[English] 日本語
Yorodumi
- PDB-5hrs: HIV Integrase Catalytic Domain containing F185K + A124N + T125A m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hrs
TitleHIV Integrase Catalytic Domain containing F185K + A124N + T125A mutations complexed with GSK0002
ComponentsIntegrase
KeywordsTRANSFERASE/INHIBITOR / Viral DNA integration / DNA Binding / LEDGF Binding / VIRAL PROTEIN / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase 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 / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
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
Chem-65P / CACODYLATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 Å
AuthorsNolte, R.T.
CitationJournal: PLoS Biol. / Year: 2016
Title: Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase.
Authors: Gupta, K. / Turkki, V. / Sherrill-Mix, S. / Hwang, Y. / Eilers, G. / Taylor, L. / McDanal, C. / Wang, P. / Temelkoff, D. / Nolte, R.T. / Velthuisen, E. / Jeffrey, J. / Van Duyne, G.D. / Bushman, F.D.
History
DepositionJan 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0157
Polymers17,9531
Non-polymers1,0636
Water1,71195
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,03114
Polymers35,9052
Non-polymers2,12612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area5990 Å2
ΔGint-54 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.517, 72.517, 65.693
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Integrase /


Mass: 17952.506 Da / Num. of mol.: 1 / Mutation: F185K, T125A, A124N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: P04585

-
Non-polymers , 5 types, 101 molecules

#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-65P / (2S)-tert-butoxy[1-(3,4-difluorobenzyl)-6-methyl-4-(5-methyl-3,4-dihydro-2H-chromen-6-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]acetic acid


Mass: 534.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H32F2N2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystals grown in 0.1M Ammonium sulfate , 0.1M Cacodylate pH 6.5, 7.5% PEG8K, 5mM MgCl2, 5mM MnCl2, and 5mM DTT Ligand dissolved at 375mM in DMSO and added to cryo buffer @5% overnight Cryo ...Details: Crystals grown in 0.1M Ammonium sulfate , 0.1M Cacodylate pH 6.5, 7.5% PEG8K, 5mM MgCl2, 5mM MnCl2, and 5mM DTT Ligand dissolved at 375mM in DMSO and added to cryo buffer @5% overnight Cryo buffer contains well buffer plus 30% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.0781 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 18851 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 37.03 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.004 / Net I/av σ(I): 30.794 / Net I/σ(I): 16.2 / Num. measured all: 137683
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.867.30.6118500.966100
1.86-1.947.30.40318721.026100
1.94-2.037.30.25918571.016100
2.03-2.137.40.16418581.015100
2.13-2.277.40.12618830.999100
2.27-2.447.40.0918750.997100
2.44-2.697.40.06218621.01100
2.69-3.087.40.06218951.009100
3.08-3.887.30.04719200.996100
3.88-506.90.03919791.00498.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
BUSTER-TNT2.11.2refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHENIXphasing
Cootmodel building
RefinementResolution: 1.86→17.86 Å / Cor.coef. Fo:Fc: 0.9499 / Cor.coef. Fo:Fc free: 0.9526 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 541 3.16 %RANDOM
Rwork0.1994 ---
obs0.1999 17100 99.88 %-
Displacement parametersBiso max: 131.11 Å2 / Biso mean: 42.02 Å2 / Biso min: 9.87 Å2
Baniso -1Baniso -2Baniso -3
1--3.1258 Å20 Å20 Å2
2---3.1258 Å20 Å2
3---6.2517 Å2
Refine analyzeLuzzati coordinate error obs: 0.227 Å
Refinement stepCycle: final / Resolution: 1.86→17.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 59 95 1206
Biso mean--53.7 54.2 -
Num. residues----139
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d522SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes168HARMONIC5
X-RAY DIFFRACTIONt_it1160HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion154SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1430SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1160HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1581HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion2.99
LS refinement shellResolution: 1.86→1.97 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2584 91 3.35 %
Rwork0.2331 2624 -
all0.2339 2715 -
obs--99.88 %

+
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