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- PDB-8fz3: Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Poly... -

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Basic information

Entry
Database: PDB / ID: 8fz3
TitleSterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form
ComponentsTranscription factor ETV6, Activated CDC42 kinase 1 fusion
KeywordsPROTEIN BINDING / Sterile Alpha Motif / Ubiquitin Associated Domain
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / cytoophidium / mesenchymal cell apoptotic process / vitellogenesis / phosphorylation / clathrin-coated vesicle / Signaling by LTK ...regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / cytoophidium / mesenchymal cell apoptotic process / vitellogenesis / phosphorylation / clathrin-coated vesicle / Signaling by LTK / epidermal growth factor receptor binding / positive regulation of peptidyl-tyrosine phosphorylation / small GTPase-mediated signal transduction / WW domain binding / hematopoietic stem cell proliferation / clathrin-coated pit / neurogenesis / Signaling by FLT3 fusion proteins / protein serine/threonine/tyrosine kinase activity / cytoplasmic vesicle membrane / RNA polymerase II transcription regulatory region sequence-specific DNA binding / non-membrane spanning protein tyrosine kinase activity / adherens junction / non-specific protein-tyrosine kinase / DNA-binding transcription repressor activity, RNA polymerase II-specific / endocytosis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / cell surface receptor signaling pathway / 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 / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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 domain-like ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / : / SAM domain-like / 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 / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
PHOSPHATE ION / Transcription factor ETV6 / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.784 Å
AuthorsAverett, J.C. / Nawarathnage, S.D. / 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: Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form, With Disordered Human ACK1 UBA Domain Fused to C-terminus
Authors: Averett, J.C. / Nawarathnage, S.D. / Moody, J.D.
History
DepositionJan 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor ETV6, Activated CDC42 kinase 1 fusion
B: Transcription factor ETV6, Activated CDC42 kinase 1 fusion
C: Transcription factor ETV6, Activated CDC42 kinase 1 fusion
D: Transcription factor ETV6, Activated CDC42 kinase 1 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4087
Polymers79,2424
Non-polymers1663
Water55831
1
A: Transcription factor ETV6, Activated CDC42 kinase 1 fusion
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. EMBO J. 2001 Aug 1;20(15):4173-82. doi: 10.1093/emboj/20.15.4173. PMID: 11483520; PMCID: PMC149168.
  • 19.8 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)19,8462
Polymers19,8111
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription factor ETV6, Activated CDC42 kinase 1 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9052
Polymers19,8111
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription factor ETV6, Activated CDC42 kinase 1 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8462
Polymers19,8111
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcription factor ETV6, Activated CDC42 kinase 1 fusion


Theoretical massNumber of molelcules
Total (without water)19,8111
Polymers19,8111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.506, 61.506, 166.139
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, Activated CDC42 kinase 1 fusion / ETS translocation variant 6 / ETS-related protein Tel1 / Tel / ACK-1 / Tyrosine kinase non-receptor protein 2


Mass: 19810.500 Da / Num. of mol.: 4 / Mutation: R45S, V77E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, TNK2, ACK1 / Plasmid: pET42 / Details (production host): Kanamycin Resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B
References: UniProt: P41212, UniProt: Q07912, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 8.2

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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: Jan 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.784→44.84 Å / Num. obs: 8929 / % possible obs: 99.84 % / Redundancy: 20 % / Biso Wilson estimate: 63.22 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1248 / Rpim(I) all: 0.02867 / Rrim(I) all: 0.1281 / Net I/σ(I): 20
Reflection shellResolution: 2.784→2.883 Å / Redundancy: 21 % / Rmerge(I) obs: 1.48 / Num. unique obs: 898 / CC1/2: 0.864 / CC star: 0.963 / Rpim(I) all: 0.3301 / Rrim(I) all: 1.516 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROC1.20.1_4487data processing
PHENIX1.20.1_4487refinement
Cootmodel building
PHASERphasing
autoPROCdata scaling
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QAR

2qar


Resolution: 2.784→44.84 Å / SU ML: 0.4651 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.8854
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2665 467 5.24 %
Rwork0.2286 8451 -
obs0.2306 8918 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.27 Å2
Refinement stepCycle: LAST / Resolution: 2.784→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 7 31 2477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752525
X-RAY DIFFRACTIONf_angle_d0.83833446
X-RAY DIFFRACTIONf_chiral_restr0.039370
X-RAY DIFFRACTIONf_plane_restr0.005439
X-RAY DIFFRACTIONf_dihedral_angle_d10.7686877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.784-2.8830.36131530.31652823X-RAY DIFFRACTION99.97
3.19-4.010.29391600.2422801X-RAY DIFFRACTION99.93
4.01-44.840.22491540.19882827X-RAY DIFFRACTION99.7
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)
14.49053392781-3.89925242766-2.22926631683.624573781772.232332204341.16837038309-0.5444684136340.1688013819531.096644800930.755491110571-0.1729654519230.0735417776986-0.174981730873-0.2061432832810.5793850459180.733363324348-0.035403780898-0.2667420529460.5444470999650.03159878597630.862853952235-30.675902816535.985775583-24.4324510633
25.00437129615-7.37804854864-2.441496938352.027103960683.309239893842.553011226271.006660271561.377282620092.37164161546-0.6597332763050.131743927977-2.80705131258-0.4870705786570.507463550799-0.1163641501520.6524127602060.0285049849459-0.2066427465090.8013577154740.06882683878521.04530814905-18.885918167232.0971099235-29.6913235986
38.81077308040.9683485652072.32564309672.845474788273.235187572127.50789884187-0.81041586168-0.649264805058-0.3222687339390.471319933225-0.25465027399-0.255563611693-0.179739798915-0.9968486650531.109840520340.5698996015850.0306475800972-0.08022507790860.5312233087370.00762080845410.4529446259441.8114180071524.3480036326-0.781487983242
44.846213701440.9185036788581.630747859897.01866472342-1.26726410278.1990960315-0.220600263301-0.854071919303-0.2533414103160.232210122290.7508272538940.253343653550.291462676725-0.506500819165-0.1667322061210.4762138245180.02608172596350.06784808957110.4204927574980.1227858097840.335205339998-3.2619150203518.4915614317-6.72868725379
57.077593324151.044205037721.814458012553.75795163665-0.4279141643965.16981422582-0.09835796608561.28634414724-0.695961535867-0.3563745182180.0286870876956-0.6164191811370.7022393519070.475787974816-0.1627037242510.4735564444810.0176367195780.06079964017270.590055881297-0.1314561215420.4536318583643.6319645605215.4437502093-14.5262480464
68.70018477263-0.01409781243360.6817580274512.269308383241.847233416121.79042018396-0.9095802048680.8240019100750.899582890897-0.3140748682470.486495620475-0.147845950803-1.31266683760.07113143267480.2479586271850.742153673399-0.116477157015-0.03300443867540.5880709373050.1595256600560.4904696893315.0633791845127.4018596422-12.7770072277
76.976608355853.300857798073.072080590595.51703376306-3.332669975437.12486105520.7056968918870.1408386889671.006217606391.02012850432-1.280001924940.103153531146-0.898987181474-0.5782648944620.3912529032790.81721474786-0.048848001852-0.1289730219620.598764302890.06542592744080.393469725672-21.389673392916.0745593234-14.3816122613
86.74101146463-1.52890615009-0.2135068922415.102804736671.036856089344.486915815880.325892288963-0.0744875330308-0.289919929004-0.132198093461-0.200480693164-0.0977899026644-0.04516796528920.175916157847-0.135801384870.469146343087-0.01583662045520.01956507779020.344481982887-0.003705121337620.279814727236-16.22802755467.70882152531-8.42598751714
99.17816597242-0.7908765161927.043972280868.93133268093-3.82907985248.177560496240.432459070125-0.998069004583-0.3935251772820.619586693711-0.343036351140.5613460161420.426519717388-0.18843963791-0.1783145081320.622973053938-0.05269187900320.1743550402950.5925966820450.1051596312130.503975047737-20.97956321186.56591503437-0.274324877688
103.167745093664.286540525322.046413996797.034819936131.740444128962.10502518640.0134782177499-1.619901588621.444080626891.83494289678-0.279053683884-0.274736329030.1965800194630.242620960265-0.1603600916780.8849337527720.227348493536-0.02417361759170.627880755167-0.1556152976160.580345343303-12.551851334126.81880698672.57798093081
117.10389595046-3.43534526724.868568910019.72587051523-1.077936972149.554940477420.8765113781261.73289178029-0.557153709084-0.927114091707-0.9938126699570.6266454670910.1683647705830.267724715138-0.1360320961150.4954129959010.195636754755-0.04856568312670.715630739393-0.1024580970880.523536112076-11.900368929933.79559821243.29399305429
120.863873315714-1.640338768590.3653744653023.428237145211.20491613089.567404254430.6091369612191.72370641318-0.75232307703-1.466991772390.8027519105472.15495602208-0.561106982341.277268982610.7058394161310.8362288641950.371654297655-0.2968454618280.960921084732-0.03976658158760.866757104005-21.838612166841.025194935-1.48129996847
132.12014450326-3.135391699660.6010580269799.6804227111-3.232978156752.139279341690.262307292621-0.4573316972280.3429637990940.600626203941-0.817320186516-1.085785799920.523195635493-0.4755106299790.4859923025670.535178982903-0.0587921282016-0.2148995710980.6343503643680.01812757500810.668211747737-10.938570825143.03505028718.55639735031
143.60004626299-2.490071587351.727904534884.801113969751.427354278928.92893694033-0.566997582381-0.55122928271.37627377203-0.34157926993-1.37959376883.814868646550.660364856803-0.08353344034040.4339132303420.6532696089370.0159077709233-0.1535768122170.552742743464-0.3276299400881.77033692102-20.943095526246.13219726449.23723801128
152.144196336451.605659550841.409123815543.025684005852.962608250193.011961635950.290171979293-0.2305100468260.6519927425491.22203778604-0.8205315978691.9807349311-0.112878139780.3150438125260.3375454685760.728800949201-0.110441091233-0.02802020208040.649819062264-0.1380578112740.818912240175-18.687299491934.899257852211.4245759967
160.506546608313-1.32510344326-0.6166252663377.81768854091.336038665830.805985386351-0.324614216556-1.079611909080.2394190970432.78767955873-0.855683800410.607281683218-0.8541650864680.2790944435271.128522534970.698916765319-0.0188606807142-0.0789219597421.081173633520.1180652302350.934821025603-16.479821342323.964497768117.88559083
173.54134666166-1.776863054521.389978357223.561658521711.959365684613.151370651070.846281328448-0.4402993281420.3580306826491.12396563223-0.108385044661-0.3501283337810.6453158647140.9842627105410.2422341587320.7683631874970.148342395847-0.1962575574350.5550376169920.04732185597350.596598481351-16.817362559324.1767205331-19.0419973894
188.80191116258-2.279623408430.8179330422369.614666966362.802907998688.69740114834-0.270817055984-0.8871408690610.8414025415661.62428975353-0.209237079351-0.982936890272-0.173376274596-0.003087736637210.4407813134820.7028459463220.0415245287751-0.1745632390470.385237727697-0.03889572475440.430128894714-23.162941888729.3534802839-18.6696638221
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 49 through 74 )DD49 - 7436 - 61
22chain 'D' and (resid 75 through 92 )DD75 - 9262 - 79
33chain 'A' and (resid 13 through 27 )AA13 - 271 - 15
44chain 'A' and (resid 28 through 41 )AA28 - 4116 - 29
55chain 'A' and (resid 42 through 74 )AA42 - 7430 - 62
66chain 'A' and (resid 75 through 90 )AA75 - 9063 - 78
77chain 'B' and (resid 13 through 20 )BB13 - 201 - 8
88chain 'B' and (resid 21 through 63 )BB21 - 639 - 51
99chain 'B' and (resid 64 through 89 )BB64 - 8952 - 77
1010chain 'C' and (resid 14 through 19 )CC14 - 191 - 6
1111chain 'C' and (resid 20 through 42 )CC20 - 427 - 29
1212chain 'C' and (resid 43 through 49 )CC43 - 4930 - 36
1313chain 'C' and (resid 50 through 63 )CC50 - 6337 - 50
1414chain 'C' and (resid 64 through 74 )CC64 - 7451 - 61
1515chain 'C' and (resid 75 through 86 )CC75 - 8662 - 73
1616chain 'C' and (resid 87 through 91 )CC87 - 9174 - 78
1717chain 'D' and (resid 14 through 19 )DD14 - 191 - 6
1818chain 'D' and (resid 20 through 48 )DD20 - 487 - 35

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