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- PDB-6jcf: Cryogenic structure of HIV-1 Integrase catalytic core domain by s... -

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Basic information

Entry
Database: PDB / ID: 6jcf
TitleCryogenic structure of HIV-1 Integrase catalytic core domain by synchrotron
ComponentsIntegrase
KeywordsVIRAL PROTEIN / HIV / HIV-1 / Integrase / cryogenic
Function / homology
Function and homology information


nucleotidyltransferase activity / HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...nucleotidyltransferase activity / HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / nucleic acid binding / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å
AuthorsPark, J.H. / Han, J. / Kim, T.H. / Yun, J.H. / Lee, W.
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 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water52229
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 area3890 Å2
ΔGint-3 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.080, 72.080, 65.192
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 / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2mM Ammonium sulfate, 0.1M sodiumcacodylate trihydrate, 30% peg 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2018
RadiationMonochromator: 0.987 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.15→36.05 Å / Num. obs: 10934 / % possible obs: 99.98 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0289 / Net I/σ(I): 33.7
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1270 / CC1/2: 0.861 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ITG

1itg


Resolution: 2.153→36.04 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 548 5.01 %
Rwork0.1997 --
obs0.2022 10934 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.153→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 8 29 1143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041133
X-RAY DIFFRACTIONf_angle_d0.591527
X-RAY DIFFRACTIONf_dihedral_angle_d12.169665
X-RAY DIFFRACTIONf_chiral_restr0.045175
X-RAY DIFFRACTIONf_plane_restr0.003189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1534-2.25140.3012660.21761270X-RAY DIFFRACTION100
2.2514-2.370.2514670.19811277X-RAY DIFFRACTION100
2.37-2.51850.2826700.2111274X-RAY DIFFRACTION100
2.5185-2.71290.1996690.18621290X-RAY DIFFRACTION100
2.7129-2.98580.2489690.22051276X-RAY DIFFRACTION100
2.9858-3.41750.2719700.20791304X-RAY DIFFRACTION100
3.4175-4.30460.2258710.18691312X-RAY DIFFRACTION100
4.3046-36.0450.2599660.19881383X-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)
13.191.1886-0.34840.47110.02422.36590.0096-0.3971-0.3143-0.0497-0.1438-0.102-0.11670.41380.00070.23140.0069-0.02430.2680.00880.286927.0323-26.9694-16.6558
23.85830.2879-1.59560.3086-0.25720.73160.2932-1.8170.59840.3256-0.20170.0168-0.22660.63450.03130.5517-0.1050.0280.8755-0.07930.380120.5964-27.041-6.6278
33.22391.40620.55170.67620.54532.6312-0.1546-0.61810.39090.2164-0.05350.2873-0.3141-0.5773-0.00490.26420.0657-0.05560.433-0.08260.335311.2938-25.5052-13.2507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 168 )
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 209 )

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