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- PDB-6ycs: Human Transcription Cofactor PC4 DNA-binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6ycs
TitleHuman Transcription Cofactor PC4 DNA-binding domain in complex with full phosphorothioate 5-10-5 2'-O-methyl DNA gapmer antisense oligonucleotide.
Components
  • (DNA (5'-D(P*(OKQ))-D(P*(OKT))-R(P*(RFJ))- ...) x 2
  • PC4 protein
KeywordsTRANSCRIPTION / DNA binding / phosphorothioate DNA / 2'-O-methyl / ASO
Function / homology
Function and homology information


negative regulation of DNA metabolic process / DNA-binding transcription factor binding => GO:0140297 / negative regulation of DNA duplex unwinding / RNA polymerase II promoter clearance / SMAD protein signal transduction / DNA duplex unwinding / positive regulation of transcription initiation by RNA polymerase II / DNA helicase activity / protein homooligomerization / single-stranded DNA binding ...negative regulation of DNA metabolic process / DNA-binding transcription factor binding => GO:0140297 / negative regulation of DNA duplex unwinding / RNA polymerase II promoter clearance / SMAD protein signal transduction / DNA duplex unwinding / positive regulation of transcription initiation by RNA polymerase II / DNA helicase activity / protein homooligomerization / single-stranded DNA binding / double-stranded DNA binding / transcription regulator complex / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
RNA polymerase II transcriptional coactivator Sub1/Tcp4-like / Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Activated RNA polymerase II transcriptional coactivator p15 / Activated RNA polymerase II transcriptional coactivator p15
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsHyjek-Skladanowska, M. / Vickers, T.A. / Napiorkowska, A. / Anderson, B. / Tanowitz, M. / Crooke, S.T. / Liang, X. / Seth, P.P. / Nowotny, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins.
Authors: Hyjek-Skladanowska, M. / Vickers, T.A. / Napiorkowska, A. / Anderson, B.A. / Tanowitz, M. / Crooke, S.T. / Liang, X.H. / Seth, P.P. / Nowotny, M.
History
DepositionMar 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.0Nov 11, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PC4 protein
B: PC4 protein
C: PC4 protein
D: PC4 protein
E: DNA (5'-D(P*(OKQ))-D(P*(OKT))-R(P*(RFJ))-D(*(OKQ)P*(OKT)P*(AS)P*(GS)P*(OKN)P*(OKN)P*(PST)P*(OKN)P*(PST)P*(GS)P*(GS)P*(AS)P*(OKT)P*(OKT))-3')
F: DNA (5'-D(P*(OKQ))-D(P*(OKT))-R(P*(RFJ))-D(*(OKQ)P*(OKT)P*(AS)P*(GS)P*(OKN)P*(OKN)P*(PST)P*(OKN)P*(PST)P*(GS)P*(GS)P*(AS)P*(OKT)P*(OKT))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7518
Polymers45,6326
Non-polymers1192
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.143, 102.143, 83.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PC4 protein / SUB1 homolog (S. cerevisiae) / isoform CRA_a / cDNA / FLJ92014 / highly similar to Homo sapiens ...SUB1 homolog (S. cerevisiae) / isoform CRA_a / cDNA / FLJ92014 / highly similar to Homo sapiens SUB1 homolog (S. cerevisiae) (SUB1) / mRNA


Mass: 8468.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PC4, SUB1, hCG_1781938 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6IBA2, UniProt: P53999*PLUS

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DNA (5'-D(P*(OKQ))-D(P*(OKT))-R(P*(RFJ))- ... , 2 types, 2 molecules EF

#2: DNA chain DNA (5'-D(P*(OKQ))-D(P*(OKT))-R(P*(RFJ))-D(*(OKQ)P*(OKT)P*(AS)P*(GS)P*(OKN)P*(OKN)P*(PST)P*(OKN)P*(PST)P*(GS)P*(GS)P*(AS)P*(OKT)P*(OKT))-3')


Mass: 5958.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*(OKQ))-D(P*(OKT))-R(P*(RFJ))-D(*(OKQ)P*(OKT)P*(AS)P*(GS)P*(OKN)P*(OKN)P*(PST)P*(OKN)P*(PST)P*(GS)P*(GS)P*(AS)P*(OKT)P*(OKT))-3')


Mass: 5798.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 14 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M LiSO4, 0.1 M BIS-TRIS pH 6.5, 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
21
ReflectionResolution: 3.05→45.68 Å / Num. obs: 8900 / % possible obs: 99.8 % / Redundancy: 25 % / CC1/2: 1 / Rmerge(I) obs: 0.184 / Net I/σ(I): 17.76
Reflection shellResolution: 3.05→3.23 Å / Mean I/σ(I) obs: 1.92 / Num. unique obs: 1401 / CC1/2: 0.72 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C62

2c62


Resolution: 3.05→45.68 Å / SU ML: 0.4392 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.3719
RfactorNum. reflection% reflection
Rfree0.3175 445 5.01 %
Rwork0.2378 --
obs0.2415 8886 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 88.2 Å2
Refinement stepCycle: LAST / Resolution: 3.05→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 586 12 2661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343330
X-RAY DIFFRACTIONf_angle_d0.82584594
X-RAY DIFFRACTIONf_chiral_restr0.0435486
X-RAY DIFFRACTIONf_plane_restr0.0053427
X-RAY DIFFRACTIONf_dihedral_angle_d31.8353394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.490.35141450.28392752X-RAY DIFFRACTION99.93
3.49-4.40.33041460.23422777X-RAY DIFFRACTION100
4.4-45.680.30221540.22832912X-RAY DIFFRACTION99.64
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)
15.7804595526.08733007887-4.593442568288.48751395746-4.051262388633.6690789821-0.256323392846-0.122821273473-0.973199245672-1.085933669750.41747143832-1.662540305380.521949407733-0.152233322523-0.02072259638590.8196867135870.03040186702650.08321766168570.674403244198-0.06494939744870.64365420523516.2182172175-35.312761057214.4639862869
23.915588812852.120610876085.640143797582.00994127452.23643057517.82263565512-0.0951708690210.202149680269-0.3738865824090.945625322749-0.135881277936-0.165761277570.5590771929162.06937293106-0.02348149758080.7206071499050.0592456457090.04954741448040.839766597643-0.004694263832840.69646027611613.9436622658-34.623400697218.7704484919
38.3803073849-4.25677921777-6.692287573027.830768617693.855296227032.009053655391.991248456943.601793287431.122527373030.05338600119041.493460161030.230118191960.6514466424570.180967158185-0.5061721916871.20717014255-0.2315804148550.4117513571812.73295488083-0.322079132970.76039857213327.2575184646-30.295247251727.6599247969
46.043830236950.4582402792837.761750994471.45869389488-0.1363856859239.968729718890.460259940009-0.329217098003-0.1572344691040.708853475739-0.28516645401-0.5866550679750.105486172113-0.318525129471-0.09596947627410.7152586693410.05954698547070.1371577849340.796719001188-0.1385945423030.51455993997111.600002941-33.14616512521.3860119934
53.343168448691.03894779188-2.816796907996.94748209883-4.524172724736.57268151385-1.497681173530.26178030622-2.35997963807-1.236350642270.4048905678120.4194001924262.11760842428-0.374176285433-0.6284649013080.984673256475-0.3368291362120.1047687629790.954054539998-0.09442967009320.8146035032292.04915369358-37.2875356976.75069766214
69.836712770223.917077715470.6726581403878.011627025414.073274608322.342542405220.5817905467763.158620678080.2943189006231.7062651649-0.7467241984780.540293853087-1.13202373140.523356435143-0.3006268515530.924914316287-0.0981589278036-0.09778806281641.059296155350.2820787627470.556910873053-1.6644385348-22.85824892764.77803683504
77.491167586186.45954116872-5.253683689396.75213933115-5.347073255964.23301311492-1.311331708691.744242344720.433809985460.2112439862011.961116410560.556643865761-0.554257023036-1.58737267646-0.9068255936840.857755298719-0.0561681665214-0.2507017198141.0146566946-0.0008478517342820.774267920092-5.86016240908-30.55520834712.5607860245
88.276577897650.44054187849-1.520957346511.860284882920.9896039983164.71514118986-0.1087778423820.8600667522451.263910504053.272679081830.3531383916631.083616167910.135956991481-0.400160182227-0.4818140826250.728606770445-0.011274598282-0.08450918171040.6637176555430.1259160472150.740573622822-1.26056632084-23.297627466115.9719127845
96.547619496413.55529760111.402760899283.78252137354-3.312337017628.59301336965-0.424714271712-0.0910166887295-0.1703666248342.047076690320.469261824895-0.489467059493-1.10486799389-0.666911795213-0.2867957782520.7166028329250.05243814631490.09201265499140.644524464420.02681801656590.672906174552-0.368345055177-28.314379149919.5737052361
107.03262596878-4.30589964866-2.458069529677.0551404727-1.788415021323.30971126569-1.45958335553-3.34911597361-4.583237461023.025784945492.250927543550.119724596091-0.475431885305-1.508311686250.24745352851.17737914601-0.1205590838880.04344326304791.609730389730.06326268592861.77134723555-12.5171155665-33.281601136130.6816645666
116.663831423141.43114817229-1.067275478154.28146410318-2.509493300215.74490478569-0.12718098568-0.3049492065-0.1463109339260.0442765398130.484735052260.6432440638720.2747236894640.00967581702653-0.1415690477980.529360402405-0.08009105772560.1029273335080.6918164935780.1078649898720.5823563751511.76652518511-29.060747694421.3838610153
128.26993302708-6.180163799411.009350259362.009188770972.661992973166.75288686871-0.3572191070841.57498053090.5782350775021.11027262661-0.839325065922-2.78424368094-0.2731037732060.1507591466570.7992327182270.595513728688-0.23881007343-0.01285274119280.9635638764470.03163734452420.51824689246812.3754136446-31.46206160185.55086175027
138.158071676720.6977441481763.76557896274.74088839341-4.911367794278.198825619351.30381888129-1.53937384229-0.9179022636741.50416565795-0.795244710981-0.680882723120.3364483603270.126377577147-0.3734945521081.23760297510.4496447707120.2222662682290.8787457290350.07648430101590.99478098424412.8003390507-34.379625300151.7705638079
144.344687423974.14449047758-4.882267290018.23503505666-5.357151018768.415541964980.855302317588-0.615552468837-0.3658496644550.98339971371-1.053744049260.581216430155-0.4472275431240.4021147053670.3859717687570.897973243359-0.282753011661-0.09672466214320.536304430036-0.08973921441050.55987652877612.8429435838-25.532046466947.3621441226
159.25072714541-2.36409108952-1.560996721141.930336440811.283768576893.87959339066-0.408709236003-1.01699343089-1.309972247170.944566977780.0679013208946-0.1877485784230.5262655742580.1611962387150.3862463431610.8803040214240.04552641344070.04102507778440.7654977177720.02932621345530.80285964992710.1123126062-29.653047235144.132548459
161.98351157943-6.72981735011-0.1394337328847.865351726713.214379544553.171470431420.358458657389-2.010113209221.001669355081.85945364034-0.308514421373-1.530310376880.804137758718-0.734078011681-0.5574358931540.642298788323-0.1735464589460.1958171495530.6587021287850.2278455115410.83397188542313.9866586993-35.347073117737.8512568611
172.17788706562-0.4813648820181.654124443986.970803432734.020319214447.65828058852-0.121823589031-3.568723473341.516336622560.754786353026-0.229627018392.14301215074-1.06212605344-0.09028861832330.3908821210880.9901593061430.3770824192470.0285218029371.2148518137-0.07850334877810.876957838174-3.16533872138-24.348663380553.9826812299
184.335506669357.46750632207-2.588591943881.988348823861.998498907961.91779042314-0.131953054328-0.9417550968912.98807456237-1.860667359051.927127221073.15646980087-1.07774711637-3.597605321820.05188463024911.20067336540.2902857804530.3791222310760.827221619188-0.05361089532871.07813880243-8.04819655919-20.092626835947.6528757799
195.419596400613.255510584045.561347077685.83059749441.969013946647.35175430033-1.68693277896-1.1911925156-1.88899799388-1.9717472019-0.244546169302-0.0696790967875-0.0151166702692-0.963876427851.13351698361.04078765970.07436425548660.4989074982960.8492120419190.225061184310.989591451101-9.20009169399-29.846297791944.7009475371
206.367711885212.188045497782.594839434658.26692958272-0.4411291837354.44812973525-0.727594012858-1.05326967387-0.513081466422-1.072200735960.167597541361-0.6876784477250.810047251439-0.001998720781791.144247420140.914292935609-0.05611863317190.2489932235561.012999021310.07160062100010.691787445925-5.35972191882-26.091965202742.1485898136
218.657201208974.295757963434.273371400893.640608810513.212482216573.29264050889-0.739523438829-0.04924604485582.31563339855-1.20067658148-0.2434614307072.10242728624-1.41182917815-0.9894151958981.581900088121.086800311650.0864709731936-0.04663396916380.8209561796670.01824900679821.55342897643-8.11609003961-20.712285130734.406532252
222.381195748740.7113471908554.470263248899.066833989884.834510031429.798438436861.2398587732-2.25793549141-2.344644955732.3089974376-1.636465698991.334000790552.24109997961-1.73720743719-0.5336348835580.9286531712290.1117646341630.4093815652881.475539754720.5896183474630.597200789114-0.396278629113-34.686580451651.8771613781
238.06306494195.980172715223.206276510724.385720566712.144201161317.47059921148-0.73756305913-0.470453390797-0.796618137349-2.48510054958-1.01256521712-0.5897818422171.61973101072-1.473321246641.353278324131.102781938050.1517639401230.06614066490851.16571277556-0.08811376597570.99473133621110.2783307419-26.222309057259.5356196527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 62 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 115 )
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 127 )
7X-RAY DIFFRACTION7chain 'B' and (resid 61 through 69 )
8X-RAY DIFFRACTION8chain 'B' and (resid 70 through 79 )
9X-RAY DIFFRACTION9chain 'B' and (resid 80 through 90 )
10X-RAY DIFFRACTION10chain 'B' and (resid 91 through 95 )
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 106 )
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 127 )
13X-RAY DIFFRACTION13chain 'D' and (resid 60 through 69 )
14X-RAY DIFFRACTION14chain 'D' and (resid 70 through 79 )
15X-RAY DIFFRACTION15chain 'D' and (resid 80 through 90 )
16X-RAY DIFFRACTION16chain 'D' and (resid 91 through 101 )
17X-RAY DIFFRACTION17chain 'D' and (resid 102 through 127 )
18X-RAY DIFFRACTION18chain 'E' and (resid 61 through 69 )
19X-RAY DIFFRACTION19chain 'E' and (resid 70 through 80 )
20X-RAY DIFFRACTION20chain 'E' and (resid 81 through 90 )
21X-RAY DIFFRACTION21chain 'E' and (resid 91 through 101 )
22X-RAY DIFFRACTION22chain 'E' and (resid 102 through 114 )
23X-RAY DIFFRACTION23chain 'E' and (resid 115 through 126 )

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