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

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Basic information

Entry
Database: PDB / ID: 8bwd
TitleCrystal structure of human Twisted gastrulation protein homolog 1 (TWSG1), crystal form 1
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 / camera-type eye development / transforming growth factor beta binding / negative regulation of cytokine production / positive regulation of transforming growth factor beta receptor signaling pathway / hemopoiesis / mesoderm formation ...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 / camera-type eye development / transforming growth factor beta binding / negative regulation of cytokine production / positive regulation of transforming growth factor beta receptor signaling pathway / hemopoiesis / mesoderm formation / negative regulation of BMP signaling pathway / positive regulation of SMAD protein signal transduction / 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 / Twisted gastrulation (Tsg) protein N-terminal domain
Similarity search - Domain/homology
Twisted gastrulation protein homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 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
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Twisted gastrulation protein homolog 1
B: Twisted gastrulation protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2363
Polymers47,1402
Non-polymers961
Water181
1
A: Twisted gastrulation protein homolog 1
hetero molecules

A: Twisted gastrulation protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3324
Polymers47,1402
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4180 Å2
ΔGint-44 kcal/mol
Surface area16360 Å2
MethodPISA
2
B: Twisted gastrulation protein homolog 1

B: 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 area4050 Å2
ΔGint-14 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.993, 97.993, 187.616
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 25 through 27 or resid 29...
d_2ens_1(chain "B" and (resid 25 through 27 or resid 29...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYASNA1 - 3
d_12ens_1ALAGLYA5 - 25
d_13ens_1GLYARGA27 - 56
d_14ens_1SERTHRA59 - 164
d_21ens_1GLYASNB1 - 3
d_22ens_1ALAGLYB5 - 25
d_23ens_1GLYARGB27 - 56
d_24ens_1SERTHRB59 - 164

NCS oper: (Code: givenMatrix: (-0.999750586203, -0.0213452496622, -0.00656853894213), (0.0222644448252, -0.975632324304, -0.218279321672), (-0.0017492522982, -0.218371124671, 0.975864228275)Vector: - ...NCS oper: (Code: given
Matrix: (-0.999750586203, -0.0213452496622, -0.00656853894213), (0.0222644448252, -0.975632324304, -0.218279321672), (-0.0017492522982, -0.218371124671, 0.975864228275)
Vector: -96.2801048256, 0.704407643229, 0.0818998387534)

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Components

#1: Protein Twisted gastrulation protein homolog 1


Mass: 23569.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TWSG1, TSG, PSEC0250 / Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q9GZX9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.85 M LiCl, 17.1% w/v PEG 6000, 85 mM HEPES pH 7.0, 3.6% 1,1,1,3,3,3-hexafluoro-2-propanol
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.627→84.864 Å / Num. obs: 8855 / % possible obs: 53 % / Redundancy: 18.8 % / Biso Wilson estimate: 82.65 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.019 / Rrim(I) all: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 2.627→2.999 Å / Rmerge(I) obs: 1.603 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 443 / Rpim(I) all: 0.377 / Rrim(I) all: 1.648 / % possible all: 8.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→42.43 Å / SU ML: 0.3495 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.4611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3054 460 5.2 %
Rwork0.259 8386 -
obs0.2616 8846 53.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.63 Å2
Refinement stepCycle: LAST / Resolution: 2.63→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 5 1 2500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262548
X-RAY DIFFRACTIONf_angle_d0.65223442
X-RAY DIFFRACTIONf_chiral_restr0.0436376
X-RAY DIFFRACTIONf_plane_restr0.0037446
X-RAY DIFFRACTIONf_dihedral_angle_d11.0058934
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.608144477686 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-3.010.4837210.4457440X-RAY DIFFRACTION8.6
3.01-3.790.31251270.30882514X-RAY DIFFRACTION48.41
3.79-42.430.30233120.24635432X-RAY DIFFRACTION99.9
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)
13.406803716150.5611074249040.4635382312867.49241574321-0.3926970789977.05509289913-0.1448986774990.04878907825530.37578247469-0.7674636618290.545575772817-0.533765557987-0.3431419636670.460644916763-0.3952992752610.722791496802-0.2006055610880.1314910722160.9255504436050.04137483053270.402027436287-37.880734547223.065420527-20.4569516343
22.711582185741.16114130119-1.161758176555.13791512656-1.022862029164.340415843270.0979091078892-0.430686246157-0.62757505048-0.0472020901001-0.240480109926-1.428125606720.7456389613160.9668039875390.05406246232640.5050978115850.0890003627028-0.01101485722960.727644571127-0.01085464015660.279592520337-33.9151527622-11.90831176712.17462442146
34.282565609960.826684125199-1.06813230774.115813211210.863418982426.181910758930.29749962245-0.0351121508511-0.74232023155-0.195103733258-0.1953323866840.226714292490.792724680915-0.61750523801-0.1121117931320.788103296433-0.081364321353-0.223335150491.03711491767-0.1860056300860.441981159763-58.8274819097-18.2941133305-24.7870686539
40.2374225166120.131920826869-0.8731589400510.0782789891553-0.4727231935043.227403420270.004552668771511.30792967316-0.925137472312-0.7111409661380.692040983780.781097140285-0.0815132223866-0.449437472625-0.9195179140561.72460546680.138270788718-0.2495039079911.58159477281-0.5332479952121.18991036848-53.1143030531-0.738231546361-20.2184729107
50.8240199540330.996447086732-1.181297032833.01613585335-1.041102761011.782320034930.318750877786-0.1528107804360.2804665225790.487733086363-0.2078544872840.97809067121-0.724047354942-1.225436527380.2122429067480.3978738467930.2275780347810.08677317350711.27511854513-0.1887740821340.124967472951-62.094989866111.14910008054.86445628154
60.4788807388840.564562937557-1.206363936030.783425092355-1.564117180043.632195268120.4817686072931.178421650760.749572521924-0.07367472113420.109761857314-0.4585333809172.770146744110.894902968232-0.1319218112231.45089060143-0.146440453735-0.137361035621.55365353391-0.2165155165151.15011716089-43.12525290634.57345055427-19.9951269349
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 79)AA25 - 791 - 55
22chain 'A' and (resid 86 through 225 )AA86 - 22562 - 164
33chain 'B' and (resid 25 through 79 )BB25 - 791 - 55
44chain 'B' and (resid 80 through 85)BB80 - 8556 - 61
55chain 'B' and (resid 86 through 225 )BB86 - 22562 - 164
66chain 'A' and (resid 80 through 85)AA80 - 8556 - 61

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