[English] 日本語
Yorodumi
- PDB-4fw2: Crystal structure of RSV three-domain integrase with disordered N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fw2
TitleCrystal structure of RSV three-domain integrase with disordered N-terminal domain
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / RNA 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 / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / 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: 2.65 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrase
B: Integrase


Theoretical massNumber of molelcules
Total (without water)59,8652
Polymers59,8652
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-25 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.400, 56.168, 65.276
Angle α, β, γ (deg.)90.00, 97.86, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 29932.424 Da / Num. of mol.: 2 / Fragment: UNP residues 1281-1550 / Mutation: C23S, 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 / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% ethanol, 100 mM imidazole-HCl, and 5% PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 18558 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.65→2.7 Å / % possible all: 98.9

-
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: 2.65→35.846 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 1855 10 %Random
Rwork0.1741 ---
all0.1812 ---
obs0.1741 17623 99.32 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.851 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1246 Å20 Å23.2711 Å2
2---9.7914 Å20 Å2
3---15.916 Å2
Refinement stepCycle: LAST / Resolution: 2.65→35.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 0 99 3402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083383
X-RAY DIFFRACTIONf_angle_d1.1284588
X-RAY DIFFRACTIONf_dihedral_angle_d15.7241249
X-RAY DIFFRACTIONf_chiral_restr0.078510
X-RAY DIFFRACTIONf_plane_restr0.005571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.72050.34951360.27441223X-RAY DIFFRACTION94
2.7205-2.80050.34231400.24361256X-RAY DIFFRACTION100
2.8005-2.89080.3091410.20821270X-RAY DIFFRACTION100
2.8908-2.99410.28941420.19711292X-RAY DIFFRACTION100
2.9941-3.11390.26291440.18161289X-RAY DIFFRACTION100
3.1139-3.25560.26051410.17981264X-RAY DIFFRACTION100
3.2556-3.42710.24171440.17391302X-RAY DIFFRACTION100
3.4271-3.64160.25561420.16881281X-RAY DIFFRACTION100
3.6416-3.92240.23561430.16891292X-RAY DIFFRACTION100
3.9224-4.31660.22031440.1511292X-RAY DIFFRACTION100
4.3166-4.93980.21491430.13421280X-RAY DIFFRACTION99
4.9398-6.21830.26211460.17721316X-RAY DIFFRACTION100
6.2183-35.8460.18851490.17241336X-RAY DIFFRACTION99
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)
13.3587-1.12792.59661.77131.29267.3140.0449-0.6661-0.65060.54450.5316-0.15940.87050.9523-0.33790.53320.1286-0.03440.35070.03080.185643.9814-8.31079.4444
22.40051.691.06497.92882.06122.4040.10550.302-0.27890.36270.09390.66620.32050.0448-0.07080.12020.01320.00540.2079-0.00640.293737.5136-23.9972-0.0403
32.7776-0.2278-1.19364.94981.02164.4767-0.096-0.0468-0.0227-0.37750.3714-0.12430.0706-0.1663-0.36340.1391-0.0383-0.01660.1705-0.010.141536.4457-18.6401-5.1571
45.33312.34876.33485.12063.50558.3646-0.3470.25351.0503-0.5740.02520.2438-0.55780.43880.5580.2708-0.00440.04690.1492-0.00950.244737.7788-6.97880.0335
50.769-0.9708-0.2236.74665.97965.94510.53150.1754-0.4093-0.06990.3188-0.95270.61240.6966-0.43530.32850.01690.03040.2304-0.1180.589248.387-19.4783-3.8516
62.3927-3.43141.885.2292-4.28499.6730.71420.28920.8937-0.37350.1038-0.9485-0.71761.1617-0.50830.5845-0.21910.16150.6413-0.07980.338448.9628-14.9414-12.7087
75.18091.92825.07065.29681.16895.07630.17320.69760.4297-1.33920.62310.1209-0.64450.3232-0.59580.3208-0.00950.14250.22960.09730.332743.2206-7.8868-10.7172
84.8092-0.5464-2.89563.04892.00853.72480.2389-0.6628-0.58740.20480.0234-0.43070.56150.6533-0.04480.3255-0.00040.05310.2717-0.04130.26349.8756-12.5926-1.9605
94.01532.4819-1.16732.52590.76192.56290.5647-0.538-0.85961.3778-0.1751-0.40580.30910.2373-0.16580.36250.0427-0.01160.24850.110.391137.9943-25.52719.0016
102.93520.7717-3.97983.8282.83219.76310.3217-0.2763-0.80550.93750.18940.19881.2593-0.5129-0.35940.48450.0321-0.10580.36750.22040.549126.3359-33.35598.0705
113.43112.2084-3.02878.4071-3.9364.8137-0.0780.3589-0.54320.9746-0.39850.59420.4271-0.39620.38810.4563-0.16350.00430.50370.14861.195723.8721-38.22362.2116
121.27872.22982.70213.99954.41996.48790.2146-0.0127-0.69910.0244-0.22661.52670.3321-1.04560.01780.2842-0.0608-0.10890.36460.03450.761623.3203-28.6354-0.7037
133.8998-2.39563.97458.7219-1.11084.29350.1116-0.8870.21350.81060.78370.7027-0.1484-0.7559-0.67990.29610.01920.06750.37080.09290.398927.5313-18.198511.0152
145.21383.27841.43825.10394.6735.06470.155-1.584-0.72632.42950.2409-0.68370.75220.8225-0.40540.93990.10540.07830.7328-0.01890.379431.4385-14.152518.6052
153.0674-1.14162.07013.15920.85135.7038-0.24780.0940.07990.98220.15690.5073-0.4362-0.09940.14370.33510.04790.08250.38340.05360.150434.2022-4.957813.4542
164.7228-0.76354.33754.0345-1.38146.24-0.01960.53920.5826-0.089-0.6534-0.7692-0.14490.68920.79570.7168-0.0383-0.23610.21910.10410.367150.202-2.619126.7674
176.1649-4.72460.96055.1646-1.96952.44760.04090.1564-0.81820.44460.1581-1.39170.3521.5575-0.20590.5124-0.0106-0.34640.94110.16031.428761.1271-12.515427.7005
187.92511.7378-1.30077.5205-2.97774.0328-0.1398-0.0611-0.6070.1717-0.1365-1.10670.29960.08780.02080.46880.06560.02820.2022-0.0360.264149.3359-9.707222.785
196.2634.9617-2.28538.6278-1.38268.3048-0.1033-0.16861.17650.31770.0518-1.1069-1.73460.87480.12590.7594-0.07010.07490.2861-0.0391.081556.2337-0.716918.8755
204.78460.9852-1.57254.29030.96314.61830.0043-0.5777-0.68850.483-0.1818-1.29731.0668-0.25020.04740.57630.0064-0.07920.2520.05940.408352.2782-11.377224.5154
213.67483.14912.72882.94963.00113.7663-0.0322-0.65180.5676-0.1375-0.26091.1301-0.6517-1.02630.37210.31550.27430.13340.64290.12570.837913.0455-6.44985.3846
220.47480.62670.11040.89910.62232.91360.48350.7903-0.3804-0.58970.04290.39760.2957-0.4706-0.04570.47260.2028-0.41170.5505-0.0290.694818.0684-15.2882-16.1816
232.37050.140.41780.77370.30631.91990.0871-0.32030.25940.0670.23710.1349-0.0861-0.2658-0.26180.08790.0664-0.00480.33850.09340.651918.3553-10.449-4.8224
242.45744.3728-4.82438.6841-8.44942.0001-0.3190.2012-0.767-0.53970.01480.06110.9431-0.76180.43660.4591-0.0042-0.24070.54650.01471.240314.1924-24.4239-11.1356
254.06015.06335.03837.14755.58796.8297-0.3627-0.1866-0.52080.37480.11391.51310.3102-0.60770.25580.24310.02680.00780.39960.16350.75318.6295-17.50340.8226
266.4107-1.40065.38331.8471-0.2447.18890.12950.0797-0.3895-0.0361-0.21630.9177-0.0418-1.24690.04010.29470.08440.13410.78580.12081.19757.5689-13.03280.3948
270.0232-0.1185-0.09680.60460.49030.47430.0074-0.48830.0585-0.0858-0.05530.66340.1307-1.1516-0.0210.3762-0.1241-0.20411.16010.07661.55075.7294-23.5809-3.6954
283.12510.3319-1.33171.65940.08961.651-0.2061-0.5231-0.67450.05520.10520.3680.1522-0.6807-0.16630.08180.0521-0.01640.62230.24570.854410.3415-13.2344-1.8779
294.8842.8965-2.46438.8083-0.09175.434-0.12191.09820.663-1.4789-0.05410.6349-0.7655-0.54280.00530.56410.2289-0.0580.4450.27760.417524.2685-4.8703-16.9698
301.2336-0.957-0.99725.07610.57321.63770.31280.05350.1113-1.13020.48080.24190.0325-0.7151-0.6811.24420.41140.28871.00450.32680.63830.4264-7.6947-24.4445
313.2315-2.4834-4.65776.31051.32387.88240.09160.4167-0.1356-0.4964-0.3087-0.1756-0.2371-0.03590.00390.51470.0982-0.02070.3049-0.04990.721929.9577-16.4917-19.4974
323.90980.32793.17272.85453.28725.92380.01550.5390.29-0.0028-0.04790.09740.07320.2571-0.05980.30820.04360.06040.27350.06590.172629.028-7.1145-7.9728
334.2974-4.8018-0.33515.3730.41070.2039-0.09290.16650.91170.56980.1224-0.09650.2121-0.0298-0.01181.0361-0.1301-0.16670.37050.25140.940925.50175.9099-4.8793
345.81653.052-1.90641.7534-0.22584.56910.4832-0.2740.6553-0.02950.12960.2462-1.2614-0.3602-0.53160.34010.08510.11510.3812-0.06640.540623.58451.36562.7628
355.11755.03273.33917.3345.39735.428-0.1495-0.750.41370.4340.20470.9837-0.9026-0.3784-0.0770.38190.13620.14740.29230.05420.429930.1487-0.506712.0003
367.3391-0.0545-0.72953.9892-1.49427.1716-0.2951-0.28210.03880.2124-0.34760.420.6391-1.10870.52070.86170.01560.15010.4-0.0610.463133.268-2.014833.5197
373.63052.06393.50154.2836-1.24619.2024-0.0629-1.02840.2450.5810.0399-0.4042-0.3311-0.7843-0.09680.89980.03580.25370.5271-0.06920.587432.6540.152942.2339
383.3681.0504-1.39773.50650.82793.1805-0.4579-0.3773-0.580.162-0.215-0.19290.54850.0870.41410.70950.00350.18250.2640.03990.264840.4213-6.054430.4942
395.0289-5.28413.068.5657-0.32896.50650.32040.21931.6055-0.2851-0.2618-0.35-1.19320.03-0.19811.050.06110.18030.36040.01690.713238.06396.795230.1875
403.6711.9347-2.85113.7786-0.13014.6979-0.1161-0.5189-0.66340.4408-0.66510.190.3302-0.10890.52560.84270.01770.15640.2640.02320.319937.5453-5.661335.519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 52:59)
2X-RAY DIFFRACTION2(chain A and resid 60:84)
3X-RAY DIFFRACTION3(chain A and resid 85:109)
4X-RAY DIFFRACTION4(chain A and resid 110:117)
5X-RAY DIFFRACTION5(chain A and resid 118:126)
6X-RAY DIFFRACTION6(chain A and resid 127:132)
7X-RAY DIFFRACTION7(chain A and resid 133:139)
8X-RAY DIFFRACTION8(chain A and resid 140:145)
9X-RAY DIFFRACTION9(chain A and resid 154:166)
10X-RAY DIFFRACTION10(chain A and resid 167:173)
11X-RAY DIFFRACTION11(chain A and resid 174:179)
12X-RAY DIFFRACTION12(chain A and resid 180:192)
13X-RAY DIFFRACTION13(chain A and resid 193:201)
14X-RAY DIFFRACTION14(chain A and resid 202:208)
15X-RAY DIFFRACTION15(chain A and resid 209:219)
16X-RAY DIFFRACTION16(chain A and resid 220:225)
17X-RAY DIFFRACTION17(chain A and resid 226:234)
18X-RAY DIFFRACTION18(chain A and resid 235:248)
19X-RAY DIFFRACTION19(chain A and resid 249:256)
20X-RAY DIFFRACTION20(chain A and resid 257:269)
21X-RAY DIFFRACTION21(chain B and resid 54:62)
22X-RAY DIFFRACTION22(chain B and resid 63:76)
23X-RAY DIFFRACTION23(chain B and resid 77:93)
24X-RAY DIFFRACTION24(chain B and resid 94:100)
25X-RAY DIFFRACTION25(chain B and resid 101:114)
26X-RAY DIFFRACTION26(chain B and resid 115:122)
27X-RAY DIFFRACTION27(chain B and resid 123:132)
28X-RAY DIFFRACTION28(chain B and resid 133:162)
29X-RAY DIFFRACTION29(chain B and resid 163:171)
30X-RAY DIFFRACTION30(chain B and resid 172:178)
31X-RAY DIFFRACTION31(chain B and resid 179:186)
32X-RAY DIFFRACTION32(chain B and resid 187:198)
33X-RAY DIFFRACTION33(chain B and resid 199:203)
34X-RAY DIFFRACTION34(chain B and resid 204:212)
35X-RAY DIFFRACTION35(chain B and resid 213:219)
36X-RAY DIFFRACTION36(chain B and resid 220:228)
37X-RAY DIFFRACTION37(chain B and resid 229:236)
38X-RAY DIFFRACTION38(chain B and resid 237:249)
39X-RAY DIFFRACTION39(chain B and resid 250:256)
40X-RAY DIFFRACTION40(chain B and resid 257:268)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more