[English] 日本語
Yorodumi
- PDB-6vlh: HIV Integrase Core domain (IN) in complex with dimer-spanning ligand -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vlh
TitleHIV Integrase Core domain (IN) in complex with dimer-spanning ligand
ComponentsIntegrase
KeywordsTRANSFERASE / Virus / Inhibitor / Complex / HIV Integrase
Function / homology
Function and homology information


DNA integration / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding
Similarity search - Function
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 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. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
IODIDE ION / Chem-R2A / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.036 Å
AuthorsGorman, M.A. / Parker, M.W.
CitationJournal: To Be Published
Title: HIV Integrase core domain (IN) in complex with dimeric spanning inhibitor
Authors: Scanlon, M. / Gorman, M.A.
History
DepositionJan 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,13218
Polymers35,7452
Non-polymers2,38816
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-128 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.306, 46.306, 139.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Integrase


Mass: 17872.305 Da / Num. of mol.: 2 / Fragment: core domain (UNP residues 50-211) / Mutation: Q53E,C56S,G124S,A125T,W131E,V151I,F185K,Q209E
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: F2WR39, RNA-directed DNA polymerase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: I
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-R2A / (2-{[3-(4-{2-[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzene-1-carbonyl)amino]ethyl}piperazine-1-carbonyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid


Mass: 761.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H39N3O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.8 M ammonium sulfate, 100 mM potassium iodide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.036→46.38 Å / Num. obs: 18621 / % possible obs: 99.3 % / Redundancy: 8 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.021 / Rrim(I) all: 0.059 / Χ2: 1.06 / Net I/σ(I): 23.8
Reflection shellResolution: 2.036→2.09 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1287 / Rpim(I) all: 0.172 / Rrim(I) all: 0.472 / Χ2: 1.2 / % possible all: 93

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998-000)refinement
XDSdata reduction
PHENIXdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.036→46.306 Å / Cross valid method: THROUGHOUT / σ(F): 8.54 / Phase error: 37.22
RfactorNum. reflection% reflection
Rfree0.2981 3644 9.96 %
Rwork0.2095 --
obs0.2226 18621 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.036→46.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 108 54 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132239
X-RAY DIFFRACTIONf_angle_d1.5333030
X-RAY DIFFRACTIONf_dihedral_angle_d18.9111278
X-RAY DIFFRACTIONf_chiral_restr0.055334
X-RAY DIFFRACTIONf_plane_restr0.008367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0387-2.07380.30731670.31281561X-RAY DIFFRACTION86
2.0738-2.11150.38381800.31411735X-RAY DIFFRACTION91
2.1115-2.15210.40091760.30871604X-RAY DIFFRACTION90
2.1521-2.19610.36511960.32321709X-RAY DIFFRACTION90
2.1961-2.24380.6431720.4581519X-RAY DIFFRACTION87
2.2438-2.2960.61721710.47991628X-RAY DIFFRACTION86
2.296-2.35340.47431860.29851654X-RAY DIFFRACTION90
2.3534-2.4170.32971940.28621666X-RAY DIFFRACTION90
2.417-2.48810.30821700.27231639X-RAY DIFFRACTION91
2.4881-2.56840.35531860.26961693X-RAY DIFFRACTION90
2.5684-2.66020.3251860.271639X-RAY DIFFRACTION90
2.6602-2.76670.29521790.26011655X-RAY DIFFRACTION90
2.7667-2.89260.3081860.22571702X-RAY DIFFRACTION90
2.8926-3.0450.22511820.20211639X-RAY DIFFRACTION90
3.045-3.23570.35851880.19871649X-RAY DIFFRACTION90
3.2357-3.48540.21721810.1831661X-RAY DIFFRACTION90
3.4854-3.83590.27641910.1471662X-RAY DIFFRACTION89
3.8359-4.39020.19821770.12981635X-RAY DIFFRACTION90
4.3902-5.52860.22871910.12881648X-RAY DIFFRACTION90
5.5286-38.55540.2821710.19771624X-RAY DIFFRACTION88

+
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