[English] 日本語
Yorodumi
- EMDB-14453: MVV strand transfer complex (STC) intasome in complex with LEDGF/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14453
TitleMVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution
Map datadeepEMhancer tight target map
Sample
  • Complex: MVV STC intasome in complex with LEDGF
    • Protein or peptide: Pol polyprotein
    • Protein or peptide: PC4 and SFRS1-interacting protein
    • DNA: DNA (5'-D(*GP*CP*TP*GP*CP*GP*AP*GP*AP*TP*CP*CP*GP*CP*TP*CP*CP*GP*GP*TP*G)-3')
    • DNA: DNA (37-MER)
    • DNA: DNA (5'-D(P*TP*TP*GP*AP*TP*TP*AP*GP*GP*GP*TP*G)-3')
  • Ligand: ZINC ION
KeywordsIntasome / Integrase / MVV / Lentivirus / HIV / strand transfer complex / LEDGF / IBD / DNA / integration / VIRAL PROTEIN
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / exoribonuclease H / exoribonuclease H activity / euchromatin / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral capsid / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / response to heat / DNA-binding transcription factor binding / DNA recombination / response to oxidative stress / DNA-directed DNA polymerase / transcription coactivator activity / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / chromatin remodeling / symbiont entry into host cell / viral translational frameshifting / chromatin binding / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / TFIIS/LEDGF domain superfamily / gag protein p24 N-terminal domain / domain with conserved PWWP motif ...Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / TFIIS/LEDGF domain superfamily / gag protein p24 N-terminal domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesVisna/maedi virus EV1 KV1772 / Homo sapiens (human) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBallandras-Colas A / Nans A / Cherepanov P
Funding support United Kingdom, United States, 2 items
OrganizationGrant numberCountry
The Francis Crick InstituteFC10061 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50AI150481 United States
CitationJournal: Nat Commun / Year: 2022
Title: Multivalent interactions essential for lentiviral integrase function.
Authors: Ballandras-Colas A / Chivukula V / Gruszka DT / Shan Z / Singh PK / Pye VE / McLean RK / Bedwell GJ / Li W / Nans A / Cook NJ / Fadel HJ / Poeschla EM / Griffiths DJ / Vargas J / Taylor IA / ...Authors: Ballandras-Colas A / Chivukula V / Gruszka DT / Shan Z / Singh PK / Pye VE / McLean RK / Bedwell GJ / Li W / Nans A / Cook NJ / Fadel HJ / Poeschla EM / Griffiths DJ / Vargas J / Taylor IA / Lyumkis D / Yardimci H / Engelman AN / Cherepanov P
History
DepositionFeb 25, 2022-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14453.png

Downloads & links

-
Map

FileDownload / File: emd_14453.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer tight target map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 320 pix.
= 441.6 Å		1.38 Å/pix.
x 320 pix.
= 441.6 Å		1.38 Å/pix.
x 320 pix.
= 441.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0018081084 - 2.1215732
Average (Standard dev.)0.0007304996 (±0.018725066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 441.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_14453_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: original volume map - no enhancement

Fileemd_14453_additional_1.map
Annotationoriginal volume map - no enhancement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Phenix local sharpen map - this map was...

Fileemd_14453_additional_2.map
AnnotationPhenix local sharpen map - this map was used for model real space refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_14453_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_14453_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MVV STC intasome in complex with LEDGF

EntireName: MVV STC intasome in complex with LEDGF
Components
  • Complex: MVV STC intasome in complex with LEDGF
    • Protein or peptide: Pol polyprotein
    • Protein or peptide: PC4 and SFRS1-interacting protein
    • DNA: DNA (5'-D(*GP*CP*TP*GP*CP*GP*AP*GP*AP*TP*CP*CP*GP*CP*TP*CP*CP*GP*GP*TP*G)-3')
    • DNA: DNA (37-MER)
    • DNA: DNA (5'-D(P*TP*TP*GP*AP*TP*TP*AP*GP*GP*GP*TP*G)-3')
  • Ligand: ZINC ION

-
Supramolecule #1: MVV STC intasome in complex with LEDGF

SupramoleculeName: MVV STC intasome in complex with LEDGF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Visna/maedi virus EV1 KV1772
Molecular weightTheoretical: 480 KDa

-
Macromolecule #1: Pol polyprotein

MacromoleculeName: Pol polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
Source (natural)Organism: Visna/maedi virus EV1 KV1772 / Strain: KV1772
Molecular weightTheoretical: 32.368826 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: WIENIPLAEE EHNKWHQDAV SLHLEFGIPR TAAEDIVQQC DVCQENKMPS TLRGSNKRGI DHWQVDYTHY EDKIILVWVE TNSGLIYAE RVKGETGQEF RVQTMKWYAM FAPKSLQSDN GPAFVAESTQ LLMKYLGIEH TTGIPWNPQS QALVERTHQT L KNTLEKLI ...String:
WIENIPLAEE EHNKWHQDAV SLHLEFGIPR TAAEDIVQQC DVCQENKMPS TLRGSNKRGI DHWQVDYTHY EDKIILVWVE TNSGLIYAE RVKGETGQEF RVQTMKWYAM FAPKSLQSDN GPAFVAESTQ LLMKYLGIEH TTGIPWNPQS QALVERTHQT L KNTLEKLI PMFNAFESAL AGTLITLNIK RKGGLGTSPM DIFIFNKEQQ RIQQQSKSKQ EKIRFCYYRT RKRGHPGEWQ GP TQVLWGG DGAIVVKDRG TDRYLVIANK DVKFIPPPKE IQKE

UniProtKB: Gag-Pol polyprotein

-
Macromolecule #2: PC4 and SFRS1-interacting protein

MacromoleculeName: PC4 and SFRS1-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.07597 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SMDSRLQRIH AEIKNSLKID NLDVNRCIEA LDELASLQVT MQQAQKHTEM ITTLKKIRRF KVSQVIMEKS TMLYNKFKNM FLVGEGDSV LEVLFQ

UniProtKB: PC4 and SFRS1-interacting protein

-
Macromolecule #3: DNA (5'-D(*GP*CP*TP*GP*CP*GP*AP*GP*AP*TP*CP*CP*GP*CP*TP*CP*CP*GP*...

MacromoleculeName: DNA (5'-D(*GP*CP*TP*GP*CP*GP*AP*GP*AP*TP*CP*CP*GP*CP*TP*CP*CP*GP*GP*TP*G)-3')
type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 7.064532 KDa
SequenceString:
(DG)(DC)(DT)(DG)(DC)(DG)(DA)(DG)(DA)(DT) (DC)(DC)(DG)(DC)(DT)(DC)(DC)(DG)(DG)(DT) (DG)(DT)(DT)

-
Macromolecule #4: DNA (37-MER)

MacromoleculeName: DNA (37-MER) / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.387863 KDa
SequenceString:
(DA)(DA)(DC)(DA)(DC)(DC)(DG)(DG)(DA)(DG) (DC)(DG)(DG)(DA)(DT)(DC)(DT)(DC)(DG)(DC) (DA)(DG)(DT)(DC)(DG)(DA)(DC)(DC)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DT)(DC)(DA)(DA) (DG) (DT)(DT)(DT)(DT)(DT)(DT)(DG)(DG) (DG)(DG)

-
Macromolecule #5: DNA (5'-D(P*TP*TP*GP*AP*TP*TP*AP*GP*GP*GP*TP*G)-3')

MacromoleculeName: DNA (5'-D(P*TP*TP*GP*AP*TP*TP*AP*GP*GP*GP*TP*G)-3') / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 7.0736 KDa
SequenceString:
(DC)(DC)(DC)(DC)(DA)(DA)(DA)(DA)(DA)(DA) (DC)(DT)(DT)(DG)(DA)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DG)

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 12 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.15 mg/mL
BufferpH: 6.5
Details: 310 mM NaCl, 3 mM CaCl2, 25 mM BisTris-HCl, pH 6.5.
GridModel: EMS Lacey Carbon / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsThe intasomes were typically assembled by incubating 7 uM MVV IN, 8 uM LEDGF/p75, and 3.75 uM annealed vDNA (or the strand transfer product mimic) in 80 mM NaCl, 40 mM potassium acetate, 3 mM CaCl2 10 uM ZnCl2, 1 mM dithiothreitol (DTT) and 25 mM BisTris-HCl, pH 6.0 in a total volume of 200 ul at 37 deg C for 10 min (to prepare samples for cryo-EM, the reaction was upscaled to a total volume of 1 ml). The opalescent mixture was supplemented with 50 mM BisTris-HCl, pH 6.5 and 190 mM NaCl and incubated on ice for 5 min to clear. If starting volume exceeded 200 ul, the mixture was concentrated by ultrafiltration in a VivaSpin device to a final volume of 200 ul. Intasomes were purified by size exclusion chromatography through a Superdex-200 10/30 column (GE Healthcare) pre-equilibrated in 310 mM NaCl, 3 mM CaCl2, 25 mM BisTris-HCl, pH 6.5.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 36232 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 121619
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

5m0r

source_name: PDB, initial_model_type: experimental model

3hph

source_name: PDB, initial_model_type: experimental model
Detailsinteractive fitting/rebuilding in coot and real space refinement in Phenix.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7z1z:
MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution

+
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