[English] 日本語
Yorodumi
- PDB-6qbv: Structure of the HTLV-2 integrase catalytic core domain in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qbv
TitleStructure of the HTLV-2 integrase catalytic core domain in complex with magnesium (dimeric form)
ComponentsIntegrase
KeywordsTRANSFERASE / retrovirus / deltaretrovirus / integration / strand-transfer / nucleotidyltransferase
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 / 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 / structural molecule activity / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Delta-retroviral matrix protein / Major core protein p19 / gag protein p24 N-terminal domain / Integrase Zinc binding domain / 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. / RNase H ...Delta-retroviral matrix protein / Major core protein p19 / gag protein p24 N-terminal domain / Integrase Zinc binding domain / 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. / 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 / 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. / 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
Similarity search - Domain/homology
Gag-Pro-Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesHuman T-cell leukemia virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsBarski, M.S. / Maertens, G.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust107005 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56γ.
Authors: Michał S Barski / Jordan J Minnell / Zuzana Hodakova / Valerie E Pye / Andrea Nans / Peter Cherepanov / Goedele N Maertens /
Abstract: Human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus and the most oncogenic pathogen. Many of the ~20 million HTLV-1 infected people will develop severe leukaemia or an ALS-like motor ...Human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus and the most oncogenic pathogen. Many of the ~20 million HTLV-1 infected people will develop severe leukaemia or an ALS-like motor disease, unless a therapy becomes available. A key step in the establishment of infection is the integration of viral genetic material into the host genome, catalysed by the retroviral integrase (IN) enzyme. Here, we use X-ray crystallography and single-particle cryo-electron microscopy to determine the structure of the functional deltaretroviral IN assembled on viral DNA ends and bound to the B56γ subunit of its human host factor, protein phosphatase 2 A. The structure reveals a tetrameric IN assembly bound to two molecules of the phosphatase via a conserved short linear motif. Insight into the deltaretroviral intasome and its interaction with the host will be crucial for understanding the pattern of integration events in infected individuals and therefore bears important clinical implications.
History
DepositionDec 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrase
B: Integrase
C: Integrase
D: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8718
Polymers74,7744
Non-polymers974
Water1,802100
1
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4364
Polymers37,3872
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrase
D: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4364
Polymers37,3872
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.315, 89.175, 65.530
Angle α, β, γ (deg.)90.000, 102.485, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Integrase /


Mass: 18693.475 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus 2 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q82441, UniProt: P03363*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 69.48 % / Description: Cubic crystals, about 0.1 mm in size
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 14% PEG 8000, 250 mM magnesium chloride

-
Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.45→58.611 Å / Num. obs: 38400 / % possible obs: 100 % / Redundancy: 3.9 % / CC1/2: 0.923 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.146 / Rrim(I) all: 0.342 / Net I/σ(I): 3
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.383 / Num. unique obs: 4309 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
Cootmodel building
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QBV

Resolution: 2.45→58.611 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.673 / SU ML: 0.258 / Cross valid method: FREE R-VALUE / ESU R: 0.301 / ESU R Free: 0.245
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 1876 4.885 %0.05
Rwork0.2326 ---
all0.235 ---
obs-38400 99.914 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.472 Å2
Baniso -1Baniso -2Baniso -3
1-5.006 Å20 Å22.061 Å2
2---4.528 Å20 Å2
3----1.267 Å2
Refinement stepCycle: LAST / Resolution: 2.45→58.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 4 100 4744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124755
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.6266444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0745571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8323.773220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35915811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4951512
X-RAY DIFFRACTIONr_chiral_restr0.1270.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023534
X-RAY DIFFRACTIONr_nbd_refined0.2240.21920
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2153
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2240.22
X-RAY DIFFRACTIONr_mcbond_it6.8126.7552320
X-RAY DIFFRACTIONr_mcangle_it9.15710.1112879
X-RAY DIFFRACTIONr_scbond_it8.8327.192435
X-RAY DIFFRACTIONr_scangle_it11.42710.493565
X-RAY DIFFRACTIONr_lrange_it13.14389.2646920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.5130.3621330.3092707X-RAY DIFFRACTION99.8594
2.513-2.5820.3231390.2882584X-RAY DIFFRACTION99.9633
2.582-2.6570.2951670.2622499X-RAY DIFFRACTION99.925
2.657-2.7390.3171160.2522483X-RAY DIFFRACTION100
2.739-2.8290.3151110.2422428X-RAY DIFFRACTION100
2.829-2.9280.3351010.2222325X-RAY DIFFRACTION99.9588
2.928-3.0380.2521180.2212237X-RAY DIFFRACTION99.8304
3.038-3.1620.2851060.2182181X-RAY DIFFRACTION99.9563
3.162-3.3020.299930.2192091X-RAY DIFFRACTION99.9085
3.302-3.4630.2381080.2081973X-RAY DIFFRACTION100
3.463-3.650.2621110.2361875X-RAY DIFFRACTION100
3.65-3.8720.286950.2351775X-RAY DIFFRACTION100
3.872-4.1380.254880.2091688X-RAY DIFFRACTION99.9437
4.138-4.4690.275780.2061553X-RAY DIFFRACTION100
4.469-4.8940.218800.1881454X-RAY DIFFRACTION100
4.894-5.470.219710.2121296X-RAY DIFFRACTION100
5.47-6.3130.309640.251161X-RAY DIFFRACTION99.9184
6.313-7.7220.298440.258982X-RAY DIFFRACTION100
7.722-10.8810.263320.263793X-RAY DIFFRACTION99.8789
10.881-58.6110.314210.326439X-RAY DIFFRACTION98.5011

+
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