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

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Basic information

Entry
Database: PDB / ID: 9ykb
TitleThe von Willebrand factor A domain of human capillary morphogenesis gene II, fused to the 1TEL crystallization chaperone, Ala-Val linker variant, expressed with SUMO tag.
ComponentsTranscription factor ETV6,Anthrax toxin receptor 2
KeywordsPEPTIDE BINDING PROTEIN / TELSAM / 1TEL / Pointed Domain / Sterile Alpha Motif domain / ETS / TEL / CMG2 / vWA Domain / Anthrax toxin receptor 2
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / collagen fibril organization / hematopoietic stem cell proliferation / uterus development / Uptake and function of anthrax toxins / single fertilization / neurogenesis / Signaling by FLT3 fusion proteins ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / collagen fibril organization / hematopoietic stem cell proliferation / uterus development / Uptake and function of anthrax toxins / single fertilization / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / endosome membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / external side of plasma membrane / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / chromatin / nucleolus / cell surface / negative regulation of transcription by RNA polymerase II / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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
Transcription factor ETV6 / Anthrax toxin receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGajjar, P. / Samarawickrama, P. / Pedroza Romo, M.J. / Keliiliki, A. / Litchfield, C. / Callahan, M. / Redd, N. / Doukov, T. / Lebedev, A. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1R15GM146209, 1R35GM155011 United States
CitationJournal: To be published
Title: 1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons
Authors: Samarawickrama, P. / Mead, D. / Ludlow, K. / Probst, R. / Doukov, T. / Moody, J.D.
History
DepositionOct 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: 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,Anthrax toxin receptor 2
C: Transcription factor ETV6,Anthrax toxin receptor 2
B: Transcription factor ETV6,Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1608
Polymers86,0273
Non-polymers1335
Water4,053225
1
A: Transcription factor ETV6,Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7243
Polymers28,6761
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Transcription factor ETV6,Anthrax toxin receptor 2


Theoretical massNumber of molelcules
Total (without water)28,6761
Polymers28,6761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Transcription factor ETV6,Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7604
Polymers28,6761
Non-polymers843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.745, 163.745, 54.246
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

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


Mass: 28675.738 Da / Num. of mol.: 3 / Mutation: R4A,V67E,K77A,R81A,A82V,C215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, ANTXR2, CMG2 / Plasmid: pET42_SUMO
Details (production host): N-term 10xHis, Kanamycin resistant
Cell (production host): BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: P41212, UniProt: P58335
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.62 % / Description: Moon like
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M BisTrisPropane, 1.5M 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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2022 / 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→141.81 Å / Num. obs: 29090 / % possible obs: 99.93 % / Redundancy: 10 % / Biso Wilson estimate: 34.15 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.5651 / Rpim(I) all: 0.1872 / Rrim(I) all: 0.5959 / Net I/σ(I): 2.41
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.3 % / Rmerge(I) obs: 4.209 / Mean I/σ(I) obs: 0.35 / Num. unique obs: 2892 / CC1/2: 0.33 / CC star: 0.704 / Rpim(I) all: 1.372 / Rrim(I) all: 4.429 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.9.8.95model building
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→2.59 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.9378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1938 1492 5.13 %
Rwork0.1786 27605 -
obs0.181 29069 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.95 Å2
Refinement stepCycle: LAST / Resolution: 2.5→2.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5990 0 5 225 6220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00636110
X-RAY DIFFRACTIONf_angle_d0.83398268
X-RAY DIFFRACTIONf_chiral_restr0.0468927
X-RAY DIFFRACTIONf_plane_restr0.00651063
X-RAY DIFFRACTIONf_dihedral_angle_d13.6132246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.21081270.21062509X-RAY DIFFRACTION95.18
2.58-2.670.19811280.18532468X-RAY DIFFRACTION95.07
2.67-2.780.18961230.19432512X-RAY DIFFRACTION95.12
2.78-2.910.20491570.1752435X-RAY DIFFRACTION93.83
2.91-3.060.19551370.17572507X-RAY DIFFRACTION94.78
3.06-3.250.20971410.16862489X-RAY DIFFRACTION94.64
3.25-3.50.18941260.16232518X-RAY DIFFRACTION95.23
3.5-3.850.18071410.15232511X-RAY DIFFRACTION94.68
3.86-4.410.13931080.15332548X-RAY DIFFRACTION95.93
4.41-5.560.20091470.18362522X-RAY DIFFRACTION94.49
5.56-141.810.24111570.22112586X-RAY DIFFRACTION94.04

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