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- PDB-7fb7: Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-... -

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Basic information

Entry
Database: PDB / ID: 7fb7
TitleCrystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine
ComponentsE3 ubiquitin-protein ligase UHRF1
KeywordsDNA BINDING PROTEIN / DNA methylation / histone modification / inhibitor
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / : / positive regulation of protein metabolic process ...histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / : / positive regulation of protein metabolic process / mitotic spindle assembly / heterochromatin / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / epigenetic regulation of gene expression / DNA methylation / replication fork / Chromatin modifications during the maternal to zygotic transition (MZT) / euchromatin / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / spindle / nuclear matrix / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / heterochromatin formation / ubiquitin-dependent protein catabolic process / histone binding / nucleic acid binding / protein ubiquitination / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / SH3 type barrels. - #30 ...: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / SH3 type barrels. - #30 / SH3 type barrels. - #140 / PUA-like superfamily / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / SH3 type barrels. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Roll / Ubiquitin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
5-amino-2,4-dimethylpyridine / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKori, S. / Arita, K. / Yoshimi, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02392 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05294 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05741 Japan
Japan Society for the Promotion of Science (JSPS)JP19J22030 Japan
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1.
Authors: Kori, S. / Shibahashi, Y. / Ekimoto, T. / Nishiyama, A. / Yoshimi, S. / Yamaguchi, K. / Nagatoishi, S. / Ohta, M. / Tsumoto, K. / Nakanishi, M. / Defossez, P.A. / Ikeguchi, M. / Arita, K.
History
DepositionJul 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: E3 ubiquitin-protein ligase UHRF1
B: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,54612
Polymers36,4992
Non-polymers1,04710
Water9,980554
1
A: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9007
Polymers18,2491
Non-polymers6516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9380 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6465
Polymers18,2491
Non-polymers3974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-11 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.120, 147.120, 110.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-493-

HOH

31A-575-

HOH

41B-409-

HOH

51B-583-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein E3 ubiquitin-protein ligase UHRF1 / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein ...Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / HuNp95 / hNp95 / RING finger protein 106 / RING-type E3 ubiquitin transferase UHRF1 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / hUHRF1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 18249.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96T88, RING-type E3 ubiquitin transferase

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Non-polymers , 5 types, 564 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-8NF / 5-amino-2,4-dimethylpyridine


Mass: 122.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES (pH7.5), 45% v/v MPD, 0.2 M Ammonium acetate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→44.14 Å / Num. obs: 157937 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 21.62 Å2 / CC1/2: 1 / Net I/σ(I): 21.2
Reflection shellResolution: 1.45→1.48 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 80771 / CC1/2: 0.768 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.19.2_4158refinement
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YYA

5yya


Resolution: 1.45→44.14 Å / SU ML: 0.1528 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1733 7925 5.02 %
Rwork0.1576 150012 -
obs0.1584 157937 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.19 Å2
Refinement stepCycle: LAST / Resolution: 1.45→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 67 554 3134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01382682
X-RAY DIFFRACTIONf_angle_d1.49263650
X-RAY DIFFRACTIONf_chiral_restr0.1192382
X-RAY DIFFRACTIONf_plane_restr0.016481
X-RAY DIFFRACTIONf_dihedral_angle_d12.5036376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.26322320.26984984X-RAY DIFFRACTION100
1.47-1.480.25892520.25945020X-RAY DIFFRACTION99.98
1.48-1.50.25422830.24574982X-RAY DIFFRACTION100
1.5-1.520.25882760.24125028X-RAY DIFFRACTION99.94
1.52-1.540.25732610.22834973X-RAY DIFFRACTION99.92
1.54-1.560.2342660.21145035X-RAY DIFFRACTION99.92
1.56-1.580.20832540.21264962X-RAY DIFFRACTION99.98
1.58-1.610.22452520.20895051X-RAY DIFFRACTION99.98
1.61-1.630.2592860.22124998X-RAY DIFFRACTION99.98
1.63-1.660.22382320.2254998X-RAY DIFFRACTION100
1.66-1.690.24343040.21475004X-RAY DIFFRACTION100
1.69-1.720.24142940.20384931X-RAY DIFFRACTION99.98
1.72-1.750.2052830.18715064X-RAY DIFFRACTION99.98
1.75-1.790.17312960.17924905X-RAY DIFFRACTION100
1.79-1.830.20982420.17695021X-RAY DIFFRACTION99.98
1.83-1.870.17832950.17134985X-RAY DIFFRACTION99.98
1.87-1.920.21942760.17244976X-RAY DIFFRACTION99.83
1.92-1.970.18562510.17065013X-RAY DIFFRACTION99.91
1.97-2.030.19772430.17775010X-RAY DIFFRACTION99.96
2.03-2.090.16572770.16694993X-RAY DIFFRACTION99.89
2.09-2.170.18042770.15435017X-RAY DIFFRACTION99.94
2.17-2.250.20572420.15595012X-RAY DIFFRACTION99.75
2.25-2.360.18732770.15894966X-RAY DIFFRACTION99.83
2.36-2.480.17812460.16135006X-RAY DIFFRACTION99.96
2.48-2.630.15792370.15845034X-RAY DIFFRACTION99.77
2.63-2.840.15932470.14995020X-RAY DIFFRACTION99.94
2.84-3.120.17292800.1434995X-RAY DIFFRACTION99.92
3.12-3.580.15432380.13455016X-RAY DIFFRACTION99.79
3.58-4.50.14262580.11575001X-RAY DIFFRACTION99.92
4.51-44.140.13692680.15355012X-RAY DIFFRACTION99.79
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)
17.204044493291.433896988910.1644173771191.166080188160.0821283812711.39664432605-0.0536785042448-0.06051878602450.245575931701-0.08936660260060.04148024126220.000581887185269-0.0677048001467-0.0057986870658-0.006300840834730.1872998245860.02203705978280.000977171568950.1759790933680.009682513176380.14802012698729.927362759340.519637287447.4460008266
25.93990637196-1.72112627915-1.64303018119.124251585141.75686176053.625179406670.0179424809844-0.0393560988758-0.3337526514030.213667378387-0.199503905302-0.6561309465490.3569678812630.105632219080.1221568419850.2020555826050.000451589188001-0.01819966632270.211884537407-0.02493775174380.2171963411924.875233679822.248261638945.4165031988
30.872417476270.2791279941120.1951815143631.831268013440.3833382222570.968737433911-0.0523700849540.0811972060471-0.0727092139656-0.0620122373345-0.0272809479244-0.02139486852970.1160306202240.03780027935060.08367294710580.1716997261960.02393955793770.009213912418730.193890472483-0.01098011736360.14270673588326.968222376931.968802149647.2201863727
43.980012746551.836136502492.225252531929.354323648545.669350491893.77720238662-0.222131829762-0.1260244911550.248291664064-0.6053942243-0.295635504670.600068382888-0.535016666518-0.6576347398070.6577836417290.2567762470090.0140261001774-0.04947759882180.221723173459-0.04116676914190.28918658299712.318504172223.536088169333.8659121489
54.968336563830.3716252318781.225303755914.963218374391.129264863185.056791267550.001788551266420.333657867394-0.214490626863-0.3842490423590.06241986487180.136076396237-0.063368344434-0.0260105300768-0.004089134275270.2208176370950.002709022097350.01006107944890.179003147234-0.04648555082590.2201819825617.307079997314.958766695429.0923364224
62.81857417335-2.27804087712-0.4811908674842.4945215279-0.5003401767637.294100650670.0304637441483-0.73282684292-1.089109374020.810291177024-0.187813797558-0.008352908352321.421249980960.00862153780579-0.02663843873490.514125074542-0.03063447007380.003373526049430.3192462952270.09469897877920.42229990627419.17515993125.7655919441643.6256968466
73.80390678611.141099201360.4297232189096.030115114162.797153324735.00783809664-0.05741812597250.225120190294-0.368810194671-0.3844827170230.2338890132-0.106558399594-0.002272454566330.236222042603-0.1629764697850.1941910088750.03138902601270.01252211963170.1412646654-0.02558381133770.21902398198520.421640713511.382189178631.6355413773
80.662303195254-1.26832013879-1.560834796764.598186657261.612351575064.59081146219-0.2465845380370.188069655419-1.03627112971-0.1596464548490.1921785188170.165275202340.532715555434-0.0956550438781-0.08563135787260.295591104557-0.004035998314540.06033821460030.155214803585-0.06333041856770.35495275673817.62112749485.8947044500229.5281035375
93.640880495274.073003409110.1033874227894.79524553321.349132115256.62616569137-0.201510442784-0.399075026613-0.774639227248-0.01974332703610.383452801108-0.9246605092610.3126444911990.784640959736-0.31070872280.3107979605890.0885515591907-0.01033976682860.275975280861-0.06909129759180.45900512450827.58051507999.1675316906834.683212676
105.777866453793.79939913021-2.244229295272.83103231312-1.727175166014.371541351450.004255872219830.04665915789870.306196236452-0.332877728517-0.00567096954760.259894334405-0.2230374248340.1398879097990.07874602943360.192441678576-0.00854407229449-0.01035381107020.144673676619-0.02491255217320.19235774455217.519542497721.209948898933.1656555421
110.979812483322-0.2775713144461.570851488383.24798090592-0.2478862367692.220070835010.216526523747-0.05462219641-0.0723520066958-0.0658629540472-0.211145660823-0.2878020658530.282340740102-0.0361905379031-0.06768581171870.1840588656310.03167490139530.02454786822270.2918667094360.04175272312110.24310917835464.176112627611.883347058152.4547462187
121.23816504745-0.307651302104-0.9495170717961.24756979107-0.5874258841981.60624614162-0.0669854415514-0.308705843123-0.209490885517-0.0666535082505-0.106165858294-0.01458758043110.1193230952960.3324613288850.2047283818550.1775834796620.0636488061942-0.008681515795480.2799753691530.016182700870.21386763308660.265669899818.244755677448.7970023728
133.30424542854-0.7865854669550.1947795247631.93640137158-0.3045922928760.964714157731-0.134579037492-0.560781055920.07342458627770.2174004438110.152960650125-0.1201800278050.01087046240660.123055536988-0.03240089790050.1622149475790.0531106471442-0.008846234723660.298423330243-0.0235102923910.13180580437747.267171967733.056758682958.5791562911
144.94983879433-2.553149593510.4434680855282.47209994531-0.4529760438315.563756773750.0196210206714-0.331990906014-1.257245382620.03292714158140.1841810343840.5554546798010.7500390177230.161705692581-0.08396071729870.23587601650.0505523823599-0.01469589161560.2638212201430.06532762387710.41425065046846.613662530219.215470799953.7667057033
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 122 through 139 )AA122 - 1391 - 18
22chain 'A' and (resid 140 through 150 )AA140 - 15019 - 29
33chain 'A' and (resid 151 through 206 )AA151 - 20630 - 76
44chain 'A' and (resid 207 through 213 )AA207 - 21377 - 83
55chain 'A' and (resid 214 through 227 )AA214 - 22784 - 97
66chain 'A' and (resid 228 through 236 )AA228 - 23698 - 106
77chain 'A' and (resid 237 through 248 )AA237 - 248107 - 118
88chain 'A' and (resid 249 through 261 )AA249 - 261119 - 131
99chain 'A' and (resid 262 through 271 )AA262 - 271132 - 141
1010chain 'A' and (resid 272 through 285 )AA272 - 285142 - 155
1111chain 'B' and (resid 128 through 180 )BB128 - 1801 - 44
1212chain 'B' and (resid 181 through 213 )BB181 - 21345 - 77
1313chain 'B' and (resid 214 through 274 )BB214 - 27478 - 138
1414chain 'B' and (resid 275 through 285 )BB275 - 285139 - 149

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