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

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Basic information

Entry
Database: PDB / ID: 8fzv
TitleThe von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Ala-Ala linker variant, expressed with SUMO tag
ComponentsTranscription factor ETV6,Anthrax toxin receptor 2
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 / 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. / 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 / 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 / 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: 3.29 Å
AuthorsPedroza Romo, M.J. / Soleimani, S. / Doukov, T. / Lebedev, A. / 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 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author

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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
B: Transcription factor ETV6,Anthrax toxin receptor 2
C: Transcription factor ETV6,Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,15894
Polymers85,9433
Non-polymers3,21591
Water724
1
A: Transcription factor ETV6,Anthrax toxin receptor 2
hetero molecules


  • defined by author
  • 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.
  • 28.7 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)28,6722
Polymers28,6481
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription factor ETV6,Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,78233
Polymers28,6481
Non-polymers1,13432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription factor ETV6,Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,70459
Polymers28,6481
Non-polymers2,05658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.557, 162.557, 56.877
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: 28647.684 Da / Num. of mol.: 3
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 35.453 Da / Num. of mol.: 90 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM sodium acetate, pH 4.6, 2.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.29→70.39 Å / Num. obs: 12820 / % possible obs: 90.65 % / Redundancy: 7.9 % / Biso Wilson estimate: 118.63 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.3371 / Net I/σ(I): 6.02
Reflection shellResolution: 3.292→3.409 Å / Rmerge(I) obs: 3.593 / Num. unique obs: 515 / CC1/2: 0.283

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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 / Resolution: 3.29→70.39 Å / SU ML: 0.4006 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.5111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3141 595 4.93 %
Rwork0.2823 11464 -
obs0.2839 12059 90.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.67 Å2
Refinement stepCycle: LAST / Resolution: 3.29→70.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 91 4 4021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00173993
X-RAY DIFFRACTIONf_angle_d0.36495446
X-RAY DIFFRACTIONf_chiral_restr0.0366632
X-RAY DIFFRACTIONf_plane_restr0.0029720
X-RAY DIFFRACTIONf_dihedral_angle_d7.56261292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.620.39281160.36042201X-RAY DIFFRACTION69.81
3.62-4.140.34561560.30473084X-RAY DIFFRACTION98.27
4.14-5.210.29451450.29283087X-RAY DIFFRACTION96.51
5.22-70.390.3011780.25663092X-RAY DIFFRACTION95.81
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)
19.50968651712-3.982227642281.075895631475.099781959141.140543676198.48017385085-0.3582425087660.538622627042-0.21023687063-0.77114860557-0.0829441738771-0.01211180205420.424115442913-1.076734900380.494988870470.704124468831-0.2983754449990.0294924904050.729263029535-0.08512151563230.72764860799163.974569950634.6745239882-19.0529468397
28.669553224362.383620034-1.047462280948.476567444991.4211742515411.2163290750.0807866595272-0.4711565567760.467160869751-0.2757246910860.0810834945841-0.09506431091510.458645956141-0.747327983676-0.1234724824440.52097150096-0.262415857657-0.0001302436062470.8382307130860.1442261573460.85292226920147.125694573911.56028628940.820413884184
33.028325966623.005751272150.3947662397615.250366359923.833437029798.301884306582.19546562358-3.04791701214-1.125969691360.3801843828891.10521333894-2.15362383625-1.54224479063.32930111878-0.7174388812960.672785150171-0.175948806418-0.6214053553421.726617716780.0560852191161.1796736066758.166116577112.22351894439.4790936538
47.88001632168-3.03806937869-0.97563233078210.0349036619-0.8632347348195.800027124380.03174153387050.4335533513620.07206553340850.247298820136-0.469521864457-1.33325668461-0.2102012760310.6831852461590.5663375521630.578813377674-0.0550849778016-0.1104900517950.4648298802340.1696444692540.76114357972414.652399183414.9755720485-2.06885323265
59.580646260152.800728696593.4480612603210.21557212895.312583632878.70307895018-0.7296912893690.327328579231-0.2832161506751.653584325770.855741472369-0.6885959531550.842695919512.67299112012-0.02213912447731.271847302810.382240020688-0.2297909160881.432488232280.01625878879560.70007452697625.634723842528.07308226525.1125938671
61.404686590780.926658539147-2.993217472272.01580384278-9.885655919617.72642655666-2.05106687889-1.8898077723-1.352932649052.281369651980.6551292095462.02209604581.67425615869-0.7588854063960.1612026310251.244014260930.06245615782920.4189478686041.97215026295-1.87498664767-3.4696646839451.336668897154.6803851722-4.52702315777
77.231453078533.48984465029-4.883714646122.09261521684-2.064391269671.9101792487-1.75649056238-1.28035201423-0.166760226097-0.3908195074580.5956926996712.86227784962.64188032142-1.418653806630.7670622195461.075270899160.3449962961220.012950378291.0418907459-0.5463015404511.3149327917153.195552722149.8312725743-8.15553072519
82.523661723885.994353778454.768884066372.512506739077.727055526312.658261546390.28014797730.02296468825411.46983476621-0.995544314207-1.725417884911.43093011025-0.195500756432-0.6955028312031.475414743181.163698588120.0735720727317-0.1259778293061.126009789550.03522383323060.8411970516658.484830788760.375764139-12.6271447815
98.252167541753.459388518023.344581673422.730142868724.913368657223.26896776278-0.1086407448680.445815798233-0.0980055545755-1.53363322276-0.0574753469931-0.245734004084-1.22144342519-0.857348801786-0.2143312389841.04408298853-0.007185586283160.03636166000660.7212333826390.05097257801430.68700961504763.393694098954.2010231762-13.9051371901
1010.47611167277.50518684228-1.348322057734.82510734419-5.212295272854.396962498640.848352781134-0.6729198689570.4220496805420.374217457536-0.244126579029-0.548349064091-0.2713468784090.689578358099-0.6225836688521.02448908847-0.08160716422080.04952072649770.694193880739-0.09764130409010.73022648182567.918714106853.9612323143-7.70696049111
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 81 )AA1 - 811 - 81
22chain 'A' and (resid 82 through 229 )AA82 - 22982 - 229
33chain 'A' and (resid 230 through 250 )AA230 - 250230 - 247
44chain 'B' and (resid 1 through 79 )BC1 - 791 - 79
55chain 'B' and (resid 80 through 253 )BC80 - 25380 - 248
66chain 'C' and (resid 8 through 12 )CD8 - 121 - 5
77chain 'C' and (resid 13 through 17 )CD13 - 176 - 10
88chain 'C' and (resid 18 through 31 )CD18 - 3111 - 24
99chain 'C' and (resid 32 through 53 )CD32 - 5325 - 46
1010chain 'C' and (resid 54 through 79 )CD54 - 7947 - 72

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