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- PDB-4jnh: A unique spumavirus gag N-terminal domain with functional propert... -

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Basic information

Entry
Database: PDB / ID: 4jnh
TitleA unique spumavirus gag N-terminal domain with functional properties of orthoretroviral Matrix and Capsid
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / Gag / coiled-coil / Env
Function / homology
Function and homology information


host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral budding via host ESCRT complex / viral release from host cell / host cell / viral nucleocapsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / DNA binding / RNA binding
Similarity search - Function
Gag polyprotein / : / : / Spumavirus gag protein, N-terminal / Spumavirus Gag polyprotein, conserved central domain / Spumavirus Gag polyprotein, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1500 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman spumaretrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.402 Å
AuthorsTaylor, I.A. / Goldstone, D.C. / Flower, T.G. / Ball, N.J.
CitationJournal: Plos Pathog. / Year: 2013
Title: A Unique Spumavirus Gag N-terminal Domain with Functional Properties of Orthoretroviral Matrix and Capsid.
Authors: Goldstone, D.C. / Flower, T.G. / Ball, N.J. / Sanz-Ramos, M. / Yap, M.W. / Ogrodowicz, R.W. / Stanke, N. / Reh, J. / Lindemann, D. / Stoye, J.P. / Taylor, I.A.
History
DepositionMar 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein
B: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)46,4862
Polymers46,4862
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-22 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.423, 94.729, 61.659
Angle α, β, γ (deg.)90.000, 93.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gag polyprotein / Pr71Gag / Gag protein / p68Gag / p3 / p3Gag


Mass: 23242.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Gene: gag / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P14349
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 10mg/ml solution of PFV-Gag-NtD in 150mM NaCl, 5% glycerol, 10mM Tris-HCl, pH 8.0 was mixed with an equal volume of crystallisation solution containing 16% PEG 6000 (w/v), 12% ethylene ...Details: 10mg/ml solution of PFV-Gag-NtD in 150mM NaCl, 5% glycerol, 10mM Tris-HCl, pH 8.0 was mixed with an equal volume of crystallisation solution containing 16% PEG 6000 (w/v), 12% ethylene glycol, 0.03M MgCl2 hexahydrate , VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2011
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Χ2: 1 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.492.80.1129930.936195.8
2.49-2.592.90.1130230.884196.5
2.59-2.730.08930410.927197.5
2.7-2.843.10.08930551.003198.7
2.84-3.023.40.07530760.999198.2
3.02-3.263.40.07130941.079198.9
3.26-3.583.40.0630981.036199.3
3.58-4.13.60.05231041.079199.7
4.1-5.163.50.04930960.988199.1
5.16-253.20.04930331.012197.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.402→23.682 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8359 / SU ML: 0.28 / σ(F): 0 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1518 4.96 %RANDOM
Rwork0.172 ---
all0.1749 30639 --
obs0.1749 30630 98.2 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.556 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 131.95 Å2 / Biso mean: 23.0467 Å2 / Biso min: 1.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.0111 Å20 Å2-0.3564 Å2
2--5.1634 Å2-0 Å2
3----3.1523 Å2
Refinement stepCycle: LAST / Resolution: 2.402→23.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 0 171 2975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082870
X-RAY DIFFRACTIONf_angle_d1.0443902
X-RAY DIFFRACTIONf_chiral_restr0.065431
X-RAY DIFFRACTIONf_plane_restr0.004525
X-RAY DIFFRACTIONf_dihedral_angle_d16.461120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.402-2.47950.25761520.17782566271896
2.4795-2.5680.28941050.20122643274897
2.568-2.67070.30381070.20582668277598
2.6707-2.79210.26531180.20842675279398
2.7921-2.9390.3011430.19882667281098
2.939-3.12280.2741580.19352610276899
3.1228-3.36330.25591460.17632662280899
3.3633-3.70060.20311510.16872638278999
3.7006-4.23340.1721450.128827052850100
4.2334-5.32360.18161430.132667281099
5.3236-23.68340.21321500.1932611276197
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)
10.005-0.00020.00560.0007-0.00010.0084-0.0069-0.014-0.0692-0.01220.0408-0.00980.0158-0.04750.06310.0992-0.04490.00090.07260.02260.1121-2.742520.259349.5964
20.1862-0.0791-0.11150.19370.0640.2768-0.02070.1125-0.07220.0547-0.07510.0207-0.0052-0.1296-0.20430.0314-0.0071-0.0050.0117-0.0679-0.0019-0.268429.351345.278
30.0668-0.054-0.00850.04470.00370.03320.0293-0.0165-0.05050.00350.02760.013-0.0152-0.02750.01460.0747-0.010.05070.09160.06240.2518-3.993233.456656.0333
40.2760.0354-0.03320.083-0.10540.14740.008-0.0307-0.174-0.0439-0.0429-0.01010.06740.0598-0.06060.05060.00160.01680.0182-0.00020.038212.416338.457850.6021
50.05990.0310.00110.02060.00020.00080.0357-0.1115-0.00830.0982-0.01470.04980.0091-0.01380.05470.1398-0.02690.06350.1679-0.0060.007120.658151.322177.7772
60.069-0.05550.03570.0445-0.02080.21730.0923-0.01350.01530.02260.02740.086-0.04010.01330.02560.1349-0.0481-0.01250.06520.02650.245142.783871.4747.8152
70.0236-0.00740.04260.1054-0.00650.0835-0.0553-0.00980.05510.0201-0.00660.049-0.02130.0497-0.1762-0.05430.0546-0.04330.05670.0910.066935.526162.852650.1193
80.00350.0105-0.00050.16780.04570.1459-0.02490.09370.0842-0.0148-0.1227-0.09330.04260.1026-0.22660.0224-0.01450.03590.14770.14250.126546.48363.091141.2969
90.2282-0.01440.02270.0121-0.00470.0736-0.01070.00460.14090.0089-0.0242-0.01310.01420.0371-0.07050.0394-0.00910.0380.03010.0170.051629.00154.1951.121
100.00430.0036-0.00810.0649-0.07260.09040.0309-0.04430.010.0897-0.0944-0.02060.04430.0129-0.03030.1419-0.10930.01640.18860.04490.041319.215742.485879.8181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 9:29)A9 - 29
2X-RAY DIFFRACTION2(chain A and resid 30:80)A30 - 80
3X-RAY DIFFRACTION3(chain A and resid 81:85)A81 - 85
4X-RAY DIFFRACTION4(chain A and resid 86:156)A86 - 156
5X-RAY DIFFRACTION5(chain A and resid 157:179)A157 - 179
6X-RAY DIFFRACTION6(chain B and resid 7:28)B7 - 28
7X-RAY DIFFRACTION7(chain B and resid 29:53)B29 - 53
8X-RAY DIFFRACTION8(chain B and resid 54:82)B54 - 82
9X-RAY DIFFRACTION9(chain B and resid 83:158)B83 - 158
10X-RAY DIFFRACTION10(chain B and resid 159:179)B159 - 179

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