[English] 日本語
Yorodumi
- PDB-6ika: HIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ika
TitleHIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:DNA:entecavir-triphosphate ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • HIV-1 RT p66 subunit
KeywordsTRANSFERASE/DNA / ENTECAVIR 5'-TRIPHOSPHATE / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / entecavir / TRANSFERASE-DNA complex / REPLICATION
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 / host cell plasma membrane / virion membrane / structural molecule activity / 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
Chem-ET9 / 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: 2.598 Å
AuthorsYasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18fk0310113 Japan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified ...Title: Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified nucleoside RT inhibitors.
Authors: Yasutake, Y. / Hattori, S.I. / Tamura, N. / Matsuda, K. / Kohgo, S. / Maeda, K. / Mitsuya, H.
History
DepositionOct 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 RT p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
C: HIV-1 RT p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,59414
Polymers255,1436
Non-polymers1,4518
Water2,684149
1
A: HIV-1 RT p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2977
Polymers127,5713
Non-polymers7264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-43 kcal/mol
Surface area47070 Å2
MethodPISA
2
C: HIV-1 RT p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2977
Polymers127,5713
Non-polymers7264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-42 kcal/mol
Surface area47660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.405, 285.405, 96.346
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 HIV-1 RT p66 subunit


Mass: 63985.387 Da / Num. of mol.: 2
Mutation: G211S, D212A, Y214F, F215Y, Q250M, I258L, F259L, C261S, C379S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / References: UniProt: D3XFN7
#2: Protein HIV-1 RT 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 (E. coli) / 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, 157 molecules

#4: Chemical ChemComp-ET9 / [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate / Entecavir 5'-triphosphate


Mass: 517.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N5O12P3
#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 58.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM Bis-Tris-HCl PH 6.0, 30-40 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 3.5-4% PEG 6000, 2.4% sucrose, 4.8% 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: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.598→50 Å / Num. obs: 89785 / % possible obs: 99.6 % / Redundancy: 5.42 % / CC1/2: 0.998 / Rrim(I) all: 0.091 / Net I/σ(I): 15.89
Reflection shellResolution: 2.598→2.76 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 14209 / CC1/2: 0.711 / Rrim(I) all: 0.844 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XN1

5xn1


Resolution: 2.598→48.869 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.232 4538 5.05 %
Rwork0.1858 --
obs0.1881 89774 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.598→48.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15682 1495 90 149 17416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01317863
X-RAY DIFFRACTIONf_angle_d1.12124572
X-RAY DIFFRACTIONf_dihedral_angle_d24.8816813
X-RAY DIFFRACTIONf_chiral_restr0.122669
X-RAY DIFFRACTIONf_plane_restr0.0072827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5982-2.62780.35641300.30842476X-RAY DIFFRACTION88
2.6278-2.65870.31471470.28212863X-RAY DIFFRACTION100
2.6587-2.69110.35631470.27422866X-RAY DIFFRACTION100
2.6911-2.72510.31091300.27072867X-RAY DIFFRACTION100
2.7251-2.7610.29951580.25772877X-RAY DIFFRACTION100
2.761-2.79880.2921440.24852870X-RAY DIFFRACTION100
2.7988-2.83880.27151480.2362866X-RAY DIFFRACTION100
2.8388-2.88120.26681760.23242753X-RAY DIFFRACTION100
2.8812-2.92620.32031620.22482880X-RAY DIFFRACTION100
2.9262-2.97420.25111610.21892832X-RAY DIFFRACTION100
2.9742-3.02540.27281740.2222833X-RAY DIFFRACTION100
3.0254-3.08040.30521600.21662857X-RAY DIFFRACTION100
3.0804-3.13970.2831230.21132882X-RAY DIFFRACTION100
3.1397-3.20380.27771730.20222847X-RAY DIFFRACTION100
3.2038-3.27340.27091570.21022860X-RAY DIFFRACTION100
3.2734-3.34950.23921300.20422864X-RAY DIFFRACTION100
3.3495-3.43330.25681620.19192847X-RAY DIFFRACTION100
3.4333-3.52610.21431520.18762842X-RAY DIFFRACTION100
3.5261-3.62980.27631640.18252835X-RAY DIFFRACTION100
3.6298-3.74690.22161380.17912883X-RAY DIFFRACTION100
3.7469-3.88080.2141480.16952826X-RAY DIFFRACTION100
3.8808-4.03610.23321810.16592843X-RAY DIFFRACTION100
4.0361-4.21970.2121570.15862845X-RAY DIFFRACTION100
4.2197-4.4420.18011300.16052882X-RAY DIFFRACTION100
4.442-4.72010.19731570.15382830X-RAY DIFFRACTION100
4.7201-5.08420.17211570.14932880X-RAY DIFFRACTION100
5.0842-5.59520.20711500.16332845X-RAY DIFFRACTION100
5.5952-6.40330.21661310.18792874X-RAY DIFFRACTION100
6.4033-8.06160.20691740.17242830X-RAY DIFFRACTION100
8.0616-48.87730.2051170.17512881X-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)
11.07590.0471-0.47170.4051-0.06592.5988-0.0858-0.05980.0864-0.01050.0372-0.09690.09950.07530.00720.20360.00060.03030.2874-0.05050.3775178.9246276.7315-147.2362
22.76970.57280.23130.97010.62571.863-0.21480.27010.2882-0.1776-0.00440.3735-0.2312-0.72610.19320.28430.0567-0.0460.6159-0.00650.5249146.5705277.4643-156.257
31.15790.1427-0.09634.15892.24024.391-0.1069-0.2484-0.3409-0.2083-0.0480.15090.1795-0.41470.17730.2553-0.0440.03120.34440.00620.3207175.4327265.5452-148.8218
41.7432-0.0112-0.1421.4451-0.4661.0006-0.06180.16660.2213-0.20650.06910.1161-0.0393-0.0533-0.01210.2703-0.05850.01850.36740.00680.3431211.9786282.9863-184.2805
50.9905-0.23940.03282.0543-0.81511.1808-0.00810.03710.0243-0.07930.0021-0.090.04430.28530.01490.2388-0.04120.05990.4096-0.00460.3551239.5662263.638-183.1524
64.12071.40940.05432.747-0.45113.31270.14630.5596-0.23-0.15-0.4635-0.24480.41480.18780.30710.35370.02250.06350.4219-0.02220.3356208.1764274.9537-192.2634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 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 1 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