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

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Basic information

Entry
Database: PDB / ID: 8bwa
TitleCrystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with platinum
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 / forebrain development / 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 / forebrain development / mesoderm formation / hemopoiesis / positive regulation of SMAD protein signal transduction / negative regulation of BMP signaling pathway / chondrocyte differentiation / negative regulation of osteoblast differentiation / BMP signaling pathway / salivary gland morphogenesis / 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 / SAD / Resolution: 3.61 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, France, European Union, 4items
OrganizationGrant numberCountry
Cancer Research UKC20724/A14414 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
Human Frontier Science Program (HFSP)LT000021/2014-L France
European Research Council (ERC)647278European Union
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 1.1Oct 23, 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)48,5059
Polymers47,1402
Non-polymers1,3667
Water00
1
A: Twisted gastrulation protein homolog 1
hetero molecules

A: Twisted gastrulation protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,70010
Polymers47,1402
Non-polymers1,5618
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4570 Å2
ΔGint-155 kcal/mol
Surface area16750 Å2
MethodPISA
2
B: Twisted gastrulation protein homolog 1
hetero molecules

B: Twisted gastrulation protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3108
Polymers47,1402
Non-polymers1,1706
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4530 Å2
ΔGint-116 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.430, 98.430, 188.160
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_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYTHRA1 - 164
d_21ens_1GLYTHRB1 - 164

NCS oper: (Code: givenMatrix: (-0.999810319277, -0.018725413673, -0.0053557772176), (0.0194310789822, -0.977757879793, -0.208834771225), (-0.00132613589644, -0.208899227824, 0.977936272964)Vector: - ...NCS oper: (Code: given
Matrix: (-0.999810319277, -0.018725413673, -0.0053557772176), (0.0194310789822, -0.977757879793, -0.208834771225), (-0.00132613589644, -0.208899227824, 0.977936272964)
Vector: -96.9273802687, 0.552845354552, 0.11792914938)

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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
Details: Protein crystals were soaked with Di-mu-iodobis(ethylenediamine)diplatinum(2) nitrate (PIP) for phasing.
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
#2: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Pt
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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.77 M LiCl, 15.5% w/v PEG 6000, 77 mM HEPES pH 7.0, 5.2% 2,2,2-trifluoroethanol. The crystal was soaked in saturated solution of di-mu-iodobis(ethylenediamine)diplatinum(2) nitrate (PIP) ...Details: 0.77 M LiCl, 15.5% w/v PEG 6000, 77 mM HEPES pH 7.0, 5.2% 2,2,2-trifluoroethanol. The crystal was soaked in saturated solution of di-mu-iodobis(ethylenediamine)diplatinum(2) nitrate (PIP) solution before data collection.
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: 1.03003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03003 Å / Relative weight: 1
ReflectionResolution: 3.61→62.72 Å / Num. obs: 6653 / % possible obs: 99.5 % / Redundancy: 25.8 % / Biso Wilson estimate: 202.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.029 / Rrim(I) all: 0.146 / Net I/σ(I): 13.6
Reflection shellResolution: 3.61→3.67 Å / Redundancy: 25.4 % / Rmerge(I) obs: 7.612 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 319 / CC1/2: 0.247 / Rpim(I) all: 1.524 / Rrim(I) all: 7.767 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.61→49.22 Å / SU ML: 0.2932 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 46.1997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3902 324 4.94 %
Rwork0.3392 6230 -
obs0.3415 6554 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 245.98 Å2
Refinement stepCycle: LAST / Resolution: 3.61→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 7 0 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232544
X-RAY DIFFRACTIONf_angle_d0.59633436
X-RAY DIFFRACTIONf_chiral_restr0.0405376
X-RAY DIFFRACTIONf_plane_restr0.004446
X-RAY DIFFRACTIONf_dihedral_angle_d11.0754934
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.214171879878 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.61-4.550.38781540.40892981X-RAY DIFFRACTION97
4.55-49.220.39071700.32763249X-RAY DIFFRACTION99.25
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)
15.2149844089-1.170948563823.320299042096.40953625165-1.433108201815.1942233309-0.03816218899950.4704392080092.70041488761-2.051366575091.09787225264-1.15272937337-0.698112737823-1.173462045350.02726898400323.73496386041-0.552801383032-0.3180575149532.571585118110.2153377404792.72470757277-38.264948976422.9157293065-20.7727312119
27.062156780460.229777141577-3.679704149673.318935658784.403803621347.942972958150.1206020792360.270562358686-0.728825323251-0.133693890472-0.73833350703-1.170259575551.312031703551.12591703926-0.08167201720582.537955151490.3343269774550.2148707431472.150233856170.521999913572.45416688408-34.2118725835-12.04771941492.15259311837
34.2177438083-0.114624900243-4.713708333338.311690203052.628948123966.43294979854-0.2495928504982.00982356849-0.107587775278-4.58210083613-0.908393128131.515797283330.689452344954-2.433769639640.6742544927223.443283727770.442659850548-0.1360068477283.0375543269-0.2641848300982.83667692691-58.9984938041-18.3404314284-24.9656607587
47.732557715030.400535464571-2.043833751284.28806135145-4.463257382539.297209088980.948377552177-0.3786052818460.1877244029411.5683172749-0.2451353928080.632781082004-2.15941319568-0.782598404434-0.8652370516453.012791847730.05537805393480.1150335701442.93679074674-0.5174352629292.44555797468-62.505920226411.24718585454.79126259678
58.23514033969-0.9034685327771.391395141562.67678323747-2.375907575832.340052096312.008376501434.051310364782.81688527662-4.45296428224-1.32611631167-3.96593572121-0.151210346228.60930810667E-60.1231913893662.99509801499-0.093710752770.7576118035523.867735922310.03691305569583.09686261019-43.59725283674.55901141843-20.1353912355
65.92684653382-5.18254893777-7.059689708587.689073703464.410405982469.34919686295-0.5325302732699.27645603055-4.310711024-5.21774651013.902019328143.15139707058-2.687724386894.89968672037-2.095718206813.75854824252-0.223389987051-1.454450601354.48413807789-0.5195104696643.43584697527-53.2812027727-0.390329075074-20.2954324731
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 86 through 225 )BB86 - 22562 - 164
55chain 'A' and (resid 80 through 85 )AA80 - 8556 - 61
66chain 'B' and (resid 80 through 85 )BB80 - 8556 - 61

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