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- PDB-9doc: The von Willebrand factor A domain of human capillary morphogenes... -

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Basic information

Entry
Database: PDB / ID: 9doc
TitleThe von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Thr-Val linker variant, at 1.2 Angstrom resolution
ComponentsTranscription factor ETV6,Capillary morphogenesis gene 2 protein
KeywordsPEPTIDE BINDING PROTEIN / TELSAM / 1TEL / Pointed Domain / Sterile Alpha Motif domain / ETS / TEL / CMG2 / vWA Domain / Anthrax toxin receptor 2 / ONCOPROTEIN
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 / Signaling by FLT3 fusion proteins / neurogenesis / 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 / Signaling by FLT3 fusion proteins / neurogenesis / 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. / Ets-domain signature 2. ...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. / 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 (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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Transcription factor ETV6 / Anthrax toxin receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsSamarawickrama, P. / Probst, R. / Ludlow, K. / 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
CitationJournal: To be published
Title: 1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons
Authors: Samarawickrama, P. / Ludlow, K. / Probst, R. / Abiodun, W. / Averett, J. / Hansen, D. / Doukov, T. / Moody, J.D.
History
DepositionSep 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor ETV6,Capillary morphogenesis gene 2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,80216
Polymers30,2341
Non-polymers56715
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.428, 101.428, 49.239
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,Capillary morphogenesis gene 2 protein


Mass: 30234.422 Da / Num. of mol.: 1 / Fragment: von Willebrand factor A domain of CMG2
Mutation: TELSAM: R80S,V112E (Uniprot numbering),vWA: C175A (Uniprot numbering)
Source method: isolated from a genetically manipulated source
Details: Tandem fusion of 1TEL followed by the vWA domain of CMG2
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, ANTXR2, CMG2 / Plasmid: pET42-His-1TEL-XhoI
Details (production host): N-term 10xHis, Kanamycin resistant
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: P41212, UniProt: P58335

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Non-polymers , 5 types, 260 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Description: Large Hexagonal prism tapered to a point at one end
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: 100 mM Bis-Tris, pH 7.25, 1350 mM Sodium Potassium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2023 / Details: Rh coated collimating mirror, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.19→43.92 Å / Num. obs: 91358 / % possible obs: 97.19 % / Redundancy: 9 % / Biso Wilson estimate: 17.06 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04722 / Rpim(I) all: 0.01608 / Rrim(I) all: 0.04997 / Net I/σ(I): 15.17
Reflection shellResolution: 1.19→1.233 Å / Rmerge(I) obs: 2.286 / Mean I/σ(I) obs: 0.62 / Num. unique obs: 7752 / CC1/2: 0.523 / CC star: 0.829 / Rpim(I) all: 0.8955 / Rrim(I) all: 2.463

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→43.92 Å / SU ML: 0.1758 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 4430 4.9 %
Rwork0.189 85986 -
obs0.1894 90416 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.27 Å2
Refinement stepCycle: LAST / Resolution: 1.19→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 28 245 2309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892133
X-RAY DIFFRACTIONf_angle_d0.92922905
X-RAY DIFFRACTIONf_chiral_restr0.0721328
X-RAY DIFFRACTIONf_plane_restr0.0077372
X-RAY DIFFRACTIONf_dihedral_angle_d12.7314778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.20.4081130.40512129X-RAY DIFFRACTION72.53
1.2-1.210.3586920.38432479X-RAY DIFFRACTION83.99
1.21-1.230.35891300.38362645X-RAY DIFFRACTION88.89
1.23-1.240.36311540.35142817X-RAY DIFFRACTION96.59
1.24-1.260.37221480.3692886X-RAY DIFFRACTION97.87
1.26-1.280.31511540.3112877X-RAY DIFFRACTION99.21
1.28-1.30.32591320.32092982X-RAY DIFFRACTION98.54
1.3-1.320.37131700.31492886X-RAY DIFFRACTION99.97
1.32-1.340.33451230.32512979X-RAY DIFFRACTION99.52
1.34-1.360.27211450.30182952X-RAY DIFFRACTION99.77
1.36-1.380.3141510.28752894X-RAY DIFFRACTION98.67
1.38-1.410.27281480.2472946X-RAY DIFFRACTION99.81
1.41-1.430.24351680.23712919X-RAY DIFFRACTION99.74
1.43-1.460.27661380.23172906X-RAY DIFFRACTION99.44
1.46-1.50.25931520.21752979X-RAY DIFFRACTION99.87
1.5-1.530.23881470.21192920X-RAY DIFFRACTION99.51
1.53-1.570.20611570.19832959X-RAY DIFFRACTION99.94
1.57-1.610.24141750.20012941X-RAY DIFFRACTION100
1.61-1.660.22981680.20122925X-RAY DIFFRACTION99.94
1.66-1.710.25391190.20062974X-RAY DIFFRACTION99.81
1.71-1.770.19681750.19862936X-RAY DIFFRACTION100
1.77-1.840.20511360.18562982X-RAY DIFFRACTION100
1.84-1.930.211500.18232874X-RAY DIFFRACTION97.33
1.93-2.030.17431400.17342903X-RAY DIFFRACTION97.78
2.03-2.160.18911620.17122858X-RAY DIFFRACTION96.76
2.16-2.320.1741490.1632838X-RAY DIFFRACTION95.77
2.32-2.560.17511630.16652969X-RAY DIFFRACTION100
2.56-2.930.17311590.17342848X-RAY DIFFRACTION95.95
2.93-3.690.17251780.16782784X-RAY DIFFRACTION94.09
3.69-43.920.16091340.16462999X-RAY DIFFRACTION96.76
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)
13.350561031560.216149631269-0.1827469406053.01608157261-0.1356235402760.837952192951-0.0545664927021-0.0837855576781-0.1564371812990.049102105460.00208287874989-0.08579933130110.0941373181040.01589380246070.0492217591960.1237738752650.004742310188410.0151531073760.109045988172-0.00902978068310.16111938048815.0083976777-16.855746591-22.1817886511
26.358602104640.7169254848991.51798378511-0.1115473197760.0724528644458-0.0976905243585-0.17561662697-0.4483635676160.3045011644450.03463386612330.004017204688780.05014536802720.000997950598437-0.07765153511360.121357943390.1705710127890.0297420607572-0.03488886956660.289299789248-0.04359373122350.25722913548538.4694197862-5.88469873441-10.9069742282
35.04663868889-0.0822903942772.072432032141.73238860327-0.004804047150081.333222595010.036605363269-0.217572925495-0.6986772406390.01602552699380.0938195694965-0.006495385218230.107025772592-0.0999803062907-0.08049047301970.1305184238620.00793408012906-0.009043333322370.2061824182240.04154470076430.27659786147949.0019210316-16.0612349109-11.6764251239
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 9 through 75 )9 - 751 - 67
22chain 'A' and (resid 76 through 170 )76 - 17068 - 162
33chain 'A' and (resid 171 through 268 )171 - 268163 - 260

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