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- PDB-6u82: Crystal Structure of the Double Homeodomain of DUX4 in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 6u82
TitleCrystal Structure of the Double Homeodomain of DUX4 in Complex with a DNA aptamer containing bulge and loop
Components
  • DNA (38-MER)
  • Double homeobox protein 4
KeywordsDNA BINDING PROTEIN/DNA / DUX tandem homeodomains / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / Zygotic genome activation (ZGA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation ...negative regulation of G0 to G1 transition / Zygotic genome activation (ZGA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / apoptotic process / regulation of transcription by RNA polymerase II / nucleolus / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Helix-turn-helix motif / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Double homeobox protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsShi, K. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Faseb J. / Year: 2020
Title: DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD.
Authors: Klingler, C. / Ashley, J. / Shi, K. / Stiefvater, A. / Kyba, M. / Sinnreich, M. / Aihara, H. / Kinter, J.
History
DepositionSep 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_alt_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double homeobox protein 4
B: DNA (38-MER)
D: Double homeobox protein 4
E: DNA (38-MER)


Theoretical massNumber of molelcules
Total (without water)54,9654
Polymers54,9654
Non-polymers00
Water00
1
A: Double homeobox protein 4
B: DNA (38-MER)


Theoretical massNumber of molelcules
Total (without water)27,4832
Polymers27,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-13 kcal/mol
Surface area12890 Å2
MethodPISA
2
D: Double homeobox protein 4
E: DNA (38-MER)


Theoretical massNumber of molelcules
Total (without water)27,4832
Polymers27,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-14 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.320, 75.670, 82.690
Angle α, β, γ (deg.)90.000, 121.600, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDBeg label alt-ID
111ARGARGPROPRO(chain 'A' and (resid 20 through 21 or (resid 22...AA20 - 444 - 28
121ALAALAPROPRO(chain 'A' and (resid 20 through 21 or (resid 22...AA47 - 15031 - 134
231ARGARGPROPRO(chain 'D' and (resid 20 through 42 or (resid 43...DC20 - 444 - 28
241ALAALAPROPRO(chain 'D' and (resid 20 through 42 or (resid 43...DC47 - 15031 - 134
152DGDGDGDG(chain 'B' and (resid 1 through 18 or (resid 19...BB1 - 171 - 17
162DGDGDGDG(chain 'B' and (resid 1 through 18 or (resid 19...BB21 - 2921 - 29
172DCDCDCDC(chain 'B' and (resid 1 through 18 or (resid 19...BB32 - 3832 - 38B
282DGDGDGDG(chain 'E' and (resid 1 through 18 or (resid 19...ED1 - 171 - 17
292DGDGDGDG(chain 'E' and (resid 1 through 18 or (resid 19...ED21 - 2921 - 29
2102DCDCDCDC(chain 'E' and (resid 1 through 18 or (resid 19...ED32 - 3832 - 38

NCS ensembles :
ID
1
2

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Components

#1: Protein Double homeobox protein 4 / Double homeobox protein 10


Mass: 15844.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUX4, DUX10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBX2
#2: DNA chain DNA (38-MER)


Mass: 11638.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Magnesium acetate, PEG8000, Sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.975 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 3.2→60.87 Å / Num. obs: 10373 / % possible obs: 98.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 87.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.6
Reflection shellResolution: 3.2→3.4 Å / Rmerge(I) obs: 1.27 / Num. unique obs: 1874 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6e8c

6e8c


Resolution: 3.21→60.87 Å / SU ML: 0.3478 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 33.6752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2796 370 4.94 %
Rwork0.2516 7122 -
obs0.2531 7492 71.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.98 Å2
Refinement stepCycle: LAST / Resolution: 3.21→60.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 1528 0 0 3743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263981
X-RAY DIFFRACTIONf_angle_d0.47825692
X-RAY DIFFRACTIONf_chiral_restr0.0295597
X-RAY DIFFRACTIONf_plane_restr0.004492
X-RAY DIFFRACTIONf_dihedral_angle_d26.78391584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.31.035210.653843X-RAY DIFFRACTION5.08
3.3-3.410.533980.4011118X-RAY DIFFRACTION15.09
3.41-3.530.3741120.3172247X-RAY DIFFRACTION29.74
3.53-3.670.4458240.3417406X-RAY DIFFRACTION50.47
3.67-3.840.3175320.349631X-RAY DIFFRACTION75.26
3.84-4.040.3217340.3366774X-RAY DIFFRACTION92.66
4.04-4.290.381260.2831834X-RAY DIFFRACTION98.17
4.29-4.620.3208400.279791X-RAY DIFFRACTION95.63
4.62-5.090.3501370.2562850X-RAY DIFFRACTION99.11
5.09-5.820.2554540.2474800X-RAY DIFFRACTION97.6
5.83-7.330.3265490.2438804X-RAY DIFFRACTION97.93
7.34-60.870.1774530.1559824X-RAY DIFFRACTION95.53
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)
10.8369377191152.10380317810.1905689334556.56011485712.741886656964.02068476604-0.1235939387270.379402857238-0.2057341693620.3224835032340.436834355043-0.6909760136230.5059799073860.418758873077-0.4426159864290.797092514192-0.6251860714-0.0895355431561.66279339729-0.0364992277770.48490881160724.8921750351-25.7433672259.0080276629
21.79407582675-0.4651113869011.658905197210.4672553248570.3655744245773.36705930943-0.6923478678520.5080162940150.524643472964-0.552744776408-0.04682485061410.409407456797-0.752898324320.02945728753770.7507365542420.897745343012-0.615284348888-0.2122928432850.842102283945-0.4291587540150.69700787941616.4259252576-11.056978434253.5111351236
31.539534966120.7639702926980.6230270932071.437372775690.9577938972270.6494201962020.1230916898480.0300519437238-0.148947799726-0.1204115587230.00163965979218-0.0474732500350.0797327772791-0.049775693225-0.07854522360790.693938358377-0.213053211587-0.3713252329770.715176966323-0.2194051309080.34832690206312.5069615571-16.746250430943.1635287573
42.38319587335-0.04592109422611.297526895920.0742622506765-0.01099731066910.999755860035-0.158275024706-0.04833404154690.4781487592420.0771023318904-0.0527285541577-0.550534090347-0.1740159203580.1119249825980.2187886988440.345925700423-0.704967872838-0.06653930802490.525862375777-0.235648724250.48705639736524.885581646-14.859698983246.2443064817
51.057624403330.8190721884570.1666745614121.082996156160.2314305051260.2555828640480.00864121724305-0.02479584253570.03408876885170.0885226927145-0.14820876496-0.03350932199520.0613064513653-0.0192912931608-0.2244758150170.191435300497-1.264236721580.009456043223720.807153362345-0.5681528311840.43944016154411.4398344552-22.558416710151.80037073
68.278998778780.79819680363-3.734421778780.49320581312-0.5878232864521.805878446310.2786515495461.09216519866-0.22628196223-0.140676185803-0.5749070377920.343087229171-0.648143846525-0.818540962160.1323194036660.954588221176-0.4822408332850.3360744726431.20412869908-0.4176853295750.5479909187135.12360889882-17.716430720143.0603559576
71.563483110611.22320889803-0.3073666664181.925681874680.3623693282213.71402072385-0.9718281787460.615828701153-0.652635569984-0.684099509735-0.3031756738-0.5675615431811.737077327660.6722619379251.17158383761.06804968318-0.2917558121330.3249501347641.060980437020.3899418849070.6819883481627.3426303489-28.515688616133.8232019901
82.16954349541.61804769497-2.697805750552.42578747871-3.967209977867.48000102526-0.610634835888-0.503614297589-0.25286309196-1.07464741358-0.191672235936-1.189299151451.645358374931.972098784470.7912650881431.41395269436-0.05169519582020.8031170130081.674192128110.2489126664471.6162006002532.4550607065-39.285413940344.4166532251
92.447338306770.5635468386-0.8289804901562.2225040553-1.255634464842.30082237886-0.0989704485375-0.0210269255951-0.2962273949820.008501742154710.09006331238440.2093811660620.292104746791-0.262132106655-0.08983300229340.82888287855-0.4287775752480.5449298833081.007732272820.3204871753720.86492859969523.1621592077-37.902236154242.0580840432
102.249403848041.64464932132-1.389540125454.339986354081.898032364773.991926693171.34794673586-1.87073850369-0.4619854252213.30601489592-1.472929514570.6128893879251.72273641705-1.18262853250.1950015925931.67095392429-0.9304917022720.02450295520241.35483367419-0.266303429530.78766380976515.4410388949-26.750655682561.9361271157
110.2110155291040.1704907997970.1032464149180.285633399414-0.2934297494330.969686844689-0.07537663121310.238354852306-0.205820660166-0.08079247778910.0842232536879-0.02830107447790.0790369463045-0.0319256033147-0.01997990960391.35204352911-0.8788695872590.444302458591.29991778281-0.5178344188870.98309282013514.6563566569-33.4375226138.7191241464
121.092758147440.5113293268880.2843427897521.156421803481.103681084091.15295181634-0.2902384786250.951495456537-0.475283423097-0.5725749005690.214842459163-0.3839761211190.2432533054840.1631147635670.1493002170970.932301218881-1.097691325110.3812244110991.07495611117-0.6741141404680.51269780226415.5687371074-33.2664801531.8026782736
133.62242383114-0.1383858640071.523849181956.455928949391.224791673142.57293928456-0.253393752394-0.5839430955971.290844100310.32249067922-0.138186632151-0.467243338779-0.0442059203167-0.09090650747690.02586379249220.854508288988-0.928051963671-0.1636460937650.95064070102-0.1981690096130.45807237818112.3558767974-33.76253021760.2876983757
143.84691473807-4.16811982015-2.293314460178.55989114294-0.4901980255683.548132442240.4486691786140.135729617872-0.008044845693590.699949083231-0.1783300994291.19046818535-0.252098377146-0.4747898977870.01209511176920.690340776814-0.4163195782870.2542832449040.59440494154-0.1155155131350.43787523378823.8632921371-25.0415906269-24.2933575474
150.677311761290.548795551128-0.7427471979250.584903613704-0.7120522520540.9129234049560.0111355640715-0.0383433669738-0.002153064993870.0803497301718-0.00115805004802-0.0164803152430.0211315528330.04854296306770.0134509428280.605153283928-0.7359524768530.2152507599330.561997248057-0.1638939476370.1305259466933.5445227271-39.5324662268-14.9174338458
160.1502941768710.154600142194-0.276774556480.367705677517-0.3548004117830.6038603985350.0563756627743-0.1092349454070.03826915212910.103689613718-0.08750021961450.0244302076211-0.1271969840140.161768148629-0.1605235824570.70336424191-0.751909117340.116322708220.766507412185-0.3199471274270.23702960654635.311914037-29.8196971035-10.4760702683
172.284994413461.475159039040.5800204098331.456508363170.4595436893070.73616210690.03411017309560.0206441641248-0.298969388591-0.02236962209380.0641351487301-0.04928806327330.382674561799-0.3106893177260.1922451324590.588377841033-1.587466055510.01205117110580.74292778277-0.4644790438890.34778225195422.5050013258-41.4806884305-16.3228370755
184.747852270011.056890923890.5295785153517.33531470381.042187891173.219941433350.266751486105-0.1589425090440.2979585475150.4490480201240.01224023468650.1902990229420.638845018637-0.131187038683-0.117609626991.18609809641-0.8230449491870.3423226959091.4005199555-0.4207022379920.68366726169325.6413936573-32.9828377703-1.14707562022
193.095865928184.12301090353-0.2146315675995.715024061690.5331680731513.11385825979-0.2384898311380.2399744693990.7833279943540.260734877290.1596900720221.18518200187-0.3066413402430.04249970065970.08185020646971.57111769884-0.6590791949220.1527358215971.36375796026-0.5355248394441.9499024755712.8198490649-9.9092374804-6.72929342493
201.558826009842.181974480930.1940817484953.211369329190.2084093764860.0467048336695-0.29082628303-0.05682107460830.770450612375-0.3253028658690.09859600788160.162550257257-0.3356479630430.8468657526350.3090002849091.564629692-0.9407542758650.6424268648241.98464149616-0.07374225324562.038033393618.9484149082-13.6143127916-13.8040113624
212.464375620551.70526424937-0.4472447840733.87063467203-0.7404604610061.20112903618-0.02605256058860.0822895619480.388926174866-0.1427377696430.2234614613120.4517431358860.0328765260338-0.133726268945-0.06706046292841.0490585341-0.872455105870.5148573208510.896977543311-0.4637052294370.98430933456413.6437496355-20.9533955702-8.23874669333
221.774449143521.68546051652-0.8180350868961.69567671129-0.5920596214390.7121164891450.616309494358-0.0895684888233-0.718636667373-0.310970840492-0.3393533606640.6781061359360.0474051631162-0.217068795960.08241539935360.73908562026-0.502966138698-0.2054507917690.761125017815-0.3403850566390.56434049894721.4696697245-33.9268138302-26.805769036
230.00192143734267-0.005103246465650.009011141872760.0672595343158-0.1716664211350.4218781740510.335106631569-0.5413142667750.4182804943070.252402477602-0.0995022539839-0.0179390463667-0.03546342553060.001866330878270.297447715321.37372614087-1.159141015470.4944590417041.84461870442-0.6164401409571.0426983337814.0831349371-30.4310652358-3.99392363731
244.73066672583.48443562892-2.241164413612.56564544321-1.609956816413.30910839925-0.0638075397111-0.5834343625180.2261617464730.677273519684-0.8482061270381.253422034080.389677435988-2.236472346850.9823917012162.02894446056-0.5985719602090.192021245212.23882888283-1.040300583721.3785594490213.3876058538-25.27641339716.7315617837
250.172036942338-0.608568948991-0.3649056499432.711787346040.8873436871111.057318582710.162811985973-0.116559626690.1103808196850.61494655203-0.3094467048270.675838881104-0.107279524839-0.1227102533140.2915347906332.00034030079-1.232106539270.8246720653011.84633535895-0.7504298062031.3408616656813.5159843918-24.62289240193.08724330979
262.35696382413.291516119612.205775773224.730605112562.924317997612.2689963207-0.20279378152-0.05042098733690.567075883476-0.227777125064-0.08120913526410.636264241224-0.2969850997570.04287923143260.5442087847550.82690018164-0.99292565904-0.02735943331840.951768701962-0.4892831475240.52753846162415.3901095646-37.5768346147-10.5896267235
278.180963708920.677711337324-0.8410812613032.57777048353-3.184260813033.93395563797-0.2896996741540.8675983673210.10883078743-1.01470942650.420248967339-0.7970851626640.300521658771-0.2051479186780.04003376098571.02297333494-0.7701270019960.1467291150661.086510360220.08628751656310.78183449284713.434603396-33.5226561206-25.371931742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 45 )
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 59 )
5X-RAY DIFFRACTION5chain 'A' and (resid 60 through 80 )
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 95 )
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 102 )
8X-RAY DIFFRACTION8chain 'A' and (resid 103 through 134 )
9X-RAY DIFFRACTION9chain 'A' and (resid 135 through 150 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'B' and (resid 6 through 15 )
12X-RAY DIFFRACTION12chain 'B' and (resid 16 through 30 )
13X-RAY DIFFRACTION13chain 'B' and (resid 31 through 38 )
14X-RAY DIFFRACTION14chain 'D' and (resid 17 through 27 )
15X-RAY DIFFRACTION15chain 'D' and (resid 28 through 45 )
16X-RAY DIFFRACTION16chain 'D' and (resid 46 through 59 )
17X-RAY DIFFRACTION17chain 'D' and (resid 60 through 85 )
18X-RAY DIFFRACTION18chain 'D' and (resid 86 through 102 )
19X-RAY DIFFRACTION19chain 'D' and (resid 103 through 115 )
20X-RAY DIFFRACTION20chain 'D' and (resid 116 through 134 )
21X-RAY DIFFRACTION21chain 'D' and (resid 135 through 150 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 5 )
23X-RAY DIFFRACTION23chain 'E' and (resid 6 through 15 )
24X-RAY DIFFRACTION24chain 'E' and (resid 16 through 20 )
25X-RAY DIFFRACTION25chain 'E' and (resid 21 through 25 )
26X-RAY DIFFRACTION26chain 'E' and (resid 26 through 30 )
27X-RAY DIFFRACTION27chain 'E' and (resid 31 through 38 )

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