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- PDB-6jcg: Room temperature structure of HIV-1 Integrase catalytic core doma... -

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Basic information

Entry
Database: PDB / ID: 6jcg
TitleRoom temperature structure of HIV-1 Integrase catalytic core domain by serial femtosecond crystallography.
ComponentsIntegrase
KeywordsVIRAL PROTEIN / HIV / HIV-1 / Integrase / Room temperature
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / 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 / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / 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 ...Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / 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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Integrase / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPark, J.H. / Shi, Y. / Han, J. / Li, X. / Kim, T.H. / Yun, J.H.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers.
Authors: Park, J.H. / Yun, J.H. / Shi, Y. / Han, J. / Li, X. / Jin, Z. / Kim, T. / Park, J. / Park, S. / Liu, H. / Lee, W.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1123
Polymers17,8381
Non-polymers2742
Water21612
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2256
Polymers35,6772
Non-polymers5484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area4000 Å2
ΔGint-7 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.275, 73.275, 66.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Integrase


Mass: 17838.338 Da / Num. of mol.: 1 / Fragment: HIV-1 Integrase catalytic core domain / Mutation: F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: F2WR52, UniProt: P12497*PLUS
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.9 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 0.2mM Ammonium sulfate, 0.1M sodiumcacodylate trihydrate, 30% PEG 8000

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 0.987 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→24.67 Å / Num. obs: 13866 / % possible obs: 99.85 % / Redundancy: 406.99 % / CC1/2: 0.9935 / R split: 0.09 / Net I/σ(I): 7.26
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 275.68 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 872 / CC1/2: 0.5506 / R split: 0.7737 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Cootmodel building
PHASERphasing
CrystFELdata scaling
Cheetahdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ITG

1itg


Resolution: 2.5→24.665 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.2117 771 10.35 %
Rwork0.1766 --
obs0.1802 7450 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 8 12 1118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031125
X-RAY DIFFRACTIONf_angle_d0.4461521
X-RAY DIFFRACTIONf_dihedral_angle_d11.981661
X-RAY DIFFRACTIONf_chiral_restr0.041176
X-RAY DIFFRACTIONf_plane_restr0.003188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61370.3111870.2629832X-RAY DIFFRACTION100
2.6137-2.75130.27311160.2327787X-RAY DIFFRACTION100
2.7513-2.92340.2842990.2236832X-RAY DIFFRACTION100
2.9234-3.14870.23851050.1954793X-RAY DIFFRACTION100
3.1487-3.46480.2311030.1845824X-RAY DIFFRACTION100
3.4648-3.96440.21790.1561857X-RAY DIFFRACTION100
3.9644-4.9880.199870.1443849X-RAY DIFFRACTION100
4.988-24.66570.1714950.1787905X-RAY DIFFRACTION100
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)
14.71241.6631-0.70351.2809-0.14222.9495-0.0145-0.3944-0.08250.1779-0.1999-0.40040.04490.0602-0.00030.39910.0309-0.02830.43330.03020.437424.5235-29.0223-15.1908
21.73520.3058-0.03211.2454-0.81960.7162-0.0724-0.39480.50080.22040.0353-0.1453-0.29780.32690.00020.4645-0.0358-0.03040.505-0.05670.455332.0308-21.6941-18.0385
35.00921.08570.52991.38610.47483.4110.062-0.9288-0.05540.44450.03160.3725-0.0915-0.4710.00170.37020.03280.02440.5454-0.05240.378213.177-29.621-10.3461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 55 through 107 )
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 208 )

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