[English] 日本語
Yorodumi
- PDB-7dbm: HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V:DNA:dG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dbm
TitleHIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V:DNA:dGTP ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • Protease
KeywordsTRANSFERASE/DNA / Entecavir 5'-triphosphate / HIV-1 / HBV / reverse transcriptase / drug resistance / TRANSFERASE-DNA complex / REPLICATION
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Pol protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Human immunodeficiency virus type 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsYasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20fk0310113 Japan
CitationJournal: J.Virol. / Year: 2021
Title: Biochemical and Structural Properties of Entecavir-Resistant Hepatitis B Virus Polymerase with L180M/M204V Mutations.
Authors: Nakajima, S. / Watashi, K. / Kato, T. / Muramatsu, M. / Wakita, T. / Tamura, N. / Hattori, S.I. / Maeda, K. / Mitsuya, H. / Yasutake, Y. / Toyoda, T.
History
DepositionOct 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Protease
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
C: Protease
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,69815
Polymers255,1756
Non-polymers1,5239
Water7,909439
1
A: Protease
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3958
Polymers127,5873
Non-polymers8085
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13280 Å2
ΔGint-51 kcal/mol
Surface area45870 Å2
MethodPISA
2
C: Protease
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3037
Polymers127,5873
Non-polymers7164
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-49 kcal/mol
Surface area46550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)283.514, 283.514, 95.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Protease / HIV-1 reverse transcriptase p66 subunit / Retropepsin


Mass: 64001.324 Da / Num. of mol.: 2 / Mutation: Q250M,Y214F,F215Y,M283V,C261S,C379S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: D3XFN5, RNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein HIV-1 RT p51 subunit / HIV-1 reverse transcriptase p51 subunit / p51 RT


Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C749S,C867S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497

-
DNA chain , 1 types, 2 molecules EF

#3: DNA chain DNA/RNA (38-MER)


Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 448 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 107363 / % possible obs: 100 % / Redundancy: 5.4 % / Rrim(I) all: 0.103 / Net I/σ(I): 10.5
Reflection shellResolution: 2.43→2.47 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5360 / Rrim(I) all: 0.819

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KDN

6kdn


Resolution: 2.43→48.469 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 5472 5.1 %
Rwork0.181 --
obs0.1832 107350 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→48.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15674 1495 94 439 17702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617858
X-RAY DIFFRACTIONf_angle_d0.81824563
X-RAY DIFFRACTIONf_dihedral_angle_d24.8016809
X-RAY DIFFRACTIONf_chiral_restr0.1532665
X-RAY DIFFRACTIONf_plane_restr0.0052829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.45760.321980.26423366X-RAY DIFFRACTION100
2.4576-2.48650.2941980.25163385X-RAY DIFFRACTION100
2.4865-2.51690.29842040.24193348X-RAY DIFFRACTION100
2.5169-2.54870.31461640.23973460X-RAY DIFFRACTION100
2.5487-2.58230.28721930.23633371X-RAY DIFFRACTION100
2.5823-2.61760.26041490.22813436X-RAY DIFFRACTION100
2.6176-2.6550.27222020.22223409X-RAY DIFFRACTION100
2.655-2.69470.27161510.2163422X-RAY DIFFRACTION100
2.6947-2.73680.24581780.22443388X-RAY DIFFRACTION100
2.7368-2.78160.27681860.21983399X-RAY DIFFRACTION100
2.7816-2.82960.2611780.21843406X-RAY DIFFRACTION100
2.8296-2.8810.2742020.22643386X-RAY DIFFRACTION100
2.881-2.93640.26321970.22323359X-RAY DIFFRACTION100
2.9364-2.99640.28692040.22583382X-RAY DIFFRACTION100
2.9964-3.06150.27721760.21543400X-RAY DIFFRACTION100
3.0615-3.13270.27781740.19983425X-RAY DIFFRACTION100
3.1327-3.2110.28371990.19833366X-RAY DIFFRACTION100
3.211-3.29780.2181640.19313398X-RAY DIFFRACTION100
3.2978-3.39490.22891780.18493435X-RAY DIFFRACTION100
3.3949-3.50440.23621970.18653377X-RAY DIFFRACTION100
3.5044-3.62960.24071690.18673388X-RAY DIFFRACTION100
3.6296-3.77490.20851710.17263417X-RAY DIFFRACTION100
3.7749-3.94660.2022110.16763351X-RAY DIFFRACTION100
3.9466-4.15460.2011830.15373398X-RAY DIFFRACTION100
4.1546-4.41470.17741680.15023379X-RAY DIFFRACTION100
4.4147-4.75530.18081900.14713435X-RAY DIFFRACTION100
4.7553-5.23330.191760.14793366X-RAY DIFFRACTION100
5.2333-5.98940.2011730.17223430X-RAY DIFFRACTION100
5.9894-7.54150.21991760.1763376X-RAY DIFFRACTION100
7.5415-48.4690.18751630.15573420X-RAY DIFFRACTION100
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)
10.8792-0.0042-0.33880.51330.03242.6381-0.07-0.03860.0607-0.00970.0048-0.07710.18670.06990.0350.22920.00280.02160.3124-0.01670.3505177.84274.7506-145.2708
22.20330.42560.02070.82310.41451.7114-0.11380.27290.1983-0.165-0.07350.3572-0.1939-0.76750.19440.35970.0549-0.02250.6879-0.03370.542145.5458275.3649-154.1607
31.81920.65170.83543.93432.49785.8978-0.1273-0.1898-0.2339-0.241-0.06020.23740.3576-0.58350.12930.3289-0.03140.0420.36480.0020.3034174.2069263.663-146.9265
41.6953-0.0589-0.18061.2231-0.44431.0932-0.07120.09550.1149-0.10210.07510.1162-0.0447-0.0646-0.01840.267-0.0287-0.01030.3696-0.01110.3203210.5811281.139-181.9587
50.9291-0.47390.18512.2125-0.74871.2201-0.0236-0.0017-0.0566-0.0472-0.0453-0.18180.08920.29440.06780.2814-0.03440.02990.44570.01240.3283238.0463261.8424-181.1702
64.21450.46420.70911.6495-0.41073.26740.1340.3282-0.4839-0.1309-0.3294-0.15620.5510.260.20210.4538-0.01350.0550.3816-0.01690.3117206.8727273.2331-189.9746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 553)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 427)
3X-RAY DIFFRACTION3(chain 'E' and resid -1 through 33)
4X-RAY DIFFRACTION4(chain 'C' and resid 2 through 553)
5X-RAY DIFFRACTION5(chain 'D' and resid 5 through 427)
6X-RAY DIFFRACTION6(chain 'F' and resid -4 through 33)

+
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