[English] 日本語
Yorodumi
- PDB-7adu: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7adu
TitleCrystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ440 (compound 5j)
Components
  • DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
  • Integrase
KeywordsVIRAL PROTEIN / Integrase / Intasome / Protein DNA complex / INSTI / Drug / HIV / Retrovirus / Integration
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding
Similarity search - Function
Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain ...Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Endonuclease III; domain 1 / SH3 type barrels. - #140 / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-R7K / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsPye, V.E. / Cherepanov, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC10061 United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2021
Title: HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants.
Authors: Smith, S.J. / Zhao, X.Z. / Passos, D.O. / Pye, V.E. / Cherepanov, P. / Lyumkis, D. / Burke Jr., T.R. / Hughes, S.H.
History
DepositionSep 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrase
B: Integrase
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,23926
Polymers99,9444
Non-polymers2,29622
Water3,333185
1
A: Integrase
B: Integrase
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules

A: Integrase
B: Integrase
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,47952
Polymers199,8878
Non-polymers4,59244
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area33530 Å2
ΔGint-499 kcal/mol
Surface area56380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.469, 159.469, 123.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Integrase / Pr125Pol


Mass: 44456.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Gene: pol / Production host: Escherichia coli (E. coli)
References: UniProt: P14350, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, Transferases; ...References: UniProt: P14350, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')


Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')


Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 7 types, 207 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-R7K / ~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-5-(hydroxymethyl)-1,4-bis(oxidanyl)-2-oxidanylidene-1,8-naphthyridine-3-carboxamide


Mass: 377.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13F2N3O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryocooled / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.62→97.64 Å / Num. obs: 48059 / % possible obs: 99.4 % / Redundancy: 14 % / Biso Wilson estimate: 52.93 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.064 / Net I/σ(I): 11.1
Reflection shellResolution: 2.62→2.66 Å / Redundancy: 14.5 % / Rmerge(I) obs: 2.2 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 33332 / CC1/2: 0.722 / Rpim(I) all: 0.857

-
Processing

Software
NameVersionClassification
PHENIXdev_3900refinement
PHENIXdev_3900refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BDZ

4bdz


Resolution: 2.62→71.32 Å / SU ML: 0.3322 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 2414 5.02 %
Rwork0.2021 45645 -
obs0.2036 48059 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.97 Å2
Refinement stepCycle: LAST / Resolution: 2.62→71.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 732 133 185 5430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235458
X-RAY DIFFRACTIONf_angle_d0.52157592
X-RAY DIFFRACTIONf_chiral_restr0.0379841
X-RAY DIFFRACTIONf_plane_restr0.0041826
X-RAY DIFFRACTIONf_dihedral_angle_d17.10852077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.670.4011440.3572557X-RAY DIFFRACTION96.36
2.67-2.730.30441470.34112618X-RAY DIFFRACTION98.71
2.73-2.790.38461340.31332644X-RAY DIFFRACTION98.79
2.79-2.860.34611510.29682605X-RAY DIFFRACTION99.21
2.86-2.940.33371420.28872664X-RAY DIFFRACTION99.19
2.94-3.030.30981200.26072658X-RAY DIFFRACTION99.5
3.03-3.130.30541360.26892682X-RAY DIFFRACTION99.47
3.13-3.240.28171330.24032664X-RAY DIFFRACTION99.64
3.24-3.370.27171370.19752680X-RAY DIFFRACTION99.61
3.37-3.520.24591530.19752648X-RAY DIFFRACTION99.57
3.52-3.710.22531370.18762697X-RAY DIFFRACTION99.79
3.71-3.940.21941460.18642683X-RAY DIFFRACTION99.4
3.94-4.240.17561550.16092680X-RAY DIFFRACTION99.51
4.24-4.670.16371550.14262710X-RAY DIFFRACTION99.31
4.67-5.340.18091540.1572736X-RAY DIFFRACTION99.72
5.35-6.730.20421260.18342787X-RAY DIFFRACTION100
6.73-71.320.21531440.19432932X-RAY DIFFRACTION99.77
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)
10.4384654473480.124654510982-0.07404773369940.491133130890.4730561880650.336537052936-0.0094183303608-0.0429182153654-0.0440778441318-0.0450404713005-0.2628006103890.1825095798520.00899976448454-0.31843902154-0.1211769823080.292479379557-0.0998963701903-0.07191918796550.410972014074-0.1153636786170.447045455674-70.19954544126.5046011573-57.570462712
20.4297156540620.03880310593020.396819409740.3489673265960.1709102508251.58403936923-0.0364120675573-0.162996497762-0.01723822571190.03353393846220.02057451932480.0001273386646130.239904467395-0.0334551102945-0.0003371776213180.28431605388-0.03084453534280.05374136880770.3012878004890.03373853113710.292526480752-35.175741260936.6124987347-8.6601981427
30.366594944845-0.222378550304-0.1856305468380.01058197335430.3355056227410.168401737278-0.350764307247-0.221671836012-0.0513978201489-0.3178323705150.1581078040670.134209109637-0.760465301634-0.303640500779-0.00207255461420.473843732276-0.01996115854920.04089146918480.533891479197-0.03549603747860.476109541742-46.755109649251.0720455624-1.95102010211
40.322601121572-0.124638415654-0.09332286294220.6874539589960.01587461029912.2494855341-0.141004919133-0.173263240465-0.1363216586290.1019851723930.1094063668030.1520861002580.961113255121-0.1496975408110.3292810394640.431537882301-0.2704874658860.08611120489140.3915087353960.04773489672150.394227771306-54.052055443225.5020427834-26.8458753871
50.577075093095-0.1102750243310.01094061062340.395533180465-0.1312584322960.768489081518-0.0635736307238-0.276344336594-0.06779045026960.111199537175-0.007414736055620.08279152574950.04169749635410.1773147625243.38365452075E-60.312334541463-0.001317062593850.01104885452410.5065902769210.02702543000920.332161396961-20.149862141939.369273099513.0309953342
60.1508438019090.3414098222560.0823015568051.330749982740.3704064760430.112831405968-0.285141777185-0.8959845918380.603792753453-0.162415640953-0.3146341017280.03266394149980.09137460297210.224387401575-0.2749002258610.3409194174750.01875478840080.1230291295421.02387359608-0.004024814098390.343651801256-13.938092890347.353950445716.4959922518
70.4195208586970.0911951890397-0.07192521467820.2292693028730.04019016251480.422921432485-0.0982525289185-0.610392203154-0.255469995410.4229405682650.1139550462630.2078070121380.244477171902-0.4113048442810.04282293277530.511060825768-0.03814993214220.1080597395410.6843030803170.07259182432090.384944359877-33.370240968132.392145400618.1270773026
80.03466883106960.002310895426290.0483310273478-0.0003673250559960.03648268728990.00676013570879-0.570795364398-0.02815642250070.231568082695-0.33510706988-0.7498344749460.2645806409730.621029491129-0.21710577762-0.0002110172739041.419584745190.07625290342120.01177481425091.08404022780.1098519298551.45999947648-29.291987178217.199121633128.4809084952
9-0.03127054970820.6528669856030.04683989184610.483695461129-0.09279099889150.763437174741-0.0417264090131-0.0892209017592-9.7056914792E-50.0646632817063-0.002836854007670.164505035705-0.222764898528-0.184093249982-0.0006733115260480.368201301603-0.04022931473150.01798520171980.343584048855-0.01293141903550.483170669029-43.774386132159.4970392056-13.913868777
100.3294567142850.293893832127-0.8483695387690.318547261792-0.537817347399-0.1013737796810.3153735870790.05263987625330.01563618779560.0662071415454-0.437551413871-0.0836643135125-0.173631438264-0.261801156094-0.01978507259830.457917101286-0.035563791509-0.03308780146160.322828833331-0.04516078439930.397638747971-41.981590418763.8015331702-16.9469379805
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 9:98)AA9 - 981 - 90
22(chain A and resid 99:280)AA99 - 28091 - 272
33(chain A and resid 281:315)AA281 - 315273 - 307
44(chain A and resid 316:375)AA316 - 375308 - 367
55(chain B and resid 116:196)BB116 - 1961 - 81
66(chain B and resid 197:215)BB197 - 21582 - 100
77(chain B and resid 216:280)BB216 - 280101 - 165
88(chain B and resid 281:297)BB281 - 297166 - 182
99(chain C and resid 1:19)CC1 - 19
1010(chain D and resid 1:17)DD1 - 17

+
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