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- PDB-5mlu: Crystal structure of the PFV GAG CBS bound to a mononucleosome -

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Basic information

Entry
Database: PDB / ID: 5mlu
TitleCrystal structure of the PFV GAG CBS bound to a mononucleosome
Components
  • (DNA (145-MER)) x 2
  • (Histone H2B) x 2
  • Histone H2A type 1
  • Histone H3.2
  • Histone H4
  • PFV GAG peptide
KeywordsDNA BINDING PROTEIN / nucleosome / GAG / prototype foamy virus (PFV) / complex / protein / DNA
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 / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / host cell / viral nucleocapsid ...host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral budding via host ESCRT complex / viral release from host cell / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / host cell / viral nucleocapsid / host cell cytoplasm / protein heterodimerization activity / symbiont entry into host cell / host cell nucleus / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Gag polyprotein / : / Spumavirus gag protein, N-terminal / Spumavirus Gag polyprotein, conserved central domain / Spumavirus Gag polyprotein, C-terminal / Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site ...Gag polyprotein / : / Spumavirus gag protein, N-terminal / Spumavirus Gag polyprotein, conserved central domain / Spumavirus Gag polyprotein, C-terminal / Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H2B 1.1 / Histone H2A type 1 / Gag polyprotein / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Simian foamy virus
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPye, V.E. / Maskell, D.P. / Lesbats, P. / Cherepanov, P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis for spumavirus GAG tethering to chromatin.
Authors: Lesbats, P. / Serrao, E. / Maskell, D.P. / Pye, V.E. / O'Reilly, N. / Lindemann, D. / Engelman, A.N. / Cherepanov, P.
History
DepositionDec 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B
M: PFV GAG peptide
I: DNA (145-MER)
J: DNA (145-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,47715
Polymers177,25711
Non-polymers2204
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59200 Å2
ΔGint-394 kcal/mol
Surface area72470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.260, 109.450, 175.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 5 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2


Mass: 11405.321 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 9566.249 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 11494.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B


Mass: 10348.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B8Y853, UniProt: P02281*PLUS
#5: Protein Histone H2B


Mass: 10478.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B8Y853, UniProt: P02281*PLUS

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Protein/peptide , 1 types, 1 molecules M

#6: Protein/peptide PFV GAG peptide


Mass: 1986.177 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian foamy virus / Production host: synthetic construct (others) / References: UniProt: P14349*PLUS

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DNA chain , 2 types, 2 molecules IJ

#7: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Widom 601 / Source: (natural) Escherichia coli (E. coli) / Plasmid details: Widow 601
#8: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Widom 601 / Source: (natural) Escherichia coli (E. coli) / Plasmid details: Widow 601

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Non-polymers , 2 types, 198 molecules

#9: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mn
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05M MnCl2, 0.04M KCl, 0.1M potassium cacodylate pH 6.0, 5% trehalose, 24% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.8→76.61 Å / Num. obs: 51308 / % possible obs: 99.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.4
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 5 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.6 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphenixphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KX5

1kx5


Resolution: 2.8→76.607 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.61
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 960 2.09 %Random selection
Rwork0.2085 ---
obs0.2094 45929 88.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→76.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6096 5945 4 194 12239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312898
X-RAY DIFFRACTIONf_angle_d0.5418677
X-RAY DIFFRACTIONf_dihedral_angle_d22.9176770
X-RAY DIFFRACTIONf_chiral_restr0.0522122
X-RAY DIFFRACTIONf_plane_restr0.0031365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94760.3522810.29173450X-RAY DIFFRACTION49
2.9476-3.13230.30661000.27165396X-RAY DIFFRACTION75
3.1323-3.37420.35431490.27827054X-RAY DIFFRACTION99
3.3742-3.71370.26361410.2297177X-RAY DIFFRACTION100
3.7137-4.25110.24831460.21257183X-RAY DIFFRACTION99
4.2511-5.35570.22781930.19477212X-RAY DIFFRACTION100
5.3557-76.63550.23411500.18217497X-RAY DIFFRACTION99
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)
10.112-0.4280.04590.6872-0.7070.6801-0.1405-0.0309-0.23730.62920.0227-0.94070.39060.2262-0.00630.5775-0.0376-0.10590.4322-0.00230.76781.9688-27.900357.295
20.0219-0.20970.05980.6191-0.08260.0380.0294-0.3246-0.33440.04890.0147-0.86450.07160.08480.00290.3902-0.0120.03740.52660.00150.5336-9.2036-25.751656.7288
30.02490.00670.06410.0035-0.00770.0181-0.4510.5465-0.52050.023-0.5423-0.38220.2191-0.15080.00020.4651-0.101-0.02530.6838-0.10590.4632-20.3565-29.76754.2391
4-0.0368-0.005-0.0366-0.0280.01090.0262-0.22590.21010.02980.8180.4416-0.0002-0.1717-0.02610.00010.9155-0.0762-0.15270.4024-0.07640.81124.617-45.457649.9963
50.23920.0697-0.1510.1248-0.03850.0425-0.02490.16460.19251.18220.1868-0.50520.4508-0.497-00.53470.019-0.16830.4985-0.02130.5972-3.9656-28.372464.0815
6-0.1981-0.2049-0.2820.39290.0846-0.02310.27630.0252-0.10380.40060.0498-0.33640.01450.07290.04170.52480.04850.18120.4344-0.03050.5713-5.7311-35.649341.7886
70.07270.0060.10780.0013-0.05430.0514-0.56880.0280.0014-1.2540.1674-0.55520.10180.28610.00010.3741-0.01550.08510.3691-0.010.6907-5.3563-24.750338.3015
80.01110.0691-0.0740.0588-0.01910.03820.01530.4439-0.2084-0.45050.2330.41370.30.2336-01.2872-0.1384-0.28730.7514-0.06560.6745-27.1396-37.67614.8655
90.783-0.81840.72440.5035-0.04750.5890.00840.247-0.2504-1.07090.08020.34050.8837-0.40260.02740.7699-0.1858-0.12520.5461-0.03360.5361-30.7507-37.404728.7699
100.0153-0.02190.04030.0426-0.0080.0999-0.1105-0.1936-0.34730.01780.15930.04970.00370.0565-00.4791-0.0718-0.01590.71530.03130.5656-28.6872-34.812641.582
11-0.0686-0.1354-0.0634-0.1289-0.1223-0.00230.1966-0.5936-0.3097-0.066-0.13080.43370.37740.019800.5802-0.06320.06161.03350.10951.0344-37.6871-34.133357.0739
120.02330.00030.0775-0.0063-0.0493-0.06080.1173-0.0497-0.41820.275-0.34660.20460.2709-0.231701.1885-0.0555-0.11841.0864-0.18470.6097-37.4814-32.529319.5602
130.0277-0.1065-0.10270.04280.05930.2895-0.48640.3855-0.3368-0.97610.451-0.0642-0.1511-0.427700.8486-0.2273-0.19250.918-0.03930.7494-38.0371-37.379329.034
140.04230.17120.080.124-0.0947-0.03980.2342-0.15560.0634-0.5998-0.1911-0.15830.0593-0.034500.8970.00230.04960.407-0.0760.4452-12.5991-28.312424.3899
150.2548-0.04890.21130.0131-0.0410.09140.6352-0.2946-0.6593-0.2118-0.2729-0.09940.33820.30380.0070.8520.00990.07620.4706-0.00750.512-15.8676-39.355830.4626
160.2015-0.0703-0.22360.16160.45421.2529-0.13070.5702-0.4229-0.2490.8388-0.0576-0.1936-0.48540.1091.89710.04140.04480.4907-0.20090.6991-19.465-46.530618.8468
170.0081-0.0683-0.02320.53070.05420.07820.1684-0.226-0.50550.82090.21581.7014-0.0179-0.65980.0446-0.9008-0.09740.44341.5690.16080.8419-47.5515-30.471859.0148
180.03060.04570.00720.0677-0.0810.1028-0.1616-0.26130.24530.05120.27020.1458-0.5722-0.65880.0495-0.01110.5762-0.27961.41250.11450.9669-44.2216-9.34542.5973
190.47980.10640.52961.07871.12620.824-0.1089-0.2510.17760.068-0.02840.5629-0.6309-0.0382-0.18550.50730.13950.07450.75580.00130.5597-35.0791-17.712449.5225
200.12270.00110.01830.02810.00130.0871-0.7944-0.27120.73640.0503-0.75980.55790.00320.2902-0.08270.1419-0.12410.3080.9380.02520.6111-23.648-16.503555.0904
210.2540.0519-0.1525-0.0072-0.04550.08370.2827-0.016-0.23390.4362-0.12250.4259-0.5341-1.04110.00010.52860.07930.11691.28170.06510.6558-42.7596-19.023756.4315
220.033-0.240.05930.1864-0.10210.119-0.61540.26920.4130.81970.34050.9657-1.1380.3966-0.3256-0.85690.5207-0.04780.7326-0.080.4696-33.319-10.108444.8809
230.04790.06910.0993-0.003-0.049-0.0341-0.56230.4040.1702-0.5934-0.0615-0.221-0.08560.1595-0.00430.74670.0474-0.21460.64640.06240.7778-32.3475-13.356631.0694
24-0.0055-0.0418-0.00280.0294-0.0223-0.01140.061-0.05030.0764-0.49560.18380.13410.0624-0.31240.00020.7913-0.016-0.17250.5521-0.07580.5742-32.7975-23.502835.9383
250.1698-0.03340.1480.039-0.0749-0.0562-0.19720.6650.1008-0.62030.0794-0.0721-0.37520.15510.00011.1874-0.03820.22060.72950.04390.7318-5.9309-6.474920.0393
260.4448-0.0495-0.34680.20540.10780.1063-0.2175-0.05610.6713-0.316-0.0385-0.2756-0.4204-0.12110.00170.65790.0374-0.03850.39190.04630.573-5.2887-2.38836.576
27-0.2523-0.206-0.49660.23980.52830.41220.02730.2350.5286-0.0790.1354-0.4293-0.2032-0.34740.0030.52370.0421-0.00550.4928-0.0210.5283-6.4289-10.679252.6533
280.1225-0.1540.0163-0.0275-0.02530.10230.7463-0.60820.62280.3198-0.0176-0.33060.14770.18710.09110.89450.15240.21680.54990.16570.50095.32-10.235128.1704
290.12580.0165-0.1850.0955-0.07290.1061-0.0416-0.06420.1933-0.5762-0.0954-0.88840.3486-0.03750.00220.4504-0.04560.14360.40520.00640.80971.6131-6.22338.1397
300.73030.1736-0.34120.4074-0.32040.26520.0883-0.05560.0831-0.3-0.0241-0.05050.1627-0.437200.84470.0849-0.16360.3834-0.00960.4467-19.9631-8.613727.9823
310.3067-0.07680.18640.0356-0.08990.1037-0.31540.83060.10110.5071-0.6335-0.5521-0.41670.3970.00431.4061-0.0111-0.07240.43510.03650.788-12.43545.311523.1892
321.47230.14760.56662.34520.10141.36850.09620.0363-0.0764-0.38550.0055-0.2259-0.0832-0.04620.11120.49970.12-0.00160.49420.13360.3914-19.4505-22.867941.217
331.32610.03770.3012.15420.17670.93390.1338-0.0309-0.109-0.2752-0.0807-0.15650.0846-0.13170.05810.48340.05530.14510.55180.12830.2276-19.1796-22.137941.1868
340.1078-0.28690.15990.11250.0223-0.0020.1303-0.25450.0266-0.3422-0.0764-0.0370.34870.53150.00631.3009-0.0926-0.08961.08750.07850.8626-27.019-44.460942.8179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 39:83)
2X-RAY DIFFRACTION2(chain A and resid 84:124)
3X-RAY DIFFRACTION3(chain A and resid 125:135)
4X-RAY DIFFRACTION4(chain B and resid 19:26)
5X-RAY DIFFRACTION5(chain B and resid 27:51)
6X-RAY DIFFRACTION6(chain B and resid 52:80)
7X-RAY DIFFRACTION7(chain B and resid 81:102)
8X-RAY DIFFRACTION8(chain C and resid 16:33)
9X-RAY DIFFRACTION9(chain C and resid 34:84)
10X-RAY DIFFRACTION10(chain C and resid 85:102)
11X-RAY DIFFRACTION11(chain C and resid 103:118)
12X-RAY DIFFRACTION12(chain D and resid 29:40)
13X-RAY DIFFRACTION13(chain D and resid 41:65)
14X-RAY DIFFRACTION14(chain D and resid 66:87)
15X-RAY DIFFRACTION15(chain D and resid 88:106)
16X-RAY DIFFRACTION16(chain D and resid 107:121)
17X-RAY DIFFRACTION17(chain E and resid 39:61)
18X-RAY DIFFRACTION18(chain E and resid 62:76)
19X-RAY DIFFRACTION19(chain E and resid 77:123)
20X-RAY DIFFRACTION20(chain E and resid 124:135)
21X-RAY DIFFRACTION21(chain F and resid 25:46)
22X-RAY DIFFRACTION22(chain F and resid 47:76)
23X-RAY DIFFRACTION23(chain F and resid 77:94)
24X-RAY DIFFRACTION24(chain F and resid 95:102)
25X-RAY DIFFRACTION25(chain G and resid 14:41)
26X-RAY DIFFRACTION26(chain G and resid 42:75)
27X-RAY DIFFRACTION27(chain G and resid 76:118)
28X-RAY DIFFRACTION28(chain H and resid 28:40)
29X-RAY DIFFRACTION29(chain H and resid 41:66)
30X-RAY DIFFRACTION30(chain H and resid 67:107)
31X-RAY DIFFRACTION31(chain H and resid 108:121)
32X-RAY DIFFRACTION32(chain I and resid -72:72)
33X-RAY DIFFRACTION33(chain J and resid -72:72)
34X-RAY DIFFRACTION34(chain M and resid 535:551)

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