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- PDB-6vcs: SRA domain of UHRF1 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 6vcs
TitleSRA domain of UHRF1 in complex with DNA
Components
  • DNA (5'-D(*GP*CP*CP*TP*GP*TP*AP*CP*AP*GP*GP*C)-3')
  • E3 ubiquitin-protein ligase UHRF1
  • UNK-UNK-UNK-UNK
KeywordsDNA BINDING PROTEIN/DNA / ligase / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / positive regulation of protein metabolic process / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / nuclear matrix / spindle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / 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 / UHRF1/2-like / Tandem tudor domain within UHRF1 / 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. / PUA-like superfamily ...: / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / 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. / PUA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDong, C. / Tempel, W. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: SRA domain of UHRF1 in complex with DNA
Authors: Dong, C. / Tempel, W. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionDec 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: E3 ubiquitin-protein ligase UHRF1
B: E3 ubiquitin-protein ligase UHRF1
C: DNA (5'-D(*GP*CP*CP*TP*GP*TP*AP*CP*AP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*TP*GP*TP*AP*CP*AP*GP*GP*C)-3')
E: E3 ubiquitin-protein ligase UHRF1
G: UNK-UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)78,95172
Polymers78,9516
Non-polymers066
Water3,333185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.995, 113.809, 133.946
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
DetailsAs per the authors the biological assembly is unknown

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Components

#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 / 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: 23698.479 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V3R / References: UniProt: Q96T88
#2: DNA chain DNA (5'-D(*GP*CP*CP*TP*GP*TP*AP*CP*AP*GP*GP*C)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide UNK-UNK-UNK-UNK


Mass: 528.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: weak electron density, which might arise from amino acid residues that may connect residues 482 and 494 in chain B.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 66 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M sodium malonate, 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→44.6 Å / Num. obs: 87819 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.093 / Net I/σ(I): 11.3
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 88.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 1.068 / Num. unique obs: 3976 / CC1/2: 0.66 / Rrim(I) all: 1.207 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bi7

3bi7


Resolution: 1.7→44.6 Å / SU ML: 0.2361 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 29.7891
Details: Strong ice rings on diffraction images. Interstrand crosslinking of the DNA, attempted prior to crystallization, appears to have failed. Signs of non-merohedral twinning. Diffraction ...Details: Strong ice rings on diffraction images. Interstrand crosslinking of the DNA, attempted prior to crystallization, appears to have failed. Signs of non-merohedral twinning. Diffraction patterns can be indexed in an apparent smaller (a,b,c=45A,114A,52A), C-centered orthorhombic cell. Protein chain E is poorly supported by electron density, compared to chains A and B. Transformation with matrix [-1 0 0, 0 1 0, 0 0 -1](52A, 0, 223A), corresponding to mutual SSM of protein chains A and B, as well as DNA strands C and D, allows interpretation of some density peaks in terms of transformed protein chain E.
RfactorNum. reflection% reflection
Rfree0.2575 4329 4.95 %
Rwork0.2367 --
obs0.2378 87428 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 478 66 185 5005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00655019
X-RAY DIFFRACTIONf_angle_d0.79386932
X-RAY DIFFRACTIONf_chiral_restr0.0555708
X-RAY DIFFRACTIONf_plane_restr0.005843
X-RAY DIFFRACTIONf_dihedral_angle_d21.44991838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.39861200.40762438X-RAY DIFFRACTION88.36
1.72-1.740.37621390.37422637X-RAY DIFFRACTION94.68
1.74-1.760.34711490.32872698X-RAY DIFFRACTION98.99
1.76-1.780.3381320.31192794X-RAY DIFFRACTION99.9
1.78-1.810.33051390.28752769X-RAY DIFFRACTION99.93
1.81-1.830.31111480.28722707X-RAY DIFFRACTION99.69
1.83-1.860.33991540.29172797X-RAY DIFFRACTION99.76
1.86-1.890.27051540.29322702X-RAY DIFFRACTION99.76
1.89-1.910.4021600.36862730X-RAY DIFFRACTION98.94
1.91-1.950.38571490.36282745X-RAY DIFFRACTION99.31
1.95-1.980.33051360.25582757X-RAY DIFFRACTION99.66
1.98-2.020.28751570.23392775X-RAY DIFFRACTION99.69
2.02-2.050.24741330.22552767X-RAY DIFFRACTION99.83
2.05-2.10.26971440.2272767X-RAY DIFFRACTION99.86
2.1-2.140.26471570.22152769X-RAY DIFFRACTION99.9
2.14-2.190.31091540.22892768X-RAY DIFFRACTION99.9
2.19-2.250.36141280.31252713X-RAY DIFFRACTION97.46
2.25-2.310.38611360.32992709X-RAY DIFFRACTION97.36
2.31-2.380.30391300.22022830X-RAY DIFFRACTION99.97
2.38-2.450.25331270.23232794X-RAY DIFFRACTION99.97
2.45-2.540.28091550.22412770X-RAY DIFFRACTION99.9
2.54-2.640.24261640.21112778X-RAY DIFFRACTION99.97
2.64-2.760.21891430.21642816X-RAY DIFFRACTION99.9
2.76-2.910.24771460.22982807X-RAY DIFFRACTION99.86
2.91-3.090.2821390.23062816X-RAY DIFFRACTION99.97
3.09-3.330.21811320.20862836X-RAY DIFFRACTION99.93
3.33-3.660.20291540.20232834X-RAY DIFFRACTION99.87
3.66-4.190.21071270.19622879X-RAY DIFFRACTION99.9
4.19-5.280.19271600.18642880X-RAY DIFFRACTION100
5.28-44.60.22891630.25423017X-RAY DIFFRACTION99.44
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)
12.39392034345-0.739052121775-0.6638270259881.41360448581-0.5447533236872.291247012870.0763945791643-0.408740122596-0.09109973960760.0393715003345-0.0517789671995-0.177160058411-0.06694252454870.444548699583-0.02809025905770.154881284549-0.022931445771-0.01944768212240.278028107510.04165392815030.18815085796719.4599533146-4.1077581145491.1843007822
20.970871121319-0.114144829312-0.449492770570.508809146470.6758422802215.14149993166-0.0551473437814-0.322151007554-0.1320877011350.133938778308-0.1768329687980.1097715198140.481998749682-0.4487927843490.2109462225710.230741580407-0.05163302256490.02685900289850.2993138448810.0220541987490.2239316426791.6612565722-2.5616249794595.0597983313
32.93046415195-0.3985778789860.4935851553624.53334797416-0.8731623680262.192846067290.0388059885622-0.2666555421640.3439604896510.422967278381-0.1108621755010.123005273081-0.5078384834780.02470929226810.08259042440060.259081212048-0.0410998913329-0.002555180450440.282936144658-0.06305551467820.1944621686447.2629755085810.070340142898.7771391235
42.358952733-0.482170835134-0.1580358452781.300216943220.6969107542852.021354905160.0654813791791-0.140609683591-0.07514592792140.0317148867286-0.05808322177490.01390894853410.00339277840194-0.03507593139610.01143748211960.115973709245-0.0230154286364-0.01570593096780.1161754483910.03023361706290.1366207949547.94192457231-1.1224403240886.9339184485
52.45792590819-0.0972211738818-1.30836633960.5326931619510.2069615424952.39659472046-0.05357166334210.121930438862-0.173543218980.0449036154633-0.0547167569773-0.08181180341120.242246079067-0.04352720777310.0737902627220.181048419389-0.0247603084727-0.02047804805430.1643469306730.02607101767940.2125962858711.8127729899-3.7691168397281.7957696972
62.250656652230.18173008831-0.7431973071951.837766514550.3869018741382.33857298130.02768025202410.196691047432-0.0906635039454-0.12264715916-0.06834149196250.05482508647920.191053982792-0.3824052932920.02487833368420.20478051755-0.0313908970065-0.001647984914450.330058280162-0.0315123386460.23684249233930.9968502993-6.07726872613134.724649261
72.32145291634-0.0172471709198-0.3612892721951.26201560294-0.3652840723011.799784130780.00783205040380.3558383428890.0572100934004-0.241372841347-0.0468810721278-0.0137172458059-0.050120903053-0.08821300372270.04431137587010.213144742439-0.001960394550990.00690432969840.255976166612-0.01396270409860.1839322213844.969018751-0.173191961571126.693087073
82.4841472870.2528258495390.04725678344871.590541908290.1299290673121.482925617710.06794083414310.1656325147480.121987102158-0.0840329808356-0.0505092530652-0.00578858500574-0.0910275292292-0.0665995197015-0.005449895132410.139599386519-8.68173447792E-50.009073809684370.153695453695-0.01239785401230.14818084275844.66844282792.82084442533133.982400302
92.51890950618-0.0139097010859-1.337974862630.393263181049-0.4796552780572.1325884457-0.101811616567-0.102993019976-0.208249202929-0.112747230558-0.02086623266880.08216670761580.239716912498-0.0461540356529-0.05563108123120.194526635306-0.0290168058821-0.01054553335140.196615131918-0.02385846756140.19675234905339.6895847803-5.05246405884141.522025158
101.226543091110.0982151090584-0.9708419045670.994970743606-2.214894776385.375687260180.1220295445420.360617059810.0868745399902-0.2329825072020.4462307930670.09643870698530.034722967968-1.11990651071-0.4638369548150.594552200029-0.0327751541901-0.1453157940340.674292151333-0.05821320897030.44230568033126.7283523717-4.98532324262109.919337914
110.772360132029-0.0297238903971-0.6353816036970.789998053121.731149776696.263172978070.0542751795155-0.2421914158020.103443152179-0.05562522232180.3747471960560.0701851953716-0.2743403564870.500148288953-0.3882956704170.5130059953960.0583786883577-0.1380040660290.7002688671590.01686950481530.44343169557725.4797020096-4.58440807592113.89822631
122.020719580830.2358712137810.6072083712680.181233552633-0.392752819061.57844354861-0.302472204853-0.540067083077-0.2434308687550.1440088441730.4368699002541.13754886652-0.570913329697-0.63690226876-0.09870335434420.5651476714420.218792642485-0.03027903102420.440379213090.1913235711080.73001808951119.5762293684-26.66253406199.4116992025
133.709063729120.117251815352-2.118146764552.450451337013.146304885865.43218590737-0.449269259182-0.6209952053870.9908915236130.824570221390.6969106173350.527934914099-1.33443932605-0.1343154108940.09359302761070.8580612408740.2230467910410.02965617290020.445988301697-0.007652550013850.47989008469728.5590135526-20.8581857293103.735273797
144.18461113357-0.1362583416630.9371707072464.83758409696-0.8236043245943.87371870172-0.3653433245080.05310167755050.1998972324920.7508475340210.328865233586-0.256690832064-0.320549830509-0.0817946604896-0.1922731218070.3019261143090.0623184899031-0.09441048511740.3505500331720.1147197539190.41002756484137.9879622401-35.8480303574101.936282361
152.07587313003-0.4651751780050.7991613881410.9183693085680.5247411776141.22448726407-0.288872788364-0.4836654949840.6869756074380.8580422120150.227450931811-0.15056928166-1.00027393033-0.0430107510476-0.1158730838531.026942693350.0706000905864-0.08378595720330.358905085308-0.02359031770650.60465168548739.4203575949-24.0824083533112.686711641
160.652766171151-0.4365333901160.2203739832970.8613892463030.4912319175390.793230451978-0.0359500892612-0.2636501870220.1386989272950.5802756730780.3974607273690.231645246475-0.6807036382690.0219866862903-0.2964456518580.7491092892820.2959629026210.1327656837060.4666958729970.06244880778010.45104535368428.6791021337-30.8374364896106.545783238
173.27652031441-0.7052418077062.347988551193.59273566435-0.1356708926291.934124551180.0832548464731-0.193289934398-0.1114528038560.3218478175730.2959814812680.209832227216-0.3418469347970.038008300569-0.2726604790970.505581225710.117617919494-8.74147489289E-70.3849152848410.063797357510.4516061641932.6382474154-33.3275665684104.369719667
184.689599004810.708004856292.011531080246.256909442930.6844464079064.01547302152-0.525199875033-0.0389848576030.2204686517260.4105382435110.451911126375-0.810935249544-0.5546509525020.4506738269690.01401781235860.5958428237040.00930780835874-0.09081182952330.302112228650.02163405292520.5093842418441.4740682681-29.2924040738107.982328998
193.355098938130.8764478303282.365227618033.866310886660.6461664354813.067007165470.112385409573-0.500051503811-0.4613626741990.9582144839180.4932445090230.517583632883-0.224094483556-0.60102854738-0.07180255736880.5571166573490.1421399213630.2560857105930.4872141688720.2971007727720.80591431141421.9424803617-39.3951565487107.928853775
200.2877159689830.1367514988730.2945646142862.148956950080.1652615473050.3017023779360.0570449874079-0.0350208019447-0.26426847994-0.06665437108210.2865327408870.2535350781920.154637293368-0.3922696516060.3564795519420.657477407898-0.1570369612370.08503532408970.6138930022020.3736249477331.1415767867814.6870846857-43.4808087481101.545999032
211.79802803904-0.1351684872840.1996427919984.998186466060.6764971218550.1180716631280.0796058030187-0.154364886353-0.657819546453-0.09167261706960.3692489223641.089598738940.237125687619-0.535915427764-0.1056019874330.667944476406-0.146408793891-0.3052441769270.4766487298420.2601570308610.97475714731715.4480867219-31.059114596287.8457334104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 414 through 462 )
2X-RAY DIFFRACTION2chain 'A' and (resid 463 through 502 )
3X-RAY DIFFRACTION3chain 'A' and (resid 503 through 526 )
4X-RAY DIFFRACTION4chain 'A' and (resid 527 through 568 )
5X-RAY DIFFRACTION5chain 'A' and (resid 569 through 612 )
6X-RAY DIFFRACTION6chain 'B' and (resid 414 through 448 )
7X-RAY DIFFRACTION7chain 'B' and (resid 449 through 511 )
8X-RAY DIFFRACTION8chain 'B' and (resid 512 through 568 )
9X-RAY DIFFRACTION9chain 'B' and (resid 569 through 616 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 12 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 12 )
12X-RAY DIFFRACTION12chain 'E' and (resid 416 through 439 )
13X-RAY DIFFRACTION13chain 'E' and (resid 440 through 462 )
14X-RAY DIFFRACTION14chain 'E' and (resid 463 through 474 )
15X-RAY DIFFRACTION15chain 'E' and (resid 475 through 526 )
16X-RAY DIFFRACTION16chain 'E' and (resid 527 through 542 )
17X-RAY DIFFRACTION17chain 'E' and (resid 543 through 568 )
18X-RAY DIFFRACTION18chain 'E' and (resid 569 through 582 )
19X-RAY DIFFRACTION19chain 'E' and (resid 583 through 591 )
20X-RAY DIFFRACTION20chain 'E' and (resid 592 through 601 )
21X-RAY DIFFRACTION21chain 'E' and (resid 602 through 613 )

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