040.25271160.205626142730100
3.6504-4.01750.21041520.187626112763100
4.0175-4.59820.19161670.161125972764100
4.5982-5.79070.23251620.172726612823100
5.7907-41.28270.23521430.19392798294199
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)
17.20943.98463.07988.38052.33365.6603-0.36190.4880.8852-0.5696-0.22170.8298-0.7304-0.36260.40290.71950.00860.04520.4203-0.10150.522517.5811-1.1683-29.2259
24.40132.46835.36063.66742.64976.5962-0.70660.68220.4698-0.58540.2860.3269-1.29940.96040.30860.4447-0.0561-0.07260.38040.04990.439516.4709-4.4638-48.7407
34.2441-2.58130.53624.7261-0.25092.74990.21890.06240.44060.155-0.0142-0.46780.19790.3955-0.26070.449-0.0375-0.07250.4167-0.05980.434930.6319-14.6447-24.2161
41.60851.10682.16971.82851.49814.46940.23860.01870.01550.16890.05290.10980.6285-0.4085-0.18540.1976-0.0416-0.00490.37160.01360.387815.4771-14.767-47.9433
56.32220.2556-0.63086.5071-1.02596.4166-0.17930.1945-0.21450.29940.046-0.63780.40011.4432-0.0160.44260.03230.05620.79-0.02860.656440.2742-24.2957-40.1353
63.32331.9931-1.20423.1862-3.30213.68430.2503-0.42820.0710.3329-0.4167-0.1761-0.38530.61020.15770.3201-0.0290.02990.4364-0.0510.444334.3965-27.2623-21.2544
74.726-2.11780.36343.36190.25953.1138-0.11980.21630.83340.20980.32190.2121-0.39630.207-0.2090.4394-0.08520.03540.54230.08060.536628.8417-9.542-45.0125
82.20641.9667-2.62744.1865-5.92848.38050.798-0.25190.23240.6463-1.067-0.2152-0.96990.0726-0.16030.32030.039-0.00050.4263-0.08150.3928.6633-19.3466-36.0284
91.86311.9933-1.88462.402-3.4715.13460.01880.1506-0.08760.1610.0620.1614-0.0398-0.5232-0.12270.3379-0.06330.00810.2994-0.04310.336123.6513-28.4971-21.1698
105.5607-1.29910.35274.1969-1.9344.8263-0.0530.6667-0.1016-0.1793-0.0797-0.25470.48190.37080.09830.2796-0.03150.06460.6758-0.1190.370533.5569-25.5502-55.0762
110.7532-0.0624-0.34610.39870.58813.74690.11930.1204-0.0496-0.20170.0144-0.03030.06810.2732-0.13890.6942-0.03630.06340.3634-0.00940.544228.5686-46.2233-25.3316
122.8652-0.1702-0.89042.8650.93612.48180.0047-0.180.14210.27560.1205-0.4149-0.93521.1483-0.28610.815-0.3206-0.06790.6999-0.02020.322224.9679-29.1453.5606
135.795-0.85690.64023.4238-3.63624.23270.2360.6357-0.0929-1.45810.04740.8641-0.1739-0.0486-0.23011.15180.041-0.18970.4517-0.03440.53593.4637-29.0644-0.5606
144.3652-2.40191.77396.9224-1.26851.9001-0.1259-0.15490.32730.59150.0542-0.2414-0.4844-0.08860.07520.6303-0.05770.11390.3234-0.07990.420613.8748-9.386-15.4221
150.52420.0083-1.59650.65741.27135.12110.00420.1280.17390.0736-0.050.5034-0.3014-0.37010.05890.42430.026-0.04430.6140.04310.6639-3.4416-8.7359-47.4421
167.40570.2781-1.84692.69060.49123.28610.07070.76580.9952-0.81150.2665-0.4575-0.70580.4411-0.2310.6637-0.21370.01070.8110.19280.520717.2055-13.9383-75.8723
175.89791.16322.05096.4939-0.8124.60050.3836-0.1086-0.39660.58750.02330.1416-0.0972-0.1838-0.21730.4718-0.0836-0.05190.7446-0.05580.463213.2604-34.0498-68.7159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )A1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 44 )A16 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 72 )A45 - 72
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 109 )A73 - 109
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 15 )B1 - 15
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 44 )B16 - 44
7X-RAY DIFFRACTION7chain 'B' and (resid 45 through 72 )B45 - 72
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 78 )B73 - 78
9X-RAY DIFFRACTION9chain 'B' and (resid 79 through 109 )B79 - 109
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 72 )C1 - 72
11X-RAY DIFFRACTION11chain 'C' and (resid 73 through 161 )C73 - 161
12X-RAY DIFFRACTION12chain 'C' and (resid 162 through 215 )C162 - 215
13X-RAY DIFFRACTION13chain 'C' and (resid 216 through 288 )C216 - 288
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 72 )D1 - 72
15X-RAY DIFFRACTION15chain 'D' and (resid 73 through 161 )D73 - 161
16X-RAY DIFFRACTION16chain 'D' and (resid 162 through 222 )D162 - 222
17X-RAY DIFFRACTION17chain 'D' and (resid 223 through 288 )D223 - 288

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