[English] 日本語
Yorodumi
- PDB-5xn2: HIV-1 reverse transcriptase Q151M:DNA:dGTP ternary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xn2
TitleHIV-1 reverse transcriptase Q151M:DNA:dGTP ternary complex
Components
  • (Pol protein) x 2
  • 38-MER DNA aptamer
KeywordsTRANSFERASE/DNA / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / entecavir / TRANSFERASE-DNA complex
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / 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 / 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 / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding
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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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. / Nucleotidyltransferase; domain 5 / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Pol protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.381 Å
AuthorsYasutake, Y. / Tamura, N. / Hayashi, H. / Maeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Sci Rep / Year: 2018
Title: HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir.
Authors: Yasutake, Y. / Hattori, S.I. / Hayashi, H. / Matsuda, K. / Tamura, N. / Kohgo, S. / Maeda, K. / Mitsuya, H.
History
DepositionMay 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pol protein
B: Pol protein
E: 38-MER DNA aptamer
C: Pol protein
D: Pol protein
F: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,01315
Polymers255,2396
Non-polymers1,7749
Water5,783321
1
A: Pol protein
B: Pol protein
E: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6778
Polymers127,6193
Non-polymers1,0585
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13280 Å2
ΔGint-47 kcal/mol
Surface area47280 Å2
MethodPISA
2
C: Pol protein
D: Pol protein
F: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3357
Polymers127,6193
Non-polymers7164
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-50 kcal/mol
Surface area47580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.694, 285.694, 96.325
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 Pol protein


Mass: 64033.387 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 100-654 / Mutation: Q151M, C162S, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: D3XFN7, UniProt: P12497*PLUS
#2: Protein Pol protein / HIV-1 reverse transcriptase p51 subunit


Mass: 51861.547 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 100-527 / Mutation: C162S, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: D3XFN7, UniProt: P12497*PLUS

-
DNA/RNA hybrid / Sugars , 2 types, 3 molecules EF

#3: DNA/RNA hybrid 38-MER DNA aptamer


Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 329 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM bis-Tris-HCl pH 6.0, 60 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 1.5-3% PEG 6000, 2-4% sucrose, 4-8% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 117205 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rpim(I) all: 0.063 / Net I/σ(I): 20.6
Reflection shellResolution: 2.38→2.52 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3G
Resolution: 2.381→48.903 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2234 5960 5.09 %
Rwork0.1885 --
obs0.1903 117194 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.381→48.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15674 1495 111 321 17601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317885
X-RAY DIFFRACTIONf_angle_d0.59524604
X-RAY DIFFRACTIONf_dihedral_angle_d22.356829
X-RAY DIFFRACTIONf_chiral_restr0.0442670
X-RAY DIFFRACTIONf_plane_restr0.0052831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3809-2.4080.35191860.30623568X-RAY DIFFRACTION95
2.408-2.43630.32351660.28283744X-RAY DIFFRACTION100
2.4363-2.4660.33752300.26923706X-RAY DIFFRACTION100
2.466-2.49720.29382330.26793637X-RAY DIFFRACTION100
2.4972-2.53010.33142190.2533734X-RAY DIFFRACTION100
2.5301-2.56480.3211770.25183674X-RAY DIFFRACTION100
2.5648-2.60140.30042010.24243769X-RAY DIFFRACTION100
2.6014-2.64020.28071780.24223699X-RAY DIFFRACTION100
2.6402-2.68150.28052150.23423740X-RAY DIFFRACTION100
2.6815-2.72540.2911620.24133710X-RAY DIFFRACTION100
2.7254-2.77240.28911970.24473733X-RAY DIFFRACTION100
2.7724-2.82280.27942070.24323728X-RAY DIFFRACTION100
2.8228-2.87710.26622060.24323683X-RAY DIFFRACTION100
2.8771-2.93590.29642160.24643688X-RAY DIFFRACTION100
2.9359-2.99970.26192120.22813746X-RAY DIFFRACTION100
2.9997-3.06950.26532270.22953652X-RAY DIFFRACTION100
3.0695-3.14620.30221670.21433720X-RAY DIFFRACTION100
3.1462-3.23120.24372240.20333690X-RAY DIFFRACTION100
3.2312-3.32630.24691820.20733748X-RAY DIFFRACTION100
3.3263-3.43360.25691900.20143727X-RAY DIFFRACTION100
3.4336-3.55630.23462110.20033685X-RAY DIFFRACTION100
3.5563-3.69870.22951850.18433720X-RAY DIFFRACTION100
3.6987-3.86690.18742000.16763734X-RAY DIFFRACTION100
3.8669-4.07070.20242190.16113655X-RAY DIFFRACTION100
4.0707-4.32560.20191970.15663746X-RAY DIFFRACTION100
4.3256-4.65940.17361950.15223722X-RAY DIFFRACTION100
4.6594-5.12780.16021930.14383693X-RAY DIFFRACTION100
5.1278-5.86870.20072030.16773701X-RAY DIFFRACTION100
5.8687-7.38990.1761850.1723762X-RAY DIFFRACTION100
7.3899-48.91290.17431770.15533720X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.8946-0.0191-0.34190.43090.06382.1645-0.0822-0.03850.0844-0.00720.0043-0.06960.1367-0.02720.06190.2712-0.00490.03380.346-0.03470.3759179.1122276.7965-147.0209
22.44070.54480.20.97730.43281.5379-0.18830.20230.2783-0.1566-0.02350.3735-0.1485-0.64220.1870.32950.0397-0.04430.666-0.03040.5326146.771277.7814-156.0196
31.65560.22190.14073.52791.6153.799-0.0905-0.1886-0.4132-0.28530.03480.02580.0768-0.44570.04150.3143-0.04180.0570.4019-0.01130.3674175.5871265.7238-148.7163
41.4906-0.0087-0.1490.9368-0.35990.9865-0.00750.1680.1255-0.13670.02050.0943-0.0681-0.0556-0.01690.3092-0.02770.04120.38240.01310.3663212.1511283.217-184.0111
50.6686-0.39550.02271.4694-0.59321.07860.03960.01880.0175-0.0552-0.0072-0.03730.03790.2668-0.02480.359-0.03060.06350.51790.00650.4661239.8692264.0205-182.9355
63.76750.82540.4511.6976-0.37323.31650.31310.4601-0.225-0.0973-0.5176-0.06150.38820.26290.21250.41420.02550.07880.4367-0.00460.3376208.4981275.1691-192.0328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 553)
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 427)
3X-RAY DIFFRACTION3(chain 'E' and resid -1 through 33)
4X-RAY DIFFRACTION4(chain 'C' and resid 3 through 553)
5X-RAY DIFFRACTION5(chain 'D' and resid 4 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