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- PDB-5nxs: Crystal Structure of Human Pro-myostatin Precursor at 4.2 A Resol... -

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Basic information

Entry
Database: PDB / ID: 5nxs
TitleCrystal Structure of Human Pro-myostatin Precursor at 4.2 A Resolution with Experimental Phases from SeMet labelling
ComponentsGrowth/differentiation factor 8
KeywordsSIGNALING PROTEIN / growth factor / TGFbeta family / cystine knot
Function / homology
Function and homology information


negative regulation of muscle hypertrophy / negative regulation of skeletal muscle tissue growth / negative regulation of myoblast proliferation / myoblast migration involved in skeletal muscle regeneration / skeletal muscle satellite cell differentiation / negative regulation of skeletal muscle satellite cell proliferation / ovulation cycle process / skeletal muscle atrophy / negative regulation of satellite cell differentiation / FOXO-mediated transcription of cell cycle genes ...negative regulation of muscle hypertrophy / negative regulation of skeletal muscle tissue growth / negative regulation of myoblast proliferation / myoblast migration involved in skeletal muscle regeneration / skeletal muscle satellite cell differentiation / negative regulation of skeletal muscle satellite cell proliferation / ovulation cycle process / skeletal muscle atrophy / negative regulation of satellite cell differentiation / FOXO-mediated transcription of cell cycle genes / response to gravity / negative regulation of myoblast differentiation / response to muscle activity / muscle organ development / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.19 Å
AuthorsCotton, T.R. / Fischer, G. / Hyvonen, M.
CitationJournal: EMBO J. / Year: 2018
Title: Structure of the human myostatin precursor and determinants of growth factor latency.
Authors: Cotton, T.R. / Fischer, G. / Wang, X. / McCoy, J.C. / Czepnik, M. / Thompson, T.B. / Hyvonen, M.
History
DepositionMay 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Growth/differentiation factor 8
B: Growth/differentiation factor 8


Theoretical massNumber of molelcules
Total (without water)76,9962
Polymers76,9962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-30 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.830, 196.830, 196.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 38497.926 Da / Num. of mol.: 2 / Fragment: Pro-Myostatin Precursor, UNP residues 43-375 / Mutation: deltaN25
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSTN, GDF8 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: O14793
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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 4.2
Details: 10 mg/mL protein, reservoir: 0.1M NaAcetate, 1M (NH4)3PO4: cryo-protection: 26% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 4.194→98.414 Å / Num. obs: 9470 / % possible obs: 100 % / Redundancy: 160.2 % / Biso Wilson estimate: 225.34 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.012 / Rrim(I) all: 0.148 / Net I/σ(I): 28.6 / Num. measured all: 1517107
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
4.194-4.267128604054720.9230.2382.7323100
11.38-98.414138.2710175140.9960.0080.09980.199.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 4.19→98.41 Å / Cor.coef. Fo:Fc: 0.654 / Cor.coef. Fo:Fc free: 0.666 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.749
RfactorNum. reflection% reflectionSelection details
Rfree0.301 478 5.05 %RANDOM
Rwork0.274 ---
obs0.276 9460 99.7 %-
Displacement parametersBiso max: 267.89 Å2 / Biso mean: 91.65 Å2 / Biso min: 5.89 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.69 Å
Refinement stepCycle: final / Resolution: 4.19→98.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 0 0 3556
Num. residues----541
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d984SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes566HARMONIC5
X-RAY DIFFRACTIONt_it3635HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion588SEMIHARMONIC5
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_contact3790SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3635HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5028HARMONIC60.53
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion24
LS refinement shellResolution: 4.19→4.68 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.238 132 5.01 %
Rwork0.22 2505 -
all-2637 -
obs--99.06 %
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)
18.9949-1.6152-2.14924.38790.35655.9725-0.06790.0809-0.8705-0.13020.13660.40550.6597-0.6175-0.06870.5050.02520.08840.3156-0.4097-0.458844.7251-10.251344.6741
20.0036-8.12772.09845.65598.07616.4724-0.14210.44920.5815-0.29350.7025-0.05040.9322-0.9017-0.56040.26270.3290.0399-0.4776-0.4559-0.579249.59515.762947.2297
310.2104-3.7392.900816.39551.770612.2750.00210.28430.18620.759-0.5969-0.6329-0.6720.49450.59480.81120.375-0.1266-0.0679-0.4559-0.46355.5435.90666.2056
40.4653-0.08762.91040-0.29860-0.00190.3951-0.08440.64640.78380.3431.03540.0394-0.78190.0797-0.3450.37110.14610.10450.797517.035611.010556.9852
56.7228-6.5947-2.11611.8099-0.74787.10660.0615-0.43130.03470.6910.05950.04440.26480.6522-0.1209-0.01760.3360.36660.55230.09880.72029.508113.540765.2744
63.85236.34430.98360-8.73120-0.1098-0.386-0.04051.23870.3756-0.48571.12971.2119-0.2658-0.7478-0.45590.4559-0.12870.26590.09861.956525.95458.4368
74.65350.8466-7.77790-8.73120-0.08560.14670.1304-0.8253-0.06070.6173-1.2152-1.03430.1462-0.7679-0.44460.3187-0.17720.22280.0867-15.296936.33553.6327
815.34716.0086-8.50340.2159-8.02870-0.0786-0.7348-0.14440.2373-0.3110.1190.232-0.04910.3896-0.6394-0.34760.4559-0.08390.3943-0.012-9.53331.375766.0485
92.9036-4.3758-7.1092.342-1.483113.8699-0.2122-0.01270.55840.59740.29740.4098-0.08530.4424-0.0852-0.1209-0.45590.4559-0.34340.04770.1593-8.43136.248459.3357
100.00718.38686.75390-8.73120-0.0694-1.18650.0211.32561.3348-1.11691.34211.3747-1.2654-0.909-0.45590.4559-0.40020.4559-0.06230.848427.415561.9293
115.09441.62723.52360-2.29686.35680.02880.0022-0.27020.4525-0.0654-0.09540.49470.17520.03670.0410.31460.20940.57050.12740.43185.381315.492672.3632
120.5618-8.7312-8.73120.0044-8.731200.1038-0.3808-0.46040.80780.8737-0.93531.23030.934-0.9774-0.3407-0.30020.45590.46780.36760.4617-8.015321.821866.195
136.71026.9872-8.73123.71770.969800.37750.2329-0.2759-0.7613-0.06220.67240.8829-0.2673-0.3153-0.8292-0.45590.45590.17160.33670.6505-15.183825.485456.081
148.93412.9981-3.684612.0752-0.65055.0874-0.08790.0594-0.65270.62140.0572-0.27220.50630.67060.0306-0.7168-0.45590.43330.04690.0590.57053.282620.02755.9767
1514.01662.7427-3.17714.2717-4.01710.14630.0281-0.14680.1761-0.30580.10410.2640.0053-0.0249-0.13210.7268-0.3676-0.34560.59690.15140.673129.1202-15.770748.1574
163.70083.74881.78558.6526-5.75895.04030.0141-0.9785-0.7070.86880.5069-0.11140.5714-0.1705-0.5210.87790.36690.03350.3083-0.45590.151548.4061-3.918456.5813
176.8455-2.92650.84877.18555.04583.32330.10940.7437-0.7777-0.2946-0.44160.66950.3697-0.81110.33210.63530.1316-0.11490.3199-0.27270.622334.9063-7.937747.4187
180.89437.16686.37237.364-3.82171.89730.0483-0.78560.375-0.09150.25140.44110.1245-0.0281-0.29980.3758-0.24430.00360.1691-0.42770.561429.1808-2.646543.0164
190.3672-1.5321-8.50633.11398.73125.47090.0441-0.4578-0.7566-0.4931.07690.9746-0.0185-0.4565-1.1210.6690.34770.3291-0.6828-0.4559-0.735348.34249.324658.1619
2010.8019-3.9353-1.17628.68344.66173.4719-0.03610.1618-0.5062-0.6760.78750.74720.7555-0.8514-0.75140.402-0.28840.03020.0821-0.45390.600732.9463-0.021547.9466
213.01942.21514.07899.54740.00029.3988-0.0170.439-0.247-0.4879-0.0469-0.28250.42280.12370.06390.54610.2513-0.40450.36450.1410.737518.4917-3.258426.7565
224.9339-6.0988-6.43726.00765.216300.0585-0.1885-0.17690.0520.0233-0.24390.39230.39-0.0818-0.026-0.2714-0.3042-0.49230.03180.860615.23131.084941.4828
2317.24086.1817.487417.6221-5.677300.03850.4792-0.74440.14390.5878-0.59930.6878-0.4527-0.6263-0.1404-0.45590.2429-0.1002-0.11490.86821.51667.96346.8927
242.07126.0769-5.923212.1082-5.4964.16620.11240.64790.32040.1737-0.4249-0.188-0.66250.34050.3125-0.4526-0.45590.3128-0.4256-0.29690.565.809224.678146.6393
250.1071-8.73128.73120.22758.73120-0.00781.04850.213-0.07280.79320.34980.5779-0.7609-0.78540.3466-0.00640.3745-0.4357-0.4255-0.33138.698615.623452.4874
2611.67252.473-8.731208.73120-0.1035-0.25570.67930.2989-1.0022-0.5105-0.48981.26121.10580.70380.41770.41080.374-0.4559-0.07863.395118.82663.7153
274.5838-0.13761.71123.8736.45899.58870.0838-0.02230.60340.29360.0770.3058-0.43840.4324-0.16090.40120.1946-0.25520.5903-0.4114-0.346353.576325.297557.6045
288.29-2.9142-0.74017.59297.790612.80260.1467-0.8868-1.00070.8806-0.66930.0053-0.08590.10530.52250.28870.40420.0023-0.5538-0.4559-0.426752.918320.209971.5803
290-1.985-1.641712.6342.99441.0580.3752-0.4074-0.04110.4619-0.1873-0.86540.15740.2435-0.18790.3890.1773-0.3492-0.0764-0.4559-0.473463.68425.783979.6062
3007.36443.556710.2662.989413.32980.0457-1.0296-1.11180.75090.63610.42491.17910.5506-0.68180.51860.31450.32870.0045-0.269-0.192257.977222.620181.6834
310-6.5548-1.93569.93626.98677.5227-0.2314-0.37150.98340.27480.02550.61050.23420.24960.2060.10830.368-0.0212-0.1753-0.4559-0.102652.920227.698368.5643
322.79141.49588.725810.43175.8067.6992-0.09420.87670.12270.24370.5625-0.80570.29040.4145-0.46830.43470.2807-0.13850.2289-0.4538-0.011562.201328.103269.0887
3311.8302-5.25732.896612.0582-3.681910.27060.0651-0.3951-0.7637-0.01550.093-0.37790.0781-0.0138-0.1580.51010.3808-0.22990.5752-0.33250.316666.679813.687376.4356
340.7622-2.3278-3.691216.39057.15118.65550.1105-0.2649-0.54860.7019-0.34550.01910.3116-0.13950.2350.62530.45590.4151-0.568-0.4559-0.523452.255618.246766.388
3512.5485.0001-2.6676.2601-2.69282.8111-0.1490.1699-0.0776-0.50730.28010.00140.101-0.1038-0.1310.2836-0.1633-0.24520.6457-0.31250.452238.790319.922144.8359
3604.1966-2.910414.81762.91047.21480.35921.1114-0.1689-1.1655-0.50770.97051.00730.70630.14840.0032-0.3007-0.205-0.0127-0.21610.571116.06097.3731.3771
3711.58024.223-2.910408.289400.37681.1588-0.0495-0.9996-0.585-0.48041.42681.17620.2082-0.7243-0.3604-0.4559-0.2998-0.45590.411924.68095.614232.7912
380-1.1169-1.90271.0315.939600.01590.08590.33060.3431-0.1937-0.0823-0.75960.87720.1778-0.26890.37730.3207-0.7955-0.4559-0.74354.14071.19736.5283
391.20330.4489-5.368408.731200.00120.0069-0.3913-0.68540.49520.59831.2623-1.143-0.4963-0.19760.07540.356-0.6887-0.45590.200442.9435-7.93833.6351
406.837-1.2413-1.12716.5795-2.13814.62590.1604-0.4005-0.92060.39840.78611.13151.30761.3939-0.9465-0.6209-0.43860.0635-0.304-0.45590.674918.93859.708743.5533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{B|44 - 56}B44 - 56
2X-RAY DIFFRACTION2{B|57 - 69}B57 - 69
3X-RAY DIFFRACTION3{B|70 - 93}B70 - 93
4X-RAY DIFFRACTION4{B|94 - 121}B94 - 121
5X-RAY DIFFRACTION5{B|122 - 151}B122 - 151
6X-RAY DIFFRACTION6{B|152 - 159}B152 - 159
7X-RAY DIFFRACTION7{B|160 - 167}B160 - 167
8X-RAY DIFFRACTION8{B|168 - 175}B168 - 175
9X-RAY DIFFRACTION9{B|187 - 201}B187 - 201
10X-RAY DIFFRACTION10{B|202 - 211}B202 - 211
11X-RAY DIFFRACTION11{B|212 - 219}B212 - 219
12X-RAY DIFFRACTION12{B|220 - 231}B220 - 231
13X-RAY DIFFRACTION13{B|232 - 246}B232 - 246
14X-RAY DIFFRACTION14{B|247 - 259}B247 - 259
15X-RAY DIFFRACTION15{B|271 - 282}B271 - 282
16X-RAY DIFFRACTION16{B|283 - 303}B283 - 303
17X-RAY DIFFRACTION17{B|304 - 313}B304 - 313
18X-RAY DIFFRACTION18{B|314 - 345}B314 - 345
19X-RAY DIFFRACTION19{B|346 - 363}B346 - 363
20X-RAY DIFFRACTION20{B|364 - 375}B364 - 375
21X-RAY DIFFRACTION21{A|44 - 52}A44 - 52
22X-RAY DIFFRACTION22{A|53 - 62}A53 - 62
23X-RAY DIFFRACTION23{A|63 - 82}A63 - 82
24X-RAY DIFFRACTION24{A|83 - 93}A83 - 93
25X-RAY DIFFRACTION25{A|94 - 118}A94 - 118
26X-RAY DIFFRACTION26{A|119 - 138}A119 - 138
27X-RAY DIFFRACTION27{A|139 - 149}A139 - 149
28X-RAY DIFFRACTION28{A|150 - 160}A150 - 160
29X-RAY DIFFRACTION29{A|161 - 184}A161 - 184
30X-RAY DIFFRACTION30{A|185 - 203}A185 - 203
31X-RAY DIFFRACTION31{A|204 - 215}A204 - 215
32X-RAY DIFFRACTION32{A|216 - 232}A216 - 232
33X-RAY DIFFRACTION33{A|235 - 248}A235 - 248
34X-RAY DIFFRACTION34{A|249 - 258}A249 - 258
35X-RAY DIFFRACTION35{A|259 - 266}A259 - 266
36X-RAY DIFFRACTION36{A|271 - 299}A271 - 299
37X-RAY DIFFRACTION37{A|300 - 316}A300 - 316
38X-RAY DIFFRACTION38{A|317 - 324}A317 - 324
39X-RAY DIFFRACTION39{A|325 - 338}A325 - 338
40X-RAY DIFFRACTION40{A|339 - 375}A339 - 375

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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