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

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Basic information

Entry
Database: PDB / ID: 8fzu
TitleThe von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Thr-Val 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 / 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: 1.9 Å
AuthorsGajjar, P.L. / Litchfield, C.M. / Callahan, M. / Redd, N. / 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)86,2525
Polymers86,1173
Non-polymers1352
Water14,898827
1
A: Transcription factor ETV6,Anthrax toxin receptor 2


  • 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)28,7061
Polymers28,7061
Non-polymers00
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)28,7452
Polymers28,7061
Non-polymers391
Water181
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)28,8022
Polymers28,7061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.096, 164.096, 54.401
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: 28705.766 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-K / POTASSIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→71.06 Å / Num. obs: 66252 / % possible obs: 90.48 % / Redundancy: 10.1 % / Biso Wilson estimate: 24.16 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1787 / Rpim(I) all: 0.05901 / Net I/σ(I): 4.67
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 2.574 / Num. unique obs: 2186 / CC1/2: 0.607 / Rrim(I) all: 2.709

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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: 1.9→71.06 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7026
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 3116 5.2 %
Rwork0.2377 56842 -
obs0.2392 59958 90.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→71.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5823 0 6 827 6656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00396015
X-RAY DIFFRACTIONf_angle_d0.66018193
X-RAY DIFFRACTIONf_chiral_restr0.0427936
X-RAY DIFFRACTIONf_plane_restr0.00451062
X-RAY DIFFRACTIONf_dihedral_angle_d10.66632157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.3599570.3119964X-RAY DIFFRACTION33.94
1.93-1.960.327510.3052914X-RAY DIFFRACTION32.69
1.96-20.3082490.3192952X-RAY DIFFRACTION33.73
2-2.030.33661520.3312587X-RAY DIFFRACTION90.76
2.03-2.070.3261660.32782781X-RAY DIFFRACTION99.93
2.07-2.110.34071670.31082849X-RAY DIFFRACTION99.97
2.11-2.160.36081490.30152852X-RAY DIFFRACTION100
2.16-2.210.34421520.29012820X-RAY DIFFRACTION100
2.21-2.260.35921560.28932854X-RAY DIFFRACTION99.83
2.26-2.330.31941370.27052818X-RAY DIFFRACTION99.93
2.33-2.390.29521410.28372871X-RAY DIFFRACTION99.93
2.39-2.470.29781490.27952867X-RAY DIFFRACTION99.93
2.47-2.560.30791210.26132872X-RAY DIFFRACTION99.97
2.56-2.660.28771810.25872815X-RAY DIFFRACTION99.93
2.66-2.780.28031800.24722840X-RAY DIFFRACTION100
2.78-2.930.30131310.25372878X-RAY DIFFRACTION99.83
2.93-3.110.29011450.24352853X-RAY DIFFRACTION100
3.11-3.350.20331240.21452899X-RAY DIFFRACTION99.97
3.35-3.690.22491750.19922851X-RAY DIFFRACTION99.97
3.69-4.220.22421760.18252868X-RAY DIFFRACTION99.93
4.23-5.320.21431530.18042906X-RAY DIFFRACTION99.93
5.32-71.060.22192040.20782931X-RAY DIFFRACTION99.52
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)
12.140569322830.829919073104-0.06510516506112.30559392954-0.3043949291061.807328447150.02256305866110.0308391943893-0.179368745062-0.0150501329278-0.0827235093148-0.152890493690.111435639030.27468851580.0333663288450.1907317725070.05212760528360.003318426691030.2130529556330.02438056470160.137987750366100.8994188537.3245274368-15.3336064269
22.45012461910.129829706761-0.1269590935784.30767692874-0.04527414187161.52128286289-0.02763612451130.0545762215992-0.170840960428-0.09079103402030.06072890742770.04465330631440.1661253919660.0110050140698-0.03131730051480.1782029874970.0366247489614-0.02396430507970.178329833514-0.007688467265030.17671359365111.69371362224.778764603813.0989063931
34.743096868781.854218463071.185804263132.801313679620.3351543450892.72508840108-0.07769149272290.9506848898820.197803030960.01249388853130.190795543250.594865131104-0.133446702729-0.883740817368-0.2144477006150.300010972564-0.02765835903340.04246530694050.3259614617590.02147405526120.181818382904141.36249259520.434843938466.552205863
41.640062733691.658798542690.05963989101093.538784750911.468386132131.23379855670.0863151035586-0.234137946167-0.09928494215640.318077929965-0.111094903017-0.1231060475520.335368288062-0.005486612012760.03919045431410.1964104058020.0271838778410.04590746359580.2248310444260.05460933848490.150941801241143.14141397110.694377849874.3200619113
51.806560418520.1645006396120.1945991581082.60072853005-0.4252902015042.463537921630.06932929109680.153918194870.00265143584527-0.111490166549-0.132765611052-0.2480760109330.2225599100620.1123813854850.04223933973060.104936634410.008570096527750.02199852914630.1717632058280.01172957121440.133894883353151.8567541529.6412839459268.055986753
61.377433720020.8333290499750.2659151727561.27561764899-0.02860412947691.61748329464-0.0108820488782-0.0417548480989-0.0215535610706-0.02679895989210.03252594641890.0807122060334-0.0107752998166-0.163774894307-0.03826034678230.09892909348070.0549862342350.01814194867840.1524907262740.007443374523170.13625633798133.30795183613.973870617441.2052582151
70.824337310502-0.4240210345270.5860058901050.667057335828-0.4138603625382.224926631320.0961475385673-0.1231995505880.3061167259730.0651262053078-0.1200859204510.255955202982-0.0494966021267-0.4570563998820.04548865490590.1773520686270.112722513520.02027572153980.3511720577830.02038509377450.272449434473122.04524520218.922501459344.5585734526
81.90220306247-1.058272428550.2740986801813.12650577324-0.6355592667491.73265040201-0.01947045332770.2835008634060.144008670942-0.1309411901490.0491263350727-0.2127120539290.07132569621940.187185796631-0.01403021082930.198411260922-0.0004098890003270.01003365174950.1953657435620.0142773582780.128357618535100.65638038458.695690074-25.9682526528
90.6598180116150.3765501427950.433551973570.7637981431580.150334433991.17677585986-0.016788307586-0.06333459366930.168522500268-0.0512800100449-0.064208444469-0.0159027251571-0.1495117276150.03283627502180.1011175155060.200909678897-0.002412718445520.01046830317630.224905990655-0.0188402405770.234565851506109.72557156463.5302362866-0.0108501054304
103.09206486779-0.4247177280580.1391425670591.626943523970.4469838898762.588318474780.02991271525710.0596882276638-0.1890269088830.00170081038470.0520367000286-0.02646201145960.1375341465180.192475158262-0.076426740240.184565247743-0.0133860221397-0.002642273601530.2086805602710.009263658470250.206261764134116.98964662860.03970503352.61351188704
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 78 )AA3 - 781 - 76
22chain 'A' and (resid 79 through 255 )AA79 - 25577 - 253
33chain 'B' and (resid 3 through 17 )BB3 - 171 - 15
44chain 'B' and (resid 18 through 45 )BB18 - 4516 - 43
55chain 'B' and (resid 46 through 78 )BB46 - 7844 - 76
66chain 'B' and (resid 79 through 208 )BB79 - 20877 - 206
77chain 'B' and (resid 209 through 255 )BB209 - 255207 - 253
88chain 'C' and (resid 2 through 64 )CC2 - 641 - 63
99chain 'C' and (resid 65 through 113 )CC65 - 11364 - 112
1010chain 'C' and (resid 114 through 256 )CC114 - 256113 - 255

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