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- PDB-8tha: 1TEL, non-compressed, double-helical crystal form -

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Basic information

Entry
Database: PDB / ID: 8tha
Title1TEL, non-compressed, double-helical crystal form
ComponentsTranscription factor ETV6,Activated CDC42 kinase 1
KeywordsTRANSCRIPTION / protein crystallization chaperone / polymer-forming / TELSAM / ETV6
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / GTPase inhibitor activity / mesenchymal cell apoptotic process / vitellogenesis / WW domain binding / clathrin-coated vesicle / hematopoietic stem cell proliferation ...regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / GTPase inhibitor activity / mesenchymal cell apoptotic process / vitellogenesis / WW domain binding / clathrin-coated vesicle / hematopoietic stem cell proliferation / small GTPase-mediated signal transduction / epidermal growth factor receptor binding / clathrin-coated pit / Signaling by FLT3 fusion proteins / protein serine/threonine/tyrosine kinase activity / neurogenesis / adherens junction / RNA polymerase II transcription regulatory region sequence-specific DNA binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytoplasmic vesicle membrane / DNA-binding transcription repressor activity, RNA polymerase II-specific / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / cell surface receptor signaling pathway / DNA-binding transcription factor activity, RNA polymerase II-specific / non-specific serine/threonine protein kinase / endosome / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / Cdc42 binding domain-like / Mig-6 domain / GTPase binding / EGFR receptor inhibitor Mig-6 / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / Cdc42 binding domain-like / Mig-6 domain / GTPase binding / EGFR receptor inhibitor Mig-6 / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Variant SH3 domain / Sterile alpha motif/pointed domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Transcription factor ETV6 / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSmith, C.P. / Wilson, E.W. / Pedroza Romo, M.J. / Averett, J.C. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)146209 United States
CitationJournal: To Be Published
Title: 1TEL, non-compressed, double-helical crystal form
Authors: Smith, C.P. / Wilson, E.W. / Pedroza Romo, M.J. / Averett, J.C. / Moody, J.D.
History
DepositionJul 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor ETV6,Activated CDC42 kinase 1


Theoretical massNumber of molelcules
Total (without water)18,8871
Polymers18,8871
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.163, 69.163, 29.131
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

#1: Protein Transcription factor ETV6,Activated CDC42 kinase 1


Mass: 18886.555 Da / Num. of mol.: 1 / Mutation: V112E,R80S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TNK2 / Plasmid: PET42_SUMO / Details (production host): Kanamycin resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: P41212, UniProt: Q07912
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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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: 1.06 Å3/Da / Density % sol: 43.4 % / Description: Narrow rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.5 M Bis-Tris, 0.35 M Mg-Formate, 5 mg/mL protein / Temp details: Room Temperature

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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: Oct 24, 2021
Details: Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.68→29.95 Å / Num. obs: 8707 / % possible obs: 93.81 % / Redundancy: 17.1 % / Biso Wilson estimate: 22.64 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07972 / Rpim(I) all: 0.01954 / Rrim(I) all: 0.08215 / Net I/σ(I): 25.74
Reflection shellResolution: 1.68→1.74 Å / Rmerge(I) obs: 1.521 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 613 / CC1/2: 0.694 / CC star: 0.905 / Rpim(I) all: 0.3905 / Rrim(I) all: 1.573

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.9.8.1model building
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→29.95 Å / SU ML: 0.2016 / Cross valid method: FREE R-VALUE / Phase error: 25.4049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 455 5.23 %
Rwork0.1824 8288 -
obs-8707 93.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.49 Å2
Refinement stepCycle: LAST / Resolution: 1.68→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms625 0 0 65 690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0106665
X-RAY DIFFRACTIONf_angle_d1.1239904
X-RAY DIFFRACTIONf_chiral_restr0.059195
X-RAY DIFFRACTIONf_plane_restr0.0097115
X-RAY DIFFRACTIONf_dihedral_angle_d12.6786240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.740.28581530.26332611X-RAY DIFFRACTION89.48
1.92-2.420.23171680.19772907X-RAY DIFFRACTION99.97
2.42-29.950.19451340.16492770X-RAY DIFFRACTION92.22
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)
17.576514990424.43955225319-2.858789473584.42055471730.3040434645393.231896035070.144398094374-0.9295779743080.263125081510.643049996316-0.156064890252-1.70478488539-0.1423583524170.1532579127180.0118363562570.631275428212-0.149864045378-0.2242122388310.367001445959-0.1250359401310.80254376114321.375854216623.68182060543.06041664305
27.01793609484-3.251760366751.929395035663.9821056043-2.498036908461.610340570640.1025000532070.3291244920420.342407929179-0.195598494975-0.144761795054-0.2486672166010.06620464126090.160891281810.002058782138130.194916181035-0.01379933089980.05259071627890.1453713431940.001566577507560.14381365135116.47065184417.6720371106-3.01644928004
35.84111822163-1.725396979150.03437162965354.30468813232-0.1102046751744.858370204470.0742007604817-0.00769658213828-0.1254832208240.05118305918410.01821746707590.1270855061350.05074349829590.0119830906497-0.07856581815670.115468134822-0.02138177271760.03507517703210.1080202166990.00558282767070.1208162513459.7829459555112.13737633421.57635985873
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 4 through 9 )4 - 91 - 6
22chain 'A' and (resid 10 through 45 )10 - 457 - 42
33chain 'A' and (resid 46 through 80 )46 - 8043 - 77

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