[English] 日本語
Yorodumi
- PDB-8bwd: Crystal structure of human Twisted gastrulation protein homolog 1... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
Yorodumi

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

Read more