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- PDB-5ji1: Crystal Structure of GDF8 -

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Basic information

Entry
Database: PDB / ID: 5ji1
TitleCrystal Structure of GDF8
ComponentsGrowth/differentiation factor 8
KeywordsCYTOKINE / GDF8 / myostatin / TGFbeta / Ligand
Function / homology
Function and homology information


negative regulation of muscle hypertrophy / negative regulation of skeletal muscle tissue growth / negative regulation of myoblast proliferation / skeletal muscle satellite cell differentiation / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / negative regulation of satellite cell differentiation / skeletal muscle atrophy / ovulation cycle process / response to gravity ...negative regulation of muscle hypertrophy / negative regulation of skeletal muscle tissue growth / negative regulation of myoblast proliferation / skeletal muscle satellite cell differentiation / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / negative regulation of satellite cell differentiation / skeletal muscle atrophy / ovulation cycle process / response to gravity / skeletal muscle tissue regeneration / negative regulation of myoblast differentiation / response to muscle activity / negative regulation of kinase activity / muscle cell cellular homeostasis / positive regulation of macrophage chemotaxis / response to testosterone / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of lamellipodium assembly / response to electrical stimulus / negative regulation of insulin receptor signaling pathway / cellular response to dexamethasone stimulus / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / response to estrogen / heparin binding / cellular response to hypoxia / response to ethanol / signaling receptor binding / positive regulation of DNA-templated transcription / protein homodimerization activity / extracellular space / extracellular region / identical protein binding
Similarity search - Function
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 / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine
Similarity search - Domain/homology
Growth/differentiation factor 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 8
B: Growth/differentiation factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6729
Polymers24,8442
Non-polymers8277
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-68 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.606, 77.739, 119.544
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 1 - 109 / Label seq-ID: 1 - 109

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Growth/differentiation factor 8 / GDF-8 / Myostatin


Mass: 12422.212 Da / Num. of mol.: 2 / Fragment: UNP residues 268-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mstn, Gdf8 / Cell (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O08689
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 55.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM 2-(N-morpholino)ethanesulfonic acid pH 6.0, 40% 2-Methyl-2,4-pentanediol
PH range: 5-10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.25→47.38 Å / Num. obs: 13830 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 44.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.032 / Rrim(I) all: 0.085 / Net I/σ(I): 18.2 / Num. measured all: 98443
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.102 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.23data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HH2

3hh2


Resolution: 2.25→36.965 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.37
RfactorNum. reflection% reflection
Rfree0.2773 985 7.15 %
Rwork0.2348 --
obs0.2377 13776 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.73 Å2 / Biso mean: 66.8889 Å2 / Biso min: 23.68 Å2
Refinement stepCycle: final / Resolution: 2.25→36.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1435 0 56 30 1521
Biso mean--84.82 53.53 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031540
X-RAY DIFFRACTIONf_angle_d0.9512076
X-RAY DIFFRACTIONf_chiral_restr0.039211
X-RAY DIFFRACTIONf_plane_restr0.006263
X-RAY DIFFRACTIONf_dihedral_angle_d15.274548
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A774X-RAY DIFFRACTION11.368TORSIONAL
12B774X-RAY DIFFRACTION11.368TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2502-2.36880.34781320.335517801912
2.3688-2.51720.35281460.31717991945
2.5172-2.71150.33081490.287617801929
2.7115-2.98430.31581300.266918231953
2.9843-3.41580.25671280.232418091937
3.4158-4.30250.26011600.192418462006
4.3025-36.96960.25211400.219719542094
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)
11.17771.53110.06172.0257-0.16942.5561-0.3228-0.22050.1671-0.27650.4815-0.23330.1077-0.0151-0.00350.5242-0.00860.02230.4650.03640.54035.8459-2.9145-36.9344
20.24850.66330.56473.10912.71462.38320.1648-0.3860.09640.34680.4530.4380.1623-1.74380.05820.42280.14040.06370.90120.39130.558-3.8798-3.956-19.5276
31.0615-0.29170.32770.9217-0.06611.4080.2110.2036-1.8365-0.8520.5250.12441.28810.32160.02210.82430.0802-0.05580.63110.10811.058711.4-16.7247-31.1697
43.67281.99022.21012.0357-0.20053.72360.368-1.31140.15450.3674-0.1337-0.076-0.05970.4090.08270.50080.001-0.03280.75150.20230.46442.7399-6.8289-11.6846
50.55940.6060.2122.2812-0.60220.9341-0.20091.1551-0.6155-0.32660.43580.11980.5889-0.4037-0.00070.7993-0.101-0.010.8659-0.05960.4937.9255-33.9605-38.4001
62.35290.5981-1.28172.37270.40261.98380.04810.7263-0.30750.09480.95030.2524-0.68681.17020.05970.4303-0.04440.05160.3538-0.15460.471618.041-32.4864-25.2871
70.1155-0.2093-0.15172.3496-1.23491.5670.1732-1.07680.9590.6404-0.7242-0.8119-1.40471.2122-0.30840.4994-0.1723-0.08120.8146-0.41850.366222.9932-32.1007-12.0379
81.48661.0403-0.46191.61040.65041.2144-0.1789-0.02980.3827-0.00460.4035-0.11840.05670.8575-0.00060.42840.01050.01980.3892-0.10210.351114.2068-32.8245-26.1565
90.5021-0.2005-0.49410.31320.47030.9631-0.48830.97150.2224-0.2342-0.88741.3046-1.4168-0.4565-0.02451.0352-0.1226-0.0570.61760.20711.03883.3216-17.5052-31.9384
102.25270.5782-0.18950.7080.58580.7726-0.0253-0.93510.36630.205-0.08010.208-0.4208-0.2802-0.00540.4969-0.06370.00360.3824-0.11910.510410.1059-31.0219-17.0258
111.4341-0.7496-0.12160.38850.06380.0093-0.3055-0.83810.2626-0.00230.55790.1175-0.6376-0.0749-0.01131.0022-0.21920.11341.6733-0.25571.094521.5113-28.05310.8805
124.58271.9449-1.57862.96451.30652.9722-0.0266-1.20890.26460.05530.03270.4824-0.7163-0.97120.09540.35030.00840.06940.4018-0.11280.41197.7647-30.7252-18.4776
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 78 )A45 - 78
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 109 )A79 - 109
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 15 )B1 - 15
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 27 )B16 - 27
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 36 )B28 - 36
8X-RAY DIFFRACTION8chain 'B' and (resid 37 through 44 )B37 - 44
9X-RAY DIFFRACTION9chain 'B' and (resid 45 through 73 )B45 - 73
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 87 )B74 - 87
11X-RAY DIFFRACTION11chain 'B' and (resid 88 through 92 )B88 - 92
12X-RAY DIFFRACTION12chain 'B' and (resid 93 through 109 )B93 - 109

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