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- PDB-4djb: A Structural Basis for the Assembly and Functions of a Viral Poly... -

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Basic information

Entry
Database: PDB / ID: 4djb
TitleA Structural Basis for the Assembly and Functions of a Viral Polymer that Inactivates Multiple Tumor Suppressors
ComponentsE4-ORF3
KeywordsVIRAL PROTEIN / Adenovirus protein / RRM-like fold / HPV E2 DBD-like protein / tumor suppressor inactivation / nucleus
Function / homologyMastadenovirus E4 ORF3 / Mastadenovirus E4/Orf3 / Mastadenovirus E4/Orf3 superfamily / Mastadenovirus E4 ORF3 protein / Alpha-Beta Plaits / 2-Layer Sandwich / identical protein binding / Alpha Beta / Probable early E4 11 kDa protein
Function and homology information
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.053 Å
AuthorsOu, H.D. / Kwiatkowski, W. / Deerinck, T.J. / Noske, A. / Blain, K.Y. / Land, H.S. / Soria, C. / Powers, C.J. / May, A.P. / Shu, X. ...Ou, H.D. / Kwiatkowski, W. / Deerinck, T.J. / Noske, A. / Blain, K.Y. / Land, H.S. / Soria, C. / Powers, C.J. / May, A.P. / Shu, X. / Tsien, R.Y. / Fitzpatrick, J.A.J. / Long, J.A. / Ellisman, M.H. / Choe, S. / O'Shea, C.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: A Structural Basis for the Assembly and Functions of a Viral Polymer that Inactivates Multiple Tumor Suppressors.
Authors: Ou, H.D. / Kwiatkowski, W. / Deerinck, T.J. / Noske, A. / Blain, K.Y. / Land, H.S. / Soria, C. / Powers, C.J. / May, A.P. / Shu, X. / Tsien, R.Y. / Fitzpatrick, J.A. / Long, J.A. / Ellisman, ...Authors: Ou, H.D. / Kwiatkowski, W. / Deerinck, T.J. / Noske, A. / Blain, K.Y. / Land, H.S. / Soria, C. / Powers, C.J. / May, A.P. / Shu, X. / Tsien, R.Y. / Fitzpatrick, J.A. / Long, J.A. / Ellisman, M.H. / Choe, S. / O'Shea, C.C.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E4-ORF3
B: E4-ORF3


Theoretical massNumber of molelcules
Total (without water)30,3012
Polymers30,3012
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-15 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.429, 67.222, 87.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsE4-ORF3 CREATES COMPLEX POLYMERIC STRUCTURES IN THE NUCLEUS.

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Components

#1: Protein E4-ORF3 / early E4 11 kDa protein


Mass: 15150.531 Da / Num. of mol.: 2 / Mutation: N82E, C71S, C86S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 5 / Gene: E4ORF3 / Plasmid: PETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04489
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG10000, 8% ethylene glycol, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 19, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.053→50 Å / Num. all: 21394 / Num. obs: 21324 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 20.4
Reflection shellResolution: 2.053→2.1 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.9 / Num. unique all: 997 / % possible all: 93.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.053→31.368 Å / SU ML: 0.24 / σ(F): 0.74 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1096 5.13 %RANDOM
Rwork0.2116 ---
obs0.2137 21324 99.38 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.535 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.663 Å2-0 Å20 Å2
2---4.6774 Å2-0 Å2
3---3.0144 Å2
Refinement stepCycle: LAST / Resolution: 2.053→31.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 0 116 2006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081922
X-RAY DIFFRACTIONf_angle_d0.9892598
X-RAY DIFFRACTIONf_dihedral_angle_d14.636711
X-RAY DIFFRACTIONf_chiral_restr0.063301
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.053-2.10030.31391390.25132416X-RAY DIFFRACTION94
2.1003-2.15280.28491570.2272447X-RAY DIFFRACTION99
2.1528-2.2110.2891660.2132523X-RAY DIFFRACTION100
2.211-2.2760.26791460.21382514X-RAY DIFFRACTION100
2.276-2.34950.27131620.21282543X-RAY DIFFRACTION100
2.3495-2.43340.25881310.22632555X-RAY DIFFRACTION100
2.4334-2.53080.26161480.22212491X-RAY DIFFRACTION100
2.5308-2.64590.24911150.22082575X-RAY DIFFRACTION100
2.6459-2.78540.27851200.21542523X-RAY DIFFRACTION100
2.7854-2.95980.27931410.22412574X-RAY DIFFRACTION100
2.9598-3.18810.26351400.23072517X-RAY DIFFRACTION100
3.1881-3.50850.26611340.21622555X-RAY DIFFRACTION100
3.5085-4.01530.28161290.20432535X-RAY DIFFRACTION100
4.0153-5.05550.20321250.17372548X-RAY DIFFRACTION100
5.0555-31.37210.2092950.222527X-RAY DIFFRACTION98

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