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- PDB-8ft8: The von Willebrand factor A domain of human capillary morphogenes... -

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Basic information

Entry
Database: PDB / ID: 8ft8
TitleThe von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Thr-Val linker variant, SUMO tag-free preparation
ComponentsTranscription factor ETV6,Anthrax toxin receptor 2 chimera
KeywordsPEPTIDE BINDING PROTEIN / TELSAM fusion / polymer forming crystallization chaperone
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Uptake and function of anthrax toxins / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transmembrane signaling receptor activity ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Uptake and function of anthrax toxins / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transmembrane signaling receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / endosome membrane / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / cell surface / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 ...Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Sterile alpha motif/pointed domain superfamily / von Willebrand factor A-like domain superfamily / DNA polymerase; domain 1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Transcription factor ETV6 / Anthrax toxin receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGajjar, P.L. / Litchfield, C.M. / Callahan, M. / Redd, N. / Doukov, T. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209-01 United States
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Increasing the bulk of the 1TEL-target linker and retaining the 10×His tag in a 1TEL-CMG2-vWa construct improves crystal order and diffraction limits.
Authors: Gajjar, P.L. / Pedroza Romo, M.J. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, ...Authors: Gajjar, P.L. / Pedroza Romo, M.J. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, T. / Lebedev, A. / Moody, J.D.
#1: Journal: Biorxiv / Year: 2023
Title: Decreasing the flexibility of the TELSAM-target protein linker and omitting the cleavable fusion tag improves crystal order and diffraction limits.
Authors: Gajjar, P.L. / Romo, M.J.P. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, T. / ...Authors: Gajjar, P.L. / Romo, M.J.P. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, T. / Lebedev, A. / Moody, J.D.
History
DepositionJan 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor ETV6,Anthrax toxin receptor 2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3647
Polymers30,0301
Non-polymers3346
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Kim CA, Phillips ML, Kim W, Gingery M, Tran HH, Robinson MA, Faham S, Bowie JU. Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression. ...Evidence: electron microscopy, Kim CA, Phillips ML, Kim W, Gingery M, Tran HH, Robinson MA, Faham S, Bowie JU. Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression. The EMBO journal. 2001 Aug 1;20(15):4173-82.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.882, 100.882, 49.754
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
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,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transcription factor ETV6,Anthrax toxin receptor 2 chimera / ETS translocation variant 6 / ETS-related protein Tel1 / Tel / Capillary morphogenesis gene 2 protein / CMG-2


Mass: 30030.176 Da / Num. of mol.: 1 / Mutation: R14A,V77E,K87A,R89A,R91T,A92V,A225V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, ANTXR2, CMG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P41212, UniProt: P58335

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Non-polymers , 5 types, 150 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2022
Details: Mirror: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2, Monochromator: Liquid nitrogen-cooled double crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→19.87 Å / Num. obs: 38098 / % possible obs: 99.56 % / Redundancy: 19 % / Biso Wilson estimate: 27.12 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05639 / Rpim(I) all: 0.01339 / Rrim(I) all: 0.05799 / Net I/σ(I): 25.28
Reflection shellResolution: 1.6→1.658 Å / Rmerge(I) obs: 0.9895 / Num. unique obs: 3766 / CC1/2: 0.939 / Rpim(I) all: 0.2253 / % possible all: 99.13

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Blu-Icedata collection
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
Coot0.9.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QAR, 1SHU

2qar

1shu


Resolution: 1.6→19.87 Å / SU ML: 0.1649 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.8698
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2042 1951 5.12 %
Rwork0.1821 36122 -
obs0.1833 38073 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.57 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 15 144 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582013
X-RAY DIFFRACTIONf_angle_d0.75832747
X-RAY DIFFRACTIONf_chiral_restr0.0474321
X-RAY DIFFRACTIONf_plane_restr0.0061351
X-RAY DIFFRACTIONf_dihedral_angle_d12.754717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.3081620.26852520X-RAY DIFFRACTION99.55
1.64-1.680.24821330.2392567X-RAY DIFFRACTION99.05
1.68-1.730.25491220.232576X-RAY DIFFRACTION99.41
1.73-1.790.28171220.21432562X-RAY DIFFRACTION99.52
1.79-1.850.25761460.22942556X-RAY DIFFRACTION99.63
1.85-1.930.22871460.20242557X-RAY DIFFRACTION99.7
1.93-2.020.19661390.20262598X-RAY DIFFRACTION99.85
2.02-2.120.2151130.18572608X-RAY DIFFRACTION99.85
2.12-2.250.1911470.18922571X-RAY DIFFRACTION99.82
2.26-2.430.19641590.17722564X-RAY DIFFRACTION99.93
2.43-2.670.23751410.19782591X-RAY DIFFRACTION100
2.67-3.060.21431450.19172595X-RAY DIFFRACTION99.64
3.06-3.850.17671190.16662632X-RAY DIFFRACTION100
3.85-19.870.19281570.16322625X-RAY DIFFRACTION98.86

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