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- PDB-8e1f: Sterile Alpha Motif Domain of Human Translocation ETS Leukemia, N... -

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Basic information

Entry
Database: PDB / ID: 8e1f
TitleSterile Alpha Motif Domain of Human Translocation ETS Leukemia, Non-Polymer Crystal Form
ComponentsTranscription factor ETV6
KeywordsGENE REGULATION / Chromatin-associated / Transcriptional Repressor
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol
Similarity search - Function
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 ...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 / Sterile alpha motif/pointed domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription factor ETV6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsWilson, E. / Nawarathnage, S. / Stewart, C. / Brown, S. / Bezzant, B. / Bunn, D. / Towne, N. / Pedroza Romo, M.J. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209-1 United States
CitationJournal: To Be Published
Title: Sterile Alpha Motif Domain of Human Translocation ETS Leukemia, Non-Polymer Crystal Form
Authors: Wilson, E. / Nawarathnage, S. / Stewart, C. / Brown, S. / Bezzant, B. / Bunn, D. / Towne, N. / Pedroza Romo, M.J. / Moody, J.D.
History
DepositionAug 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Mar 8, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor ETV6
B: Transcription factor ETV6
C: Transcription factor ETV6
D: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,97614
Polymers38,5564
Non-polymers42010
Water3,567198
1
A: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8195
Polymers9,6391
Non-polymers1804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7954
Polymers9,6391
Non-polymers1563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6742
Polymers9,6391
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6883
Polymers9,6391
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.954, 61.954, 167.574
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 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel


Mass: 9638.910 Da / Num. of mol.: 4 / Fragment: Sterile Alpha Motif Domain, residues 47-126 / Mutation: R35S, V67E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1 / Plasmid: pET42_SUMO
Details (production host): appends N-terminal 10xHis-SUMO tag
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P41212
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.41 Å3/Da / Density % sol: 48.96 % / Description: Rod-like
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 200mM MgSO4 Heptahydrate, 20% w/v Polyethylene Glycol 3,350

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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: Dec 1, 2020 / Details: Rh coated collimating mirror, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled Si(111) double crystal monochromator, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.16→38.69 Å / Num. obs: 19209 / % possible obs: 98.47 % / Redundancy: 20.2 % / Biso Wilson estimate: 33.66 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1397 / Rpim(I) all: 0.0318 / Rrim(I) all: 0.1433 / Net I/σ(I): 17.04
Reflection shellResolution: 2.16→2.237 Å / Redundancy: 19.3 % / Rmerge(I) obs: 1.488 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 1954 / CC1/2: 0.829 / CC star: 0.952 / Rpim(I) all: 0.3457 / Rrim(I) all: 1.528 / % possible all: 100

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Processing

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

2qar


Resolution: 2.16→38.69 Å / SU ML: 0.2112 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 930 4.85 %Random within each shell
Rwork0.1975 18286 --
obs-19184 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.93 Å2
Refinement stepCycle: LAST / Resolution: 2.16→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 18 198 2776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212654
X-RAY DIFFRACTIONf_angle_d1.0943616
X-RAY DIFFRACTIONf_chiral_restr0.0564388
X-RAY DIFFRACTIONf_plane_restr0.0059460
X-RAY DIFFRACTIONf_dihedral_angle_d14.3351952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.16-2.240.3316814.150.26221951100
2.27-2.420.2261580.212601100
2.42-2.60.24851370.2209265299.86
2.6-2.860.24871270.2332264099.86
2.86-3.280.2461350.20822657100
3.28-4.130.21631220.1733240390.37
4.13-38.690.21031300.1825265399.5
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)
18.64693941616-1.20142680309-0.05211579545417.08498986847-1.010216500064.832386879140.07911463729450.2832419336390.460452290193-0.739956039221-0.378308088875-0.124238483351-0.3338663811890.6285107473050.2313411393780.414954300934-0.0753278158024-0.04965836937710.3243145550.01799585753130.37150032025630.240589522633.708505514913.5151667016
28.188266451212.056835558940.1505574445079.579158634670.1076463890965.85326862819-0.423551093784-0.275198532061.075349030530.2480181893020.0972322697711-0.230153264125-0.813932228330.3139234428260.3756911327620.420316626697-0.060846297372-0.1165139932040.3173703537950.02502843878410.52990000024529.854749038841.811565939917.5982961577
39.658064758566.37620722239-3.400239174035.33476663092-5.105874748518.45073936742-0.106896321663-0.1474838846421.565257881230.96243580628-0.05897135247460.717424632508-0.872044047158-0.355784669483-0.09847334018290.330613244850.0223780183161-0.08032535782510.297796787891-0.050856176980.46134283050621.33316422834.642273262919.8650810752
44.906191647984.34290953214-3.410917301294.72879189875-1.629585084664.536858109830.01689541943140.503882055451.59534695354-0.07470177206020.7102943027550.706922121145-0.701462432696-0.953527522248-0.2553771078580.6932012246148.93991162192E-50.02205940209280.3549123335370.110550946850.50446048432413.957443057427.877694093221.0788441365
56.96455482455-0.1552679752630.1121011147434.17962105102-0.3452997284145.33954411608-0.146795576081-0.301256821766-0.5048614885730.145844884692-0.3331672619180.08938383698650.438460220386-0.1079167655840.2461829941820.229184689566-0.02725911453440.02336728187490.3416746494090.01306212074890.2787311492830.1210515356.2572219973113.5554592861
67.1715966046-0.3824446920450.09390453356732.03431959033-0.3210176377285.61931793759-0.117089534092-1.15510866147-0.8267002725040.5295490532180.0680836142756-0.1744915584320.294617505994-0.008116484949090.1995504880130.2426077069350.04588808494250.006657853039960.5682899135890.123132084090.35910819211438.283353843.9097909383618.4980570075
73.6675306754-1.29748383090.8363939331135.818678499492.195004386731.85911956095-0.120260231336-1.15933265455-0.9036157964311.13818525676-0.113912992849-1.194194329340.1470870320140.8954624758030.06879806586030.4480139783430.186119769754-0.1129523153920.7363522051550.188361559730.81786124222446.82037394290.29624737542120.0528487638
89.52741938848-0.959431414236-0.1641364546417.736850392781.879337265133.56941823044-0.6281060546940.0586350233910.555517293712-0.04238951238960.0541365687576-0.191694100333-0.09812649678810.3679130292470.2870825251460.296902012562-0.0400509004310.009225044513230.3533704984570.0447953144710.40085738037943.475359895712.578983168511.6320584799
92.409074159612.37072345302-1.35340752862.53748483711-0.3648108393915.24285669705-0.268340690965-0.272220871575-0.488231051824-0.334545116213-0.279819987954-1.016787611360.1558733542630.7919848744710.5211968421480.272057427982-0.005033716165960.04324530465810.4174914915920.1166778900120.4709224001351.13725091094.94834664639.75742943118
105.84472400688-1.915042262335.490389537134.66587961087-0.8478253220425.277350015230.5415527024720.823987704866-1.05836513606-0.572401763867-0.392576999431-0.6242247729420.6421819123360.521522976101-0.1582151825130.3730255056380.03252225171040.04455813776980.362081686872-0.001148530743160.44373920233738.35133739180.4378055949127.16442346395
118.518829575791.39621192084-1.303164951677.01254227469-2.904080457713.375290350330.08920441472480.1649909402720.475484911262-0.122845216055-0.2602370903120.149071427296-0.1990954077940.253525342710.1516380868830.342398818348-0.0127655496951-0.03253258164780.27877453730.02116000811140.187292943703-2.0725071107124.4235331655-7.97919653695
125.003080092820.1941554682920.9481044294992.960113600760.1039711743563.59467903506-0.0129101647218-0.110358328616-0.182163527746-0.0478223390897-0.007867069546370.1240487630440.0609012913780.06222752057350.008985767826320.2280071278720.0118994289560.01082593039070.2169916566750.01307482122080.232108942209-0.03032937634617.15823221650.99785861125
134.59650678784-2.576675308791.790035095158.24053744582-2.600735667934.506549955650.0632229549769-0.4686275810370.1705510740160.451501447704-0.2098011571550.163641115963-0.425308785214-0.05001538592360.07247720284630.2882928402020.007246338989750.01952619341480.336769706031-0.02805330902460.21609540712-4.6294706463622.24285257237.43606062507
144.39348480926-2.270306908235.871108534178.699102038980.9400380209899.96171953702-0.112940903568-0.3967407329810.0944995107958-0.307106189508-0.152729230832-0.107738753813-0.8130804490220.0461881268840.2422389642470.339545900816-0.0506818217504-0.04067808530810.352347331269-0.02358508327170.23388370308821.794461010615.86161340916.52251383531
153.08913026647-0.7651629137051.161562393742.71600291801-1.232912906624.038418177540.0484770090191-0.07611060119160.02122010808650.0307833268526-0.0800780307302-0.0518953919773-0.122123571331-0.141017607360.04855930929080.242037793585-0.0150754590395-0.003769655709460.23397927891-0.01733979126750.2165428768615.35813023019.504470781740.460162539038
169.12534812439-0.265420523742-4.43001226136.956755262464.646310805435.07397848195-0.076790720663-0.334354517992-0.475616226249-0.01631112259590.110168052839-0.4717501108630.7053694043080.53805817651-0.004814873507940.2663531758190.0349862366327-0.00928125849420.214859922550.02369545796410.36684700812520.9206127676-0.839205612369-1.16395212436
178.420668693481.552060659940.8390984315039.91084768295-0.9238924766055.96167038714-0.04197011872120.571918630399-0.690885122334-0.916284357345-0.008907310685710.1513587971710.4984570945710.1367855820650.05234083810660.3756213606170.037623006086-0.02412245093070.304155533185-0.07110525584160.24487511555316.10435213833.51923055735-11.8395512272
184.14728863533-3.231508667475.646550096368.86710037606-2.390579722188.398272119170.3146065979450.846772182320.436001730548-1.13723637501-0.304137651524-0.3663562751140.1045547110050.7496842880670.07923785293890.3413826258740.02212355249890.06033121392570.3653462779730.0228698582230.30048723618823.97290344028.94538051256-6.42178451598
193.024817915682.17022749946-2.015591793177.55161305545-2.428028072153.266078949550.2028936034370.5787992645030.663173632411-0.382483984724-0.397337537197-0.607501686342-1.223912265460.9612456671070.2715294870080.414319102262-0.01470681850350.0425181425780.619011928830.2383983330030.76936221485532.021927595212.5272231484-0.398828246519
204.149262561952.313685275760.8056620638926.06178367399-1.024226345978.79533906672-0.1001761420410.01989593172940.252639983732-0.341729182023-0.1452646597720.5555340087920.0753929734737-0.5587959693290.2596074684510.305524009999-0.0481434122361-0.02730316077630.256079194775-0.01111860649840.3391462885220.40168670722.947572933913.699394169
212.04529002819-6.834702300972.81454662184.53591215242-1.8969212927.98988179909-0.06827766910040.5234561695360.058374873485-1.060870723140.06392121119030.6638534437240.0186791340564-0.06314214781980.03066335688320.542729501344-0.13471792198-0.09921768326780.3092284769960.06099838277710.46939769867522.622381392531.04302523738.7494883072
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 46 through 66 )CC46 - 6632 - 52
22chain 'C' and (resid 67 through 77 )CC67 - 7753 - 63
33chain 'C' and (resid 78 through 89 )CC78 - 8964 - 75
44chain 'C' and (resid 90 through 94 )CC90 - 9476 - 80
55chain 'D' and (resid 15 through 30 )DD15 - 301 - 16
66chain 'D' and (resid 31 through 45 )DD31 - 4517 - 31
77chain 'D' and (resid 46 through 51 )DD46 - 5132 - 37
88chain 'D' and (resid 52 through 66 )DD52 - 6638 - 52
99chain 'D' and (resid 67 through 77 )DD67 - 7753 - 63
1010chain 'D' and (resid 78 through 94 )DD78 - 9464 - 80
1111chain 'A' and (resid 16 through 30 )AA16 - 301 - 15
1212chain 'A' and (resid 31 through 66 )AA31 - 6616 - 51
1313chain 'A' and (resid 67 through 94 )AA67 - 9452 - 79
1414chain 'B' and (resid 16 through 23 )BB16 - 231 - 8
1515chain 'B' and (resid 24 through 58 )BB24 - 589 - 43
1616chain 'B' and (resid 59 through 66 )BB59 - 6644 - 51
1717chain 'B' and (resid 67 through 77 )BB67 - 7752 - 62
1818chain 'B' and (resid 78 through 89 )BB78 - 8963 - 74
1919chain 'B' and (resid 90 through 94 )BB90 - 9475 - 79
2020chain 'C' and (resid 15 through 30 )CC15 - 301 - 16
2121chain 'C' and (resid 31 through 45 )CC31 - 4517 - 31

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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