[English] 日本語
Yorodumi
- PDB-6oe3: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oe3
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-7-fluoro-2-naphthonitrile (JLJ635), a Non-nucleoside Inhibitor
Components(HIV-1 REVERSE TRANSCRIPTASE, ...) x 2
KeywordsTRANSFERASE / NNRTIs / HIV-1 / drug design
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / 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. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-M9A / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBertoletti, N. / Kudalkar, S.N. / Anderson, K.S. / Cisneros Trigo, J.A. / Jorgensen, W.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049551 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141572 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI044616 United States
CitationJournal: Antiviral Res. / Year: 2019
Title: Structural and pharmacological evaluation of a novel non-nucleoside reverse transcriptase inhibitor as a promising long acting nanoformulation for treating HIV.
Authors: Kudalkar, S.N. / Ullah, I. / Bertoletti, N. / Mandl, H.K. / Cisneros, J.A. / Beloor, J. / Chan, A.H. / Quijano, E. / Saltzman, W.M. / Jorgensen, W.L. / Kumar, P. / Anderson, K.S.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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: HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5665
Polymers114,0292
Non-polymers5383
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-43 kcal/mol
Surface area45540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.311, 69.572, 104.830
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
HIV-1 REVERSE TRANSCRIPTASE, ... , 2 types, 2 molecules AB

#1: Protein HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT / p66 RT


Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S, C258Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT


Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): GOLD / References: UniProt: P03366

-
Non-polymers , 4 types, 16 molecules

#3: Chemical ChemComp-M9A / 5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-7-fluoronaphthalene-2-carbonitrile


Mass: 417.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H16FN3O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.45 Å3/Da / Density % sol: 64.4 % / Description: thin plate
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES pH 6.0, 18% PEG 8,000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 34181 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 18.2 Å2 / CC1/2: 0.996 / Rsym value: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5280 / CC1/2: 0.63 / Rsym value: 1.098 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TW3

5tw3


Resolution: 2.9→43.171 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.4
RfactorNum. reflection% reflection
Rfree0.2729 1701 4.99 %
Rwork0.228 --
obs0.2303 34093 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→43.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7550 0 37 13 7600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067794
X-RAY DIFFRACTIONf_angle_d0.82110651
X-RAY DIFFRACTIONf_dihedral_angle_d14.84646
X-RAY DIFFRACTIONf_chiral_restr0.0511182
X-RAY DIFFRACTIONf_plane_restr0.0071383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8983-2.98360.47591280.48382451X-RAY DIFFRACTION90
2.9836-3.07990.43181440.34832718X-RAY DIFFRACTION99
3.0799-3.18990.38431430.29472740X-RAY DIFFRACTION100
3.1899-3.31760.34371430.30342718X-RAY DIFFRACTION99
3.3176-3.46850.34541430.29562729X-RAY DIFFRACTION99
3.4685-3.65130.33341420.28872686X-RAY DIFFRACTION98
3.6513-3.87990.36921300.2992539X-RAY DIFFRACTION92
3.8799-4.17930.29071420.22352700X-RAY DIFFRACTION98
4.1793-4.59940.21291440.17662730X-RAY DIFFRACTION99
4.5994-5.2640.20621460.16932775X-RAY DIFFRACTION100
5.264-6.62820.26271460.20892765X-RAY DIFFRACTION99
6.6282-43.17540.21141500.17752841X-RAY DIFFRACTION99
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)
13.47470.58850.79423.9075-0.72425.495-0.2527-0.53290.030.4732-0.16710.0853-0.44160.0530.41690.74770.1069-0.12620.8257-0.12020.7099458.228218.1103237.9692
23.8017-1.07770.44598.8879-0.93716.6405-0.4514-0.9889-0.05740.83890.0268-0.9236-0.12280.15330.44280.75340.1585-0.13011.2238-0.13350.8231466.694610.4059243.0965
34.1396-5.12114.86846.3773-6.30817.68450.2261-0.6889-0.80740.2628-0.13120.1322-0.0367-0.6704-0.13790.86840.1018-0.27742.20160.66971.3213459.8844-1.2501250.5145
43.52840.77620.14721.94330.11930.415-0.1339-0.5015-0.59050.16330.0036-0.18650.29310.22070.13250.73540.15150.05440.66070.11130.6339444.947-0.0226232.9035
54.43953.00245.21142.45123.38366.16310.6534-0.91640.2764-0.6289-0.12290.1015-0.50640.024-0.60391.4347-0.186-0.07821.3952-0.05531.3449422.424810.1179255.0648
63.44871.4809-0.51471.3221-1.62642.9224-0.2622-0.2434-0.47810.25860.04160.02950.2765-0.25740.17730.86640.03380.26750.55670.06740.9095415.7127-3.3155232.6081
74.7754-1.7627-2.99622.33762.2353.8043-0.1024-0.05110.0421-0.13070.0546-0.15010.2221-0.18720.03910.5578-0.04030.04560.58210.07580.8193391.175816.435237.5244
83.2806-1.13570.11455.6761-0.16594.8905-0.33830.06210.32490.37030.1084-0.1406-0.15780.0160.22230.49820.0186-0.04950.53010.06280.5293435.162622.2631215.2213
94.151-1.67671.24082.7454-1.27572.1919-0.29850.34430.32960.46590.1387-0.0402-0.4678-0.00640.1870.6059-0.02710.04510.4970.06060.5318434.275926.0042211.1202
108.7812-1.05611.03013.57131.09176.76410.04510.7944-0.1461-0.05360.03230.32090.0976-0.4021-0.07520.5603-0.058-0.00080.70130.15630.6224424.074137.1137196.2255
114.6290.8811-1.64952.2292-0.36143.46830.06390.5891.0704-0.64030.17220.1269-0.4977-0.4825-0.31070.7940.07430.19720.97360.3491.0097389.097637.3165224.5681
126.08920.9903-1.96930.9148-1.18471.59390.33970.12731.31990.06320.09280.2181-0.4075-0.4557-0.44960.77650.077-0.03460.71210.14220.9519397.641536.4234222.171
135.3553-2.367-1.68555.8365-3.90445.0452-1.29572.1657-1.518-1.99330.22192.24250.2656-1.28220.57850.8436-0.2233-0.34340.9665-0.12871.1268407.24715.9363211.5602
145.38280.5712-1.59137.2885-0.93944.34570.0276-0.0889-0.39150.7515-0.07590.0116-0.0629-0.12430.10750.67320.02510.05620.51970.0290.5581413.689625.1112218.9668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:29)
2X-RAY DIFFRACTION2(chain A and resid 30:63)
3X-RAY DIFFRACTION3(chain A and resid 64:72)
4X-RAY DIFFRACTION4(chain A and resid 73:282)
5X-RAY DIFFRACTION5(chain A and resid 283:290)
6X-RAY DIFFRACTION6(chain A and resid 291:392)
7X-RAY DIFFRACTION7(chain A and resid 393:552)
8X-RAY DIFFRACTION8(chain B and resid 5:95)
9X-RAY DIFFRACTION9(chain B and resid 96:159)
10X-RAY DIFFRACTION10(chain B and resid 160:237)
11X-RAY DIFFRACTION11(chain B and resid 238:281)
12X-RAY DIFFRACTION12(chain B and resid 282:356)
13X-RAY DIFFRACTION13(chain B and resid 357:369)
14X-RAY DIFFRACTION14(chain B and resid 370:428)

+
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