[English] 日本語
Yorodumi
- PDB-7uyn: Crystal structure of B-form alien DNA 5'-CTTBPPBBSSZZSAAG in a ho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uyn
TitleCrystal structure of B-form alien DNA 5'-CTTBPPBBSSZZSAAG in a host-guest complex with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase
Components
  • DNA (5'-D(*CP*TP*TP*(IGU)P*(1WA)P*(1WA)P*(IGU)P*(IGU))-3')
  • DNA (5'-D(P*(JSP)P*(JSP)P*(1W5)P*(1W5)P*(JSP)P*AP*AP*G)-3')
  • reverse transcriptase
KeywordsDNA BINDING PROTEIN/DNA / unnatural DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


host cell late endosome membrane / virion assembly / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination ...host cell late endosome membrane / virion assembly / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / : / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / 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. / 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
DNA / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGeorgiadis, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1939086 United States
CitationJournal: Philos.Trans.R.Soc.Lond.B Biol.Sci. / Year: 2023
Title: Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form.
Authors: Shukla, M.S. / Hoshika, S. / Benner, S.A. / Georgiadis, M.M.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*(IGU)P*(1WA)P*(1WA)P*(IGU)P*(IGU))-3')
G: DNA (5'-D(P*(JSP)P*(JSP)P*(1W5)P*(1W5)P*(JSP)P*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)35,0133
Polymers35,0133
Non-polymers00
Water2,774154
1
A: reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*(IGU)P*(1WA)P*(1WA)P*(IGU)P*(IGU))-3')
G: DNA (5'-D(P*(JSP)P*(JSP)P*(1W5)P*(1W5)P*(JSP)P*AP*AP*G)-3')

A: reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*(IGU)P*(1WA)P*(1WA)P*(IGU)P*(IGU))-3')
G: DNA (5'-D(P*(JSP)P*(JSP)P*(1W5)P*(1W5)P*(JSP)P*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)70,0266
Polymers70,0266
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_475-x-1,-y+2,z1
Unit cell
Length a, b, c (Å)54.854, 146.480, 46.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

-
Components

#1: Protein reverse transcriptase


Mass: 30023.531 Da / Num. of mol.: 1 / Fragment: N-terminal fragment (UNP residues 683-937)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Gene: gag-pro-pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UN00
#2: DNA chain DNA (5'-D(*CP*TP*TP*(IGU)P*(1WA)P*(1WA)P*(IGU)P*(IGU))-3')


Mass: 2502.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*(JSP)P*(JSP)P*(1W5)P*(1W5)P*(JSP)P*AP*AP*G)-3')


Mass: 2486.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.05 M ADA, pH 6.5, 9% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.65→73.24 Å / Num. obs: 46199 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 24.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Net I/σ(I): 14.7 / Num. measured all: 578693 / Scaling rejects: 215
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.65-1.6811.61.3392610722550.6970.4081.4022.3
9.04-73.2410.30.05835943490.9970.0170.0629.5

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MIK

6mik


Resolution: 1.65→30.46 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 2213 4.8 %
Rwork0.2221 43915 -
obs0.2233 46128 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.37 Å2 / Biso mean: 33.2227 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: final / Resolution: 1.65→30.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 334 0 154 2477
Biso mean---30.28 -
Num. residues----264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.690.37191170.358827192836
1.69-1.730.31421580.304226992857
1.73-1.770.30571410.277826882829
1.77-1.820.29921440.248727082852
1.82-1.870.30981250.24827102835
1.87-1.930.22311210.233927312852
1.93-20.26911310.227227142845
2-2.080.27511240.235727292853
2.08-2.170.26031340.223627352869
2.17-2.290.24231290.218927312860
2.29-2.430.28561460.221827312877
2.43-2.620.2311480.224927532901
2.62-2.880.29271360.242127672903
2.88-3.30.27441490.236727532902
3.3-4.150.21731620.203927882950
4.16-30.460.20071480.193529593107

+
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