[English] 日本語
Yorodumi
- PDB-2fd0: HIV-1 DIS kissing-loop in complex with lividomycin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fd0
TitleHIV-1 DIS kissing-loop in complex with lividomycin
ComponentsHIV-1 DIS RNA
KeywordsRNA / HIV-1 / aminoglycoside / antibiotics
Function / homology: / Chem-LIV / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEnnifar, E. / Paillart, J.C. / Marquet, R. / Dumas, P.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell.
Authors: Ennifar, E. / Paillart, J.C. / Bodlenner, A. / Walter, P. / Weibel, J.-M. / Aubertin, A.-M. / Pale, P. / Dumas, P. / Marquet, R.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 DIS RNA
B: HIV-1 DIS RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6469
Polymers14,9312
Non-polymers1,7157
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.137, 115.335, 95.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-90-

K

21B-2032-

HOH

-
Components

#1: RNA chain HIV-1 DIS RNA


Mass: 7465.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in subtype F HIV-1
#2: Chemical ChemComp-LIV / (2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R ,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMET HYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL / LIVIDOMYCIN A / O-2-AMINO-2,3-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL-(1,4)-O-[BETA-D-MANNOPYRANOSYL-(1,4)-O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPY RANOSYL-(1,3)-BETA-D-RIBOFURANOSYL-(1,5)-2-DEOXY-D-STREPTAMINE / Lividomycin


Mass: 761.770 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H55N5O18 / Comment: antibiotic*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MPD, KCl, MgCl2, Na Cacodylate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 310K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91946 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91946 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 26564 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 33.8 Å2 / Rsym value: 0.061 / Net I/σ(I): 26.4
Reflection shellHighest resolution: 1.8 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.273 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FCY

2fcy


Resolution: 1.8→9.94 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1031896.48 / Data cutoff high rms absF: 1031896.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1542 5.8 %RANDOM
Rwork0.245 ---
obs0.245 26457 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2637 Å2 / ksol: 0.4016 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--2.32 Å20 Å2
3----2.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.8→9.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 980 109 90 1179
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d8.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 97 2.2 %
Rwork0.357 4233 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramwater.top
X-RAY DIFFRACTION2luc.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4bru_rep.parambru.top
X-RAY DIFFRACTION5lividomycin.paramlividomycin.top

+
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