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- PDB-5ntu: Crystal Structure of human Pro-myostatin Precursor at 2.6 A Resolution -

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Basic information

Entry
Database: PDB / ID: 5ntu
TitleCrystal Structure of human Pro-myostatin Precursor at 2.6 A Resolution
ComponentsGrowth/differentiation factor 8
KeywordsSIGNALING PROTEIN / growth factor / signalling protein / 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 / 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 / FOXO-mediated transcription of cell cycle genes ...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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.58 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
DepositionApr 28, 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

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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)77,13725
Polymers75,7632
Non-polymers1,37423
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS confirms disulphide linked dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint6 kcal/mol
Surface area30520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.157, 36.301, 120.448
Angle α, β, γ (deg.)90.000, 104.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-510-

HOH

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Components

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


Mass: 37881.328 Da / Num. of mol.: 2 / Fragment: Pro-Myostatin Precursor / Mutation: G319A, K320A, K217A, Q218A, E220A
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) / References: UniProt: O14793
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 10% PEG6000, 0.1M HEPES: cryo-protection: 70% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.575→76.264 Å / Num. obs: 22474 / % possible obs: 97.7 % / Redundancy: 4 % / Biso Wilson estimate: 95.66 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.034 / Rrim(I) all: 0.071 / Net I/σ(I): 11.7 / Num. measured all: 90386
Reflection shell
Resolution (Å)Redundancy (%)CC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
2.575-2.624.20.5830.4931.037199.6
6.989-76.2643.60.9970.0220.046199.1

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→28.27 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.576 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.554 / SU Rfree Blow DPI: 0.297 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1118 5.01 %RANDOM
Rwork0.215 ---
obs0.217 22310 97.7 %-
Displacement parametersBiso max: 201.34 Å2 / Biso mean: 100.2 Å2 / Biso min: 46.99 Å2
Baniso -1Baniso -2Baniso -3
1--2.6578 Å20 Å20.5284 Å2
2---2.5218 Å20 Å2
3---5.1796 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.58→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 86 30 4515
Biso mean--91.21 76.07 -
Num. residues----581
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1488SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes651HARMONIC5
X-RAY DIFFRACTIONt_it4579HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion634SEMIHARMONIC5
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_contact4752SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4579HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6207HARMONIC60.55
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion20.72
LS refinement shellResolution: 2.58→2.71 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.264 137 4.6 %
Rwork0.215 2843 -
all-2980 -
obs--99.87 %
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)
10.8039-4.5203-1.46354.7513-4.434-0.80390.0343-0.1657-0.04530.1974-0.11350.10090.1302-0.250.07930.35650.1638-0.00550.2738-0.2799-0.1498-35.7648-13.4213.3769
2-0.4374-0.32971.41261.2073-5.55671.95830.02260.38770.3302-0.12350.02470.5099-0.2486-0.2902-0.04730.14340.4040.12450.5495-0.02230.0863-31.2581-7.8145-2.3201
35.32415.698-1.0480.98383.25058.91080.0062-0.0927-0.0776-0.0252-0.02660.02260.0769-0.25950.02040.1411-0.06850.03490.2651-0.012-0.0855-22.3817-19.5425-10.6306
41.65212.5634-2.90246.0308-0.6240.45690.0348-0.09740.07680.1358-0.0542-0.2156-0.01660.05270.01940.3512-0.16310.14670.1788-0.29410.0061-19.1176-26.9599.4713
59.7542-1.02984.36024.78880.72892.50880.05820.0825-0.273-0.3469-0.2212-0.01620.38310.00410.163-0.16180.11510.133-0.11340.0185-0.1488-3.1595-29.393842.3165
63.2469-4.6174.477811.3265-1.29118.85860.1446-0.4378-0.8089-0.2793-0.11210.60660.5725-0.0767-0.0324-0.1550.10430.06220.00170.1098-0.06314.9426-34.909139.1793
76.8548-1.51051.20152.4963-0.40451.49110.1012-0.66340.36840.3725-0.1495-0.52090.11180.96670.0483-0.2651-0.0579-0.01180.41830.0810.095518.996-25.363855.1843
8-0.99342.97472.24021.53432.26694.4948-0.06170.0312-0.1751-0.0180.1206-0.27620.23750.1667-0.05890.18340.43230.20.14060.14490.461519.3769-47.002145.0487
91.65263.48973.22424.1886-3.23395.37550.1683-0.49720.49330.1341-0.436-0.1552-0.35470.7120.2677-0.4248-0.0210.04240.47690.00670.203122.5977-23.763152.2465
105.93632.4061.568702.59517.6214-0.0336-0.2736-0.4132-0.2517-0.2906-0.71270.95550.38060.3242-0.28080.17080.1197-0.00780.1855-0.0511.3894-33.586441.7498
111.31674.88720.88667.1771-0.98240.36830.0821-0.46080.00360.4919-0.1856-0.4738-0.11170.63990.1034-0.13380.1355-0.10740.4858-0.01930.156720.7897-32.378356.7033
121.32731.35547.08170-4.70018.7699-0.0378-0.1708-0.1340.1988-0.3149-0.0820.49720.250.3528-0.2599-0.01530.02160.1733-0.0588-0.067910.7243-28.869461.468
132.1209-0.4635-3.4514.56136.505-1.80960.15780.0229-0.3797-0.0125-0.2834-0.48970.1857-0.03360.1256-0.3288-0.01040.0470.01540.0122-0.11796.9025-27.388849.7512
14-2.80256.13715.00050.0265.71383.71670.01790.3231-0.0665-0.44570.01360.22880.0407-0.3685-0.03150.11020.1363-0.10210.44520.04810.3001-10.5652-30.564127.3811
15-0.6018-4.35631.15691.65225.96020.6568-0.03090.2147-0.3458-0.33470.11430.29920.3913-0.3019-0.08340.2878-0.3266-0.03740.0491-0.22390.3537-38.8332-31.543423.0905
162.29830.17420.98331.35372.58.22180.17210.5310.1688-0.162-0.1920.08840.2067-0.54980.0199-0.1773-0.0084-0.14890.6411-0.1936-0.2033-35.391-18.27914.2656
171.6664-2.48820.35520-0.73432.8137-0.23230.4875-0.3326-0.16040.58610.01670.20820.1464-0.35380.0445-0.3158-0.21710.1332-0.1427-0.0678-35.1119-23.951520.0743
180.39562.1024-1.41393.8583-1.80047.4154-0.1427-0.18230.1792-0.22180.22290.66370.1059-0.9208-0.0802-0.10380.0407-0.0549-0.0929-0.09540.0482-31.898-26.835142.3751
192.99480.4547-3.103801.01496.97740.26551.0743-0.0744-0.2791-0.1227-0.3046-0.3491-0.3043-0.14280.11170.08590.08560.4391-0.1719-0.0141-24.5805-14.53134.2367
204.4624-1.8357-1.80540.2360.86367.6520.02860.6038-0.144-0.1524-0.11270.05620.02060.32780.0841-0.0138-0.0532-0.04160.0564-0.1938-0.0248-24.9344-19.621713.245
210.84552.27162.82475.2673-2.72561.83990.09810.01620.02550.0424-0.13080.86470.2025-0.77790.0328-0.16960.0123-0.03020.0127-0.02830.0192-29.8938-15.679742.5314
222.2336-3.2518-1.849400.26921.94710.37940.0034-0.5743-0.1444-0.14060.26320.20430.3014-0.23870.00570.02060.0235-0.08870.0339-0.0715-14.5939-28.516645.6696
233.45570.1943-1.60531.22270.9632-1.0512-0.0432-0.56380.44420.1338-0.1397-0.6014-0.14960.47980.1828-0.15080.02120.00050.0999-0.0353-0.03990.0962-23.058555.3643
24-1.16331.65332.117700.72011.1633-0.00970.23680.57670.12160.2001-0.1148-0.4844-0.0827-0.19030.0186-0.08160.06480.060.01850.177-1.214-12.492744.7694
251.38210.5178-2.74454.85384.01450.39760.15220.06690.22390.7887-0.46030.0737-0.09220.21390.30810.2152-0.00010.07720.4166-0.1066-0.0755-18.7533-9.30123.274
264.70260.64491.45564.39054.16853.34270.0332-0.32250.1041-0.0072-0.0485-0.1139-0.25710.06370.01530.43010.28620.1960.272-0.07640.2045-14.5593-0.6961-8.1513
271.14130.5633-0.84390-1.03540.23250.0327-0.0709-0.03510.07580.001-0.0383-0.0130.0125-0.0336-0.1511-0.0676-0.0660.50530.0089-0.1647-8.1701-11.9434-5.5959
281.8592-1.37360.47091.20580.64776.55380.009-0.0965-0.00440.04770.05940.0066-0.6673-0.5506-0.0685-0.1012-0.07460.1282-0.2128-0.0655-0.0822-14.3303-14.0733-27.3399
290.42741.1258-0.63752.20150.62261.38490.0027-0.0109-0.0171-0.0277-0.02460.0525-0.03150.00560.02190.5323-0.1383-0.01930.2136-0.30730.3893-6.57463.8018-19.5976
302.7311-0.7254-2.09621.99760.56088.2519-0.0916-0.31690.12240.06890.0866-0.03570.1141-0.20860.0049-0.0381-0.00920.1331-0.2424-0.07820.0889-10.2471-16.6197-27.3728
315.88841.3206-3.36080-1.30942.11480.0937-0.194-0.14970.0347-0.1539-0.3443-0.14060.53170.0602-0.03880.09550.14730.06920.21270.0137-10.1375-12.8981-16.0283
320.8303-4.2403-1.061.39642.94441.01110.01890.12740.0752-0.024-0.0739-0.0412-0.1198-0.10590.0550.2651-0.1151-0.04450.4363-0.45590.213-7.17880.4744-7.1903
3311.0936-0.9795-3.13698.1638-1.31252.131-0.06970.04970.3528-0.21630.07340.2169-0.4854-0.6147-0.00370.2928-0.00140.107-0.0354-0.04930.0212-17.3327-8.592-28.7666
341.1995-0.5064-0.53750.35070.39090.57570.0151-0.07540.03130.10920.00310.0593-0.0776-0.0569-0.0182-0.17620.11220.27450.3311-0.13530.0618-26.4823-12.743-20.2755
350.1229-0.22062.76214.32660.33382.52740.0227-0.6266-0.00020.43440.062-0.2274-0.16350.0941-0.0847-0.09140.03150.16760.3598-0.0424-0.1798-14.6635-10.4199-1.0928
368.5955-0.4587-2.14165.9179-1.44062.74680.01470.48520.5137-1.021-0.40720.7401-0.0374-0.41370.39250.06870.1388-0.1319-0.2695-0.08750.061-29.9366-2.549735.3995
377.8322-1.51093.39873.1187-0.51291.22840.1018-0.58850.3003-0.2103-0.0433-0.2726-0.1251-0.082-0.0585-0.110.05220.0325-0.1137-0.0452-0.1494-16.1652-16.450348.2635
381.1991-4.8385-0.94994.0992-0.94652.32810.09880.5556-0.5072-0.5395-0.32890.54570.0776-0.05580.23010.07090.0791-0.1124-0.1361-0.071-0.0277-25.542-12.058732.7926
3911.5907-2.0812-2.51382.14164.69095.1437-0.0139-0.5088-0.5196-0.00540.010.21290.46560.29370.0039-0.21050.04370.0456-0.0270.0133-0.0689-5.2759-26.520945.3732
401.3518-3.04-0.10593.90951.38614.69970.22250.35810.214-0.7529-0.29860.1224-0.47940.02110.07610.13290.1108-0.0209-0.0830.0297-0.1009-18.9634-14.964931.8623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|47 - 62}A47 - 62
2X-RAY DIFFRACTION2{A|63 - 79}A63 - 79
3X-RAY DIFFRACTION3{A|80 - 92}A80 - 92
4X-RAY DIFFRACTION4{A|93 - 109}A93 - 109
5X-RAY DIFFRACTION5{A|110 - 136}A110 - 136
6X-RAY DIFFRACTION6{A|137 - 154}A137 - 154
7X-RAY DIFFRACTION7{A|155 - 174}A155 - 174
8X-RAY DIFFRACTION8{A|175 - 187}A175 - 187
9X-RAY DIFFRACTION9{A|188 - 200}A188 - 200
10X-RAY DIFFRACTION10{A|201 - 222}A201 - 222
11X-RAY DIFFRACTION11{A|223 - 235}A223 - 235
12X-RAY DIFFRACTION12{A|236 - 247}A236 - 247
13X-RAY DIFFRACTION13{A|248 - 255}A248 - 255
14X-RAY DIFFRACTION14{A|256 - 270}A256 - 270
15X-RAY DIFFRACTION15{A|271 - 283}A271 - 283
16X-RAY DIFFRACTION16{A|284 - 301}A284 - 301
17X-RAY DIFFRACTION17{A|302 - 315}A302 - 315
18X-RAY DIFFRACTION18{A|316 - 342}A316 - 342
19X-RAY DIFFRACTION19{A|343 - 358}A343 - 358
20X-RAY DIFFRACTION20{A|359 - 375}A359 - 375
21X-RAY DIFFRACTION21{B|42 - 58}B42 - 58
22X-RAY DIFFRACTION22{B|59 - 74}B59 - 74
23X-RAY DIFFRACTION23{B|75 - 87}B75 - 87
24X-RAY DIFFRACTION24{B|88 - 96}B88 - 96
25X-RAY DIFFRACTION25{B|107 - 125}B107 - 125
26X-RAY DIFFRACTION26{B|134 - 149}B134 - 149
27X-RAY DIFFRACTION27{B|150 - 155}B150 - 155
28X-RAY DIFFRACTION28{B|156 - 174}B156 - 174
29X-RAY DIFFRACTION29{B|175 - 187}B175 - 187
30X-RAY DIFFRACTION30{B|188 - 200}B188 - 200
31X-RAY DIFFRACTION31{B|201 - 211}B201 - 211
32X-RAY DIFFRACTION32{B|212 - 224}B212 - 224
33X-RAY DIFFRACTION33{B|225 - 244}B225 - 244
34X-RAY DIFFRACTION34{B|245 - 250}B245 - 250
35X-RAY DIFFRACTION35{B|251 - 268}B251 - 268
36X-RAY DIFFRACTION36{B|269 - 283}B269 - 283
37X-RAY DIFFRACTION37{B|284 - 303}B284 - 303
38X-RAY DIFFRACTION38{B|304 - 348}B304 - 348
39X-RAY DIFFRACTION39{B|349 - 361}B349 - 361
40X-RAY DIFFRACTION40{B|362 - 375}B362 - 375

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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