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- PDB-6zx9: Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from ... -

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Basic information

Entry
Database: PDB / ID: 6zx9
TitleCrystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396)
Components
  • DDB1- and CUL4-associated factor 1
  • DNA damage-binding protein 1
  • Vpr protein fused to T4 lysozyme
KeywordsVIRAL PROTEIN / viral protein Vpr / viral hijacking of human ubiquitin ligase CRL4 / DDB1 / DCAF1
Function / homology
Function and homology information


cell competition in a multicellular organism / V(D)J recombination / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding ...cell competition in a multicellular organism / V(D)J recombination / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / ectopic germ cell programmed cell death / ubiquitin-like ligase-substrate adaptor activity / positive regulation of viral genome replication / proteasomal protein catabolic process / viral release from host cell by cytolysis / viral life cycle / peptidoglycan catabolic process / positive regulation of gluconeogenesis / post-translational protein modification / B cell differentiation / nuclear estrogen receptor binding / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / fibrillar center / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cell wall macromolecule catabolic process / cellular response to UV / rhythmic process / lysozyme / lysozyme activity / Antigen processing: Ubiquitination & Proteasome degradation / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / eukaryotic translation initiation factor 2alpha kinase activity / host cell cytoplasm / chromosome, telomeric region / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein ubiquitination / defense response to bacterium / protein serine kinase activity / DNA repair / apoptotic process / centrosome / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / host cell nucleus / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal ...: / Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Lysozyme / Armadillo-like helical / Lysozyme-like domain superfamily / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Vpr protein / Endolysin / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5197288426 Å
AuthorsSchwefel, D. / Banchenko, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHW 1851/1-1 Germany
CitationJournal: Plos Pathog. / Year: 2021
Title: Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses.
Authors: Banchenko, S. / Krupp, F. / Gotthold, C. / Burger, J. / Graziadei, A. / O'Reilly, F.J. / Sinn, L. / Ruda, O. / Rappsilber, J. / Spahn, C.M.T. / Mielke, T. / Taylor, I.A. / Schwefel, D.
History
DepositionJul 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: 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: DNA damage-binding protein 1
B: DDB1- and CUL4-associated factor 1
C: Vpr protein fused to T4 lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,62412
Polymers197,8213
Non-polymers8029
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-23 kcal/mol
Surface area72430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.898, 95.540, 98.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127241.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein kinase VPRBP / Vpr-interacting protein


Mass: 40876.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF1, KIAA0800, RIP, VPRBP / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#3: Protein Vpr protein fused to T4 lysozyme / Lysis protein / Lysozyme / Muramidase


Mass: 29703.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Simian immunodeficiency virus
Gene: vpr / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P00720, UniProt: A4UDG5, lysozyme

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Non-polymers , 3 types, 262 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2.
PH range: 7.8-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→79.07 Å / Num. obs: 85560 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 54.6751512341 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.78
Reflection shellResolution: 2.52→2.56 Å / Num. unique obs: 6264 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSXDSAPPdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZUE, 1QT6

6zue

1qt6


Resolution: 2.5197288426→79.0659625889 Å / SU ML: 0.440095094398 / Cross valid method: FREE R-VALUE / σ(F): 1.32551474912 / Phase error: 29.4127757546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.260498009517 3948 4.65522120555 %
Rwork0.216112029271 80860 -
obs0.218135520807 84808 99.1894831639 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.2991472108 Å2
Refinement stepCycle: LAST / Resolution: 2.5197288426→79.0659625889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13548 0 49 253 13850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042088631835713866
X-RAY DIFFRACTIONf_angle_d0.8108429397918769
X-RAY DIFFRACTIONf_chiral_restr0.04852752225732117
X-RAY DIFFRACTIONf_plane_restr0.004326236951832425
X-RAY DIFFRACTIONf_dihedral_angle_d23.64702607667215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.55050.4463746743111510.4111499802792729X-RAY DIFFRACTION96.5147453083
2.5505-2.58270.4092495559841570.3903387618712811X-RAY DIFFRACTION97.3433912758
2.5827-2.61670.3996917791341480.3786282965812771X-RAY DIFFRACTION98.1176470588
2.6167-2.65260.3830003438831360.3596700321662865X-RAY DIFFRACTION97.9758406791
2.6526-2.69050.3418074673511140.3541382009092825X-RAY DIFFRACTION98.0320213476
2.6905-2.73060.3826385785391300.3409352603352846X-RAY DIFFRACTION98.7392169874
2.7306-2.77330.4314440156571530.3406562284212793X-RAY DIFFRACTION98.4625668449
2.7733-2.81880.3529131711031350.3358484080682859X-RAY DIFFRACTION98.551678736
2.8188-2.86740.3282100971371250.3180207854932849X-RAY DIFFRACTION98.9683860233
2.8674-2.91950.3446947459971540.3081654113782884X-RAY DIFFRACTION99.5086799869
2.9195-2.97570.3581589803821220.2785906378482874X-RAY DIFFRACTION99.0740740741
2.9757-3.03640.3149681105911430.28156259162841X-RAY DIFFRACTION99.5330220147
3.0364-3.10250.3032979852751410.2595970614322892X-RAY DIFFRACTION99.4426229508
3.1025-3.17460.3245146963141460.2583287116562883X-RAY DIFFRACTION99.5399277029
3.1746-3.2540.275204217181630.242932842882833X-RAY DIFFRACTION99.5018266357
3.254-3.3420.2736821921051270.2257137552412918X-RAY DIFFRACTION99.640052356
3.342-3.44030.2958804397341590.227626209722836X-RAY DIFFRACTION99.5678191489
3.4403-3.55140.2786339794841580.2241496234872891X-RAY DIFFRACTION99.7383055283
3.5514-3.67830.2527121754641560.2152278366712903X-RAY DIFFRACTION99.8694090761
3.6783-3.82560.2357787050621400.2043211121792920X-RAY DIFFRACTION99.8043052838
3.8256-3.99970.2620619636151370.1906232710252889X-RAY DIFFRACTION99.8021108179
3.9997-4.21050.2465255951231370.1801499011372920X-RAY DIFFRACTION99.9346191566
4.2105-4.47430.2041298583291350.1577620669622954X-RAY DIFFRACTION99.9352960207
4.4743-4.81980.1789293795251450.146078120072922X-RAY DIFFRACTION100
4.8198-5.30470.17977992571250.1566128795352980X-RAY DIFFRACTION100
5.3047-6.07210.2249473439681240.1870201209212990X-RAY DIFFRACTION99.9678972713
6.0721-7.64920.2385266676991440.1948512925053022X-RAY DIFFRACTION99.8423210344
7.6492-79.06590.2061773637341430.1757186977633160X-RAY DIFFRACTION99.7282608696
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)
10.3593543672070.174360077235-0.1176574710220.299377895508-0.01530573179160.173712044947-0.04728969774490.06870381011490.133748704310.0149388652230.01071091582540.1742455509460.04140919127880.025939527399-0.001153484475350.274535768590.0150218773431-0.02298442260440.2643546592440.00769117203790.330721200658541.64521.52426.374
20.0093710474348-0.1154980881240.00527831801832-0.02697687567250.01939354116850.319133764876-0.14306459734-0.03476235466030.02364107619380.0402914691930.1640226371790.1113021651430.563773564539-0.1679555467890.1201896284280.59922432506-0.175246425547-0.1680059825960.385322847505-0.0819533060554-0.580832264728562.5770.085-22.724
30.3800600278430.261657838504-0.03427553825050.5563066005780.2359046004270.282282642152-0.005500071432870.06716657305430.0431985843462-0.07130594729560.106476580835-0.07651464322290.00481192400684-0.01328663259610.01638308839920.2191906190750.007616166681520.01441063831920.2819868381880.01360198373450.240391709307573.82418.68517.827
40.00285477712690.00884390103869-0.00182531631120.00710640180693-0.003824899043840.000766163524193-0.0974295771660.02115155348350.107287951172-0.0457345555551-0.0590871660941-0.0457382815260.118164581681-0.1641766001072.92164813879E-70.363647200015-0.010554672346-0.009223454505640.429033583236-0.02330136025650.387145342653571.51926.02436.845
50.0164927068720.00917925358897-0.01385545880130.01472006135390.004978594459680.0151237852173-0.0721060253062-0.07104256569420.0603986073151-0.221366580956-0.0345763447346-0.141356404113-0.04653977055140.0627401258251-0.00068336281790.371194504166-0.040377604934-0.112290417470.372104289621-0.01035922404550.661402379864581.6658.20536.987
60.0122524205752-0.0297119683875-0.04003962505640.06342319873220.089614184280.16708761462-0.2659394628-0.2304078234520.3554303150970.0287277705349-0.1674405274510.219424636387-0.112320819419-0.256844403403-0.01698596972170.4135740892060.0984970309763-0.1710375871840.537549729916-0.2403124332060.877426916347559.42259.9645.13
70.00693010694476-0.0127396435932-0.003168552459020.01777075850830.006078724070780.00496504349247-0.176088170937-0.01934640102880.001001549923520.0505497385039-0.179408643510.07616861366040.0931932679088-0.1577762568165.06034339097E-80.5120469823650.03393045533650.1019427650810.513555751571-0.1306749876610.643085639903562.74543.41548.97
80.00337237215721-0.004584282665370.002793644759380.00805384184678-0.0009071057376190.000256036234982-0.0990840073028-0.0189795761760.03622675097040.0857439798833-0.0115796765773-0.0058187321266-0.0384945198508-0.04687177813582.92977816E-70.569122245815-0.001759909787250.03710693735150.378383621874-0.05804677443390.494238690102574.17939.00548.113
90.0217518957591-9.18344025469E-50.009844643169580.00523616259995-0.005189564714130.01509036354-0.0484438710976-0.0664244311231-0.0866455870930.1489318865030.00164757581222-0.1213928265320.01244448578710.135671237762-1.85047949516E-70.4375781011930.0144262435383-0.138075980520.3686555465450.01665881791020.562844833531585.49240.36243.595
100.03045922055860.0679049987810.004879669457350.40618011449-0.07161242803050.3374500129940.09344255846990.104343507144-0.162219964055-0.376579055982-0.463391272811-0.109184305356-0.0564290511226-0.028036761397-0.2723857774760.7067825697490.1669963281190.1277958015870.5166068578290.01212779257830.612192096987590.17264.9467.051
110.008191145707470.0134302491750.00510573746840.0122689194656-0.0005690010184120.00405104812366-0.114203526223-0.05432754286210.113029315411-0.09446468027149.54162473901E-5-0.02451991877-0.030014775839-0.06574830808127.441349050870.611039445565-0.0976070724803-0.1910509847840.466255271473-0.03510905567160.672824667499591.42771.38745.886
120.0742405058805-0.0087167855931-0.02863373707180.0234104034355-0.01764738970970.054463601828-0.0390590473553-0.0391619535378-0.0341111345130.0391552734179-0.1288182026740.01373295464330.004200303606750.0448006494607-0.04847486115580.304544402476-0.087777880628-0.09397383186750.499723345241-0.1295167550210.605141507412592.66363.9355.779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:365 )A-1 - 365
2X-RAY DIFFRACTION2( CHAIN A AND RESID 366:698 )A366 - 698
3X-RAY DIFFRACTION3( CHAIN A AND RESID 699:1140 )A699 - 1140
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1046:1086 )B1046 - 1086
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1087:1171 )B1087 - 1171
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1172:1264 )B1172 - 1264
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1265:1332 )B1265 - 1332
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1333:1359 )B1333 - 1359
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1360:1399 )B1360 - 1399
10X-RAY DIFFRACTION10( CHAIN C AND RESID -165:4 )C-165 - 4
11X-RAY DIFFRACTION11( CHAIN C AND RESID 5:37 )C5 - 37
12X-RAY DIFFRACTION12( CHAIN C AND RESID 38:91 )C38 - 91

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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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