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- PDB-7uaj: Crystal structure of apo HPV16 E6 -

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Basic information

Entry
Database: PDB / ID: 7uaj
TitleCrystal structure of apo HPV16 E6
ComponentsMaltose/maltodextrin-binding periplasmic protein,Protein E6
KeywordsVIRAL PROTEIN / Apo conformation
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / PDZ domain binding / : / outer membrane-bounded periplasmic space / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / periplasmic space / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA damage response / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / membrane / identical protein binding / metal ion binding
Similarity search - Function
E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Protein E6 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsShen, Q. / Leonard, P.G. / Cross, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Disorder-to-order transition of the interdomain linker of HPV E6 upon E6AP binding reshapes p53 binding pocket
Authors: Shen, Q. / Leonard, P.G. / Cross, J.B.
History
DepositionMar 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Protein E6
B: Maltose/maltodextrin-binding periplasmic protein,Protein E6
C: Maltose/maltodextrin-binding periplasmic protein,Protein E6
D: Maltose/maltodextrin-binding periplasmic protein,Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,53716
Polymers243,6444
Non-polymers1,89212
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.110, 88.680, 109.610
Angle α, β, γ (deg.)106.610, 90.160, 102.760
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 371 or resid 381...
21(chain B and ((resid 2 and (name N or name...
31(chain C and ((resid 2 and (name N or name...
41(chain D and ((resid 2 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 371 or resid 381...A2 - 371
121(chain A and (resid 2 through 371 or resid 381...A381 - 452
131(chain A and (resid 2 through 371 or resid 381...A456
211(chain B and ((resid 2 and (name N or name...B2
221(chain B and ((resid 2 and (name N or name...B2 - 601
231(chain B and ((resid 2 and (name N or name...B2 - 601
241(chain B and ((resid 2 and (name N or name...B2 - 601
251(chain B and ((resid 2 and (name N or name...B2 - 601
261(chain B and ((resid 2 and (name N or name...B2 - 601
311(chain C and ((resid 2 and (name N or name...C2
321(chain C and ((resid 2 and (name N or name...C2 - 601
331(chain C and ((resid 2 and (name N or name...C2 - 601
341(chain C and ((resid 2 and (name N or name...C2 - 601
351(chain C and ((resid 2 and (name N or name...C2 - 601
361(chain C and ((resid 2 and (name N or name...C2 - 601
411(chain D and ((resid 2 and (name N or name...D2
421(chain D and ((resid 2 and (name N or name...D2 - 601
431(chain D and ((resid 2 and (name N or name...D2 - 601
441(chain D and ((resid 2 and (name N or name...D2 - 601
451(chain D and ((resid 2 and (name N or name...D2 - 601
461(chain D and ((resid 2 and (name N or name...D2 - 601

NCS oper:
IDCodeMatrixVector
1given(-0.999780794026, 0.0190585111597, -0.00866816301563), (-0.00459991298963, -0.603837621962, -0.797094076696), (-0.0204255892982, -0.796879476116, 0.603792924641)-14.8172457378, 61.7932293983, 30.9501020083
2given(-0.999021823099, -0.0306072354189, -0.0319154212161), (-0.0438845790974, 0.597529389368, 0.800645222654), (-0.00543513466606, 0.801262644818, -0.598288085566)-13.23940196, 29.0473143127, -17.3027020941
3given(0.999726742938, 0.0211818455984, -0.00988781426459), (0.0214175871214, -0.999473363816, 0.0243778995084), (-0.00936623808042, -0.0245830111987, -0.999653914685)-2.13607149983, 92.3258194842, 15.2787635979

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein,Protein E6 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 60911.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Human papillomavirus type 16
Strain: K12 / Gene: malE, b4034, JW3994, E6 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P03126
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Zn
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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, 8% ethylene glycol and 10% PEG 8000 at pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→82.67 Å / Num. obs: 42715 / % possible obs: 91.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 109.37 Å2 / CC1/2: 0.919 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.075 / Rrim(I) all: 0.144 / Net I/σ(I): 5.7 / Num. measured all: 159101 / Scaling rejects: 205
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.25-3.371.6891707345780.4010.9941.960.993.3
12.16-82.670.05431698570.8860.040.06713.697.2

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Processing

Software
NameVersionClassification
MOSFLMv 7.3.0data reduction
Aimlessv 0.7.4data scaling
PHASERv 2.8.3phasing
PHENIXv 1.20.1-4887-000refinement
PDB_EXTRACTv 3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XR8

4xr8


Resolution: 3.25→52.39 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 34.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2824 2134 5.02 %
Rwork0.2559 40390 -
obs0.2572 42524 91.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.72 Å2 / Biso mean: 121.5343 Å2 / Biso min: 51.12 Å2
Refinement stepCycle: final / Resolution: 3.25→52.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16117 0 100 0 16217
Biso mean--101.28 --
Num. residues----2041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.25-3.330.39731510.38082684283592
3.33-3.410.38521380.37212724286292
3.41-3.50.39451670.35842637280490
3.5-3.60.38231370.35052615275290
3.6-3.720.39711200.32572478259883
3.72-3.850.33011390.30412683282291
3.85-4.010.34961430.30192780292395
4.01-4.190.32831610.27142794295595
4.19-4.410.27311450.26442774291995
4.41-4.690.25271610.25032749291094
4.69-5.050.30421440.23352669281392
5.05-5.560.26811100.2492497260783
5.56-6.360.2811350.26172820295595
6.36-8.010.23241410.23282823296496
8.01-52.390.21041420.18842663280590

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