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- PDB-8bwi: Crystal structure of human Twisted gastrulation protein homolog 1... -

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Basic information

Entry
Database: PDB / ID: 8bwi
TitleCrystal structure of human Twisted gastrulation protein homolog 1 (TWSG1), crystal form 2
ComponentsTwisted gastrulation protein homolog 1
KeywordsSIGNALING PROTEIN / Twisted gastrulation protein homolog 1 (TWSG1) / Transforming Growth Factor beta (TGF-beta) signalling pathway / extracellular protein / disulfide rich domains.
Function / homology
Function and homology information


negative regulation of CD4-positive, alpha-beta T cell activation / regulation of BMP signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of BMP signaling pathway / transforming growth factor beta binding / camera-type eye development / negative regulation of cytokine production / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of SMAD protein signal transduction / hemopoiesis ...negative regulation of CD4-positive, alpha-beta T cell activation / regulation of BMP signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of BMP signaling pathway / transforming growth factor beta binding / camera-type eye development / negative regulation of cytokine production / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of SMAD protein signal transduction / hemopoiesis / mesoderm formation / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / chondrocyte differentiation / BMP signaling pathway / salivary gland morphogenesis / forebrain development / ossification / heparin binding / extracellular space
Similarity search - Function
Twisted gastrulation (Tsg) protein / Twisted gastrulation (Tsg) protein conserved region
Similarity search - Domain/homology
Twisted gastrulation protein homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMalinauskas, T. / Rudolf, A.F. / Moore, G. / Eggington, H. / Belnoue-Davis, H. / El Omari, K. / Woolley, R.E. / Griffiths, S.C. / Duman, R. / Wagner, A. ...Malinauskas, T. / Rudolf, A.F. / Moore, G. / Eggington, H. / Belnoue-Davis, H. / El Omari, K. / Woolley, R.E. / Griffiths, S.C. / Duman, R. / Wagner, A. / Leedham, S.J. / Baldock, C. / Ashe, H. / Siebold, C.
Funding support United Kingdom, European Union, France, 4items
OrganizationGrant numberCountry
Cancer Research UKC20724/A14414 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
European Research Council (ERC)647278European Union
Human Frontier Science Program (HFSP)LT000021/2014-L France
CitationJournal: Nat Commun / Year: 2024
Title: Molecular mechanism of BMP signal control by Twisted gastrulation.
Authors: Malinauskas, T. / Moore, G. / Rudolf, A.F. / Eggington, H. / Belnoue-Davis, H.L. / El Omari, K. / Griffiths, S.C. / Woolley, R.E. / Duman, R. / Wagner, A. / Leedham, S.J. / Baldock, C. / Ashe, H.L. / Siebold, C.
History
DepositionDec 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Twisted gastrulation protein homolog 1


Theoretical massNumber of molelcules
Total (without water)23,5701
Polymers23,5701
Non-polymers00
Water00
1
A: Twisted gastrulation protein homolog 1

A: Twisted gastrulation protein homolog 1


Theoretical massNumber of molelcules
Total (without water)47,1402
Polymers47,1402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3780 Å2
ΔGint-15 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.250, 92.250, 95.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

#1: Protein Twisted gastrulation protein homolog 1


Mass: 23569.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TWSG1, TSG, PSEC0250 / Plasmid: pHLsec / Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q9GZX9

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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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.0 M K/Na tartrate, 0.1 M MES pH 6.0 / PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 3.4→48.08 Å / Num. obs: 3626 / % possible obs: 99.4 % / Redundancy: 15.6 % / Biso Wilson estimate: 99.38 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.069 / Rrim(I) all: 0.265 / Net I/σ(I): 8.2
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 15.4 % / Rmerge(I) obs: 5.961 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 254 / CC1/2: 0.436 / Rpim(I) all: 1.551 / Rrim(I) all: 6.167 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→46.12 Å / SU ML: 0.6835 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3424 132 4.5 %
Rwork0.2955 2802 -
obs0.2977 2934 81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.51 Å2
Refinement stepCycle: LAST / Resolution: 3.4→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 0 0 1266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331292
X-RAY DIFFRACTIONf_angle_d0.67941744
X-RAY DIFFRACTIONf_chiral_restr0.0441190
X-RAY DIFFRACTIONf_plane_restr0.0039226
X-RAY DIFFRACTIONf_dihedral_angle_d10.7415475
LS refinement shellResolution: 3.4→46.12 Å
RfactorNum. reflection% reflection
Rfree0.3424 132 -
Rwork0.2955 2802 -
obs--81 %
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)
13.581876196032.25077053505-1.625562770642.50341399961-0.7661375563991.22825769809-0.4217812435821.243432821170.894493605369-0.4342939973960.4568254083930.880667022164-1.022401367680.131615222354-0.4701944318750.87369854771-0.74812506419-0.1115627822931.223128242610.4373434417451.11264293096-36.104145425220.0473846144-23.1182963848
26.47333479752-0.29950929505-4.995651141850.03963527392810.2384935545863.870819543561.040349673631.510286240740.0670221866830.00657512292351-0.660939058857-0.2892490236670.328777532393-0.346388809309-0.271615325962.042297738520.23213882505-0.001347780839071.453141929510.3435047080182.23413826943-41.71331210632.01608400697-19.7202036771
34.00905185759-0.3290845187290.9523640689082.356380255760.1468692639674.306229255190.249463744499-0.0460176868724-0.304251686347-0.4118653764430.0810982873268-0.7110070598050.7174274191450.893768449699-0.1782730125760.5398537145610.07285598441050.06107080667950.5706551526990.06117949264150.851488819365-32.0798325216-11.5552147373.44009011025
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 79 )25 - 791 - 55
22chain 'A' and (resid 80 through 85 )80 - 8556 - 61
33chain 'A' and (resid 86 through 226 )86 - 22662 - 165

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