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- PDB-4fw1: Crystal structure of two-domain RSV INTEGRASE covalently linked w... -

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Basic information

Entry
Database: PDB / ID: 4fw1
TitleCrystal structure of two-domain RSV INTEGRASE covalently linked with DNA
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Integrase, C-terminal domain superfamily, retroviral / Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal ...Integrase, C-terminal domain superfamily, retroviral / Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / SH3 type barrels. / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsShi, K. / Aihara, H.
CitationJournal: Plos One / Year: 2013
Title: A possible role for the asymmetric C-terminal domain dimer of Rous sarcoma virus integrase in viral DNA binding.
Authors: Shi, K. / Pandey, K.K. / Bera, S. / Vora, A.C. / Grandgenett, D.P. / Aihara, H.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase


Theoretical massNumber of molelcules
Total (without water)49,5012
Polymers49,5012
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-29 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.800, 67.480, 126.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Integrase / RSV integrase / IN / pp32


Mass: 24750.496 Da / Num. of mol.: 2 / Fragment: UNP residues 1329-1580 / Mutation: S124D, C125A, E157C, R166K, F199K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Strain: Prague C / Gene: gag-pro-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03354
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% Ethanol, 10% PEG4,000, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.86→46 Å / Num. obs: 39849 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→35.77 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 1994 5 %
Rwork0.175 --
obs0.175 39848 99.2 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.12 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6325 Å2-0 Å20 Å2
2---5.9779 Å20 Å2
3---5.3455 Å2
Refinement stepCycle: LAST / Resolution: 1.86→35.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 0 240 3601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073473
X-RAY DIFFRACTIONf_angle_d1.0414722
X-RAY DIFFRACTIONf_dihedral_angle_d13.3791283
X-RAY DIFFRACTIONf_chiral_restr0.074524
X-RAY DIFFRACTIONf_plane_restr0.005594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90760.37461140.31352564X-RAY DIFFRACTION95
1.9076-1.95910.29071390.25592671X-RAY DIFFRACTION99
1.9591-2.01680.28211560.21462669X-RAY DIFFRACTION100
2.0168-2.08190.25551390.19642654X-RAY DIFFRACTION100
2.0819-2.15630.2321290.17392695X-RAY DIFFRACTION100
2.1563-2.24260.24241630.16562685X-RAY DIFFRACTION100
2.2426-2.34470.23191280.16952720X-RAY DIFFRACTION100
2.3447-2.46820.21921370.17512701X-RAY DIFFRACTION100
2.4682-2.62280.22121380.16622707X-RAY DIFFRACTION100
2.6228-2.82530.21641470.1682708X-RAY DIFFRACTION100
2.8253-3.10940.24321380.17142730X-RAY DIFFRACTION100
3.1094-3.5590.23851430.17312754X-RAY DIFFRACTION100
3.559-4.48260.17961500.14562759X-RAY DIFFRACTION99
4.4826-35.7710.20391730.17912837X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.0294-1.11591.78734.4662-4.41184.41580.1561-0.4939-0.1410.8893-0.2613-0.4306-0.3409-0.1394-0.04470.3445-0.0796-0.01650.22950.02550.2608-5.31326.65990.6537
24.19942.2069-0.13642.7702-0.65261.68260.1209-0.1501-0.23020.1655-0.1395-0.2696-0.04270.15150.01630.14920.0088-0.0150.17110.00810.17888.42115.114-6.8124
33.05250.4826-0.63392.37890.57432.22870.1522-0.03120.23760.11030.0428-0.0725-0.2531-0.0155-0.23290.1927-0.0150.01820.1611-0.00180.15336.227723.2565-7.826
40.37180.9963-0.24.8965-2.73742.26190.1786-0.16590.15990.1074-0.21640.5171-0.0941-0.4070.00680.1311-0.02690.03780.1967-0.02490.1346-5.652517.1028-7.3652
52.89692.44881.64188.47095.45185.17790.1859-1.0919-0.14321.32330.1151-0.9949-0.39640.3925-0.02840.3166-0.094-0.00880.30680.0180.20854.459417.95514.6688
64.8635-3.1452-0.22026.7193-1.10963.15150.1774-0.85840.8571.2844-0.1208-0.2807-0.31670.0419-0.04020.3721-0.09330.04650.3146-0.0640.25996.273226.02513.5097
73.53153.26850.58414.44793.72797.35410.4929-0.36731.22250.3235-0.36730.7097-0.7508-0.1739-0.16460.2701-0.03710.09570.2502-0.080.3716-3.790228.02810.3758
82.2465-0.65652.11577.3138-1.67282.17220.3981-0.1576-0.14550.7177-0.4158-0.15240.41680.1166-0.15350.3132-0.05120.07920.2893-0.0150.2419-0.760719.02815.6617
95.0751-2.0695-5.10743.87392.26835.1572-0.0692-0.2245-0.65170.33390.1712-0.27610.65550.0785-0.16360.26-0.012-0.04480.23860.04060.334910.18777.3859-4.2296
102.88461.78110.41781.18180.98176.74440.2318-0.2098-1.02960.1030.2585-1.24680.76311.2035-0.03340.11350.1004-0.03520.1882-0.01240.486816.19597.7005-13.1504
114.3454.60340.40966.4977-2.9558.8742-0.00480.6578-0.698-1.15880.1612-1.3142-0.54821.2426-0.23070.39650.03440.20610.4743-0.12380.420219.0967.9236-21.5465
124.37122.7417-1.25073.9283-1.2412.0255-0.23230.4323-0.1433-0.46590.3674-0.4355-0.04170.2834-0.08920.1834-0.03650.06090.2911-0.05550.19512.916913.2574-19.687
132.85563.7788-0.50915.0216-1.04827.87990.5448-0.2421-1.4070.2858-0.1408-0.69291.92980.9998-0.32240.78620.0106-0.09130.6081-0.3351.34563.57-2.9274-12.2344
146.663-2.4584-2.28191.34280.27942.4728-0.68240.9404-2.0978-1.0893-0.05870.77221.0384-0.50020.62260.3254-0.09880.02420.2416-0.10670.4518-3.00711.476-13.1965
153.66682.634-2.84185.867-5.14268.0225-0.44950.6007-0.0637-0.4720.38320.02350.5385-0.48870.03010.152-0.04450.03720.19130.00780.2194-9.95531.9447-7.0196
165.21232.1314.80674.65721.01764.6742-0.1661-0.51580.15250.80320.18510.07770.0894-0.39330.06290.28650.04520.02650.2511-0.02090.2392-10.144-8.481810.9149
172.07672.10522.40834.1873.06327.35150.3009-0.53390.18810.40470.3162-0.2508-0.00260.1662-0.42231.02710.1342-0.47131.1240.03270.88750.2343-6.832323.1049
184.3374-1.9985-0.72834.7970.76175.8554-0.1113-0.5392-0.06720.53490.0997-0.57840.40840.73860.11960.25010.0405-0.04220.3132-0.00080.2497-4.3987-5.853910.1533
197.6841.1066-3.11636.9009-0.94656.4690.1309-0.28950.52530.67890.21680.2547-0.1454-0.2601-0.39530.2603-0.00590.01590.3272-0.02010.2254-9.2390.027212.8699
203.59833.79472.02024.39762.66682.41310.5837-0.1136-0.60021.5942-0.0043-1.12890.37060.5974-0.43740.35830.0355-0.09990.33590.05710.5312-2.6065-11.16112.5889
214.61223.0303-4.82296.9733-3.1965.0476-0.34370.9411-0.3848-0.68670.73531.00280.6931-0.9198-0.18320.3248-0.1032-0.06950.27360.0160.3045-9.18658.0023-29.5773
220.7740.55740.27343.3273.99735.13160.08980.18180.0681-0.67430.2559-0.0508-0.60820.1162-0.33760.3332-0.03190.04080.20680.00570.2325-1.443429.8235-26.9942
232.27920.5106-0.35182.9767-0.25722.72350.1082-0.03580.0645-0.31230.1543-0.0019-0.2454-0.0942-0.23660.2049-0.01450.02190.1969-0.02710.1715-4.084821.4905-25.9316
246.1579-2.56020.66363.8616-2.96232.77270.48410.07620.4849-0.1872-0.4371-0.7335-0.94140.2352-0.22430.3622-0.05890.10890.2311-0.07540.23368.141122.6432-30.2486
252.0520.7452-0.22263.4743-0.55954.8003-0.0639-0.109-0.1074-0.26780.1715-0.1185-0.0545-0.2059-0.11350.1708-0.0220.00930.2049-0.02470.1525-0.822512.1983-27.763
262.1566-1.07371.62682.45191.59586.30210.06680.73650.4094-1.11880.2086-0.1903-0.54090.1052-0.33040.5258-0.0680.0550.38310.0420.22073.012421.2258-39.8915
275.51382.7684-0.86362.9288-2.58563.3402-0.17820.3622-0.2803-0.13370.3733-0.88020.0510.1934-0.19320.3788-0.0250.06830.2231-0.06530.22298.989411.1985-34.7756
286.0685-0.7459-1.87423.49540.35071.7333-0.11440.25331.1575-1.15620.0170.6289-0.2745-1.10820.07730.59230.078-0.20550.4192-0.07230.4899-5.902717.257-39.7619
294.2013-0.3753-0.73874.39023.94674.0941-0.16070.23270.2302-0.8888-0.23141.2993-0.5597-0.77160.36760.34910.0434-0.10250.26710.06640.3578-11.55127.7172-25.1736
301.7208-1.8119-2.68963.93242.87924.20730.0198-0.3990.3197-0.02410.01680.2159-0.17870.0969-0.13210.20520.18940.34040.2739-0.29930.5345-7.937737.6785-13.0766
312.1009-2.56570.62893.1634-1.11236.90910.09570.05881.5325-0.1954-0.0706-0.39-0.9113-0.1671-0.00950.4159-0.01910.07090.1699-0.00820.5089-1.308139.2851-17.3433
329.86046.91921.15829.531.04092.97930.1216-0.32080.51190.3786-0.1560.2943-0.1342-0.24010.11440.16870.03240.01730.17680.01060.2064-6.143624.9267-14.6839
334.47843.3098-2.88154.34710.18074.65690.0987-0.406-0.67730.0925-0.27531.43090.0683-1.76160.27470.23820.0064-0.01060.75010.14420.7712-21.512617.5381-19.8723
343.5882-3.3101-1.33263.74110.65572.3212-0.30180.10550.01220.3664-0.09421.28610.2862-0.88780.37470.2031-0.060.00850.36490.01510.3615-16.069211.9542-18.2942
353.30152.0431-1.74253.45650.44421.9737-0.15250.50720.0926-0.32470.65520.72280.4742-0.6232-0.40310.1314-0.0614-0.00470.2610.0130.2229-13.03973.6859-13.6495
361.69451.2470.44982.1212-1.68093.6039-0.143-0.04030.1911-0.4841-0.21310.17010.7794-0.55570.20410.4987-0.09650.12940.27-0.11150.3769-11.3658-17.6923-5.9142
370.4236-0.67380.52663.0506-2.33251.78490.1889-0.1074-0.67740.23960.00630.40570.5648-0.2343-0.0271.3534-0.44580.44580.2656-0.1110.8863-12.7349-29.8207-2.6442
386.50950.61750.36746.17110.75382.5005-0.33590.0871-0.0614-0.46630.0432-0.05790.6685-0.41940.38310.2718-0.07190.08060.2639-0.09510.294-10.2541-15.6676-1.4412
392.03091.64941.20943.49410.95255.8014-0.39510.178-0.7867-0.0560.00170.49010.2995-1.03080.34840.219-0.02770.07640.4-0.07350.4473-15.1273-15.74091.5823
405.0233-0.94683.49812.909-1.25486.50460.13340.4378-0.1550.1482-0.11580.1232-0.03320.4313-0.02730.4129-0.0340.12860.3029-0.07320.3657-6.5777-21.3488-4.236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 52:58)
2X-RAY DIFFRACTION2(chain A and resid 59:87)
3X-RAY DIFFRACTION3(chain A and resid 88:105)
4X-RAY DIFFRACTION4(chain A and resid 106:117)
5X-RAY DIFFRACTION5(chain A and resid 118:122)
6X-RAY DIFFRACTION6(chain A and resid 123:128)
7X-RAY DIFFRACTION7(chain A and resid 129:139)
8X-RAY DIFFRACTION8(chain A and resid 140:145)
9X-RAY DIFFRACTION9(chain A and resid 154:163)
10X-RAY DIFFRACTION10(chain A and resid 164:168)
11X-RAY DIFFRACTION11(chain A and resid 169:175)
12X-RAY DIFFRACTION12(chain A and resid 176:198)
13X-RAY DIFFRACTION13(chain A and resid 199:205)
14X-RAY DIFFRACTION14(chain A and resid 206:210)
15X-RAY DIFFRACTION15(chain A and resid 211:219)
16X-RAY DIFFRACTION16(chain A and resid 220:226)
17X-RAY DIFFRACTION17(chain A and resid 227:232)
18X-RAY DIFFRACTION18(chain A and resid 233:249)
19X-RAY DIFFRACTION19(chain A and resid 250:261)
20X-RAY DIFFRACTION20(chain A and resid 262:269)
21X-RAY DIFFRACTION21(chain B and resid 54:61)
22X-RAY DIFFRACTION22(chain B and resid 62:74)
23X-RAY DIFFRACTION23(chain B and resid 75:94)
24X-RAY DIFFRACTION24(chain B and resid 95:103)
25X-RAY DIFFRACTION25(chain B and resid 104:120)
26X-RAY DIFFRACTION26(chain B and resid 121:127)
27X-RAY DIFFRACTION27(chain B and resid 128:139)
28X-RAY DIFFRACTION28(chain B and resid 140:154)
29X-RAY DIFFRACTION29(chain B and resid 155:170)
30X-RAY DIFFRACTION30(chain B and resid 171:176)
31X-RAY DIFFRACTION31(chain B and resid 177:182)
32X-RAY DIFFRACTION32(chain B and resid 183:199)
33X-RAY DIFFRACTION33(chain B and resid 200:205)
34X-RAY DIFFRACTION34(chain B and resid 206:211)
35X-RAY DIFFRACTION35(chain B and resid 212:219)
36X-RAY DIFFRACTION36(chain B and resid 220:227)
37X-RAY DIFFRACTION37(chain B and resid 228:233)
38X-RAY DIFFRACTION38(chain B and resid 234:244)
39X-RAY DIFFRACTION39(chain B and resid 245:259)
40X-RAY DIFFRACTION40(chain B and resid 260:269)

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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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