[English] 日本語
Yorodumi
- PDB-4hiv: Structure of actinomycin D d(ATGCGGCAT) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hiv
TitleStructure of actinomycin D d(ATGCGGCAT) complex
Components
  • ACTINOMYCIN D
  • DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3')
KeywordsDNA/ANTIBIOTIC / Double helix DNA / Nucleotide flipping-out / sharp kink / left-handed twist / CGG tripleat repeat / Neurological disease / DNA-ANTIBIOTIC complex
Function / homologyActinomycin D / : / DNA
Function and homology information
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsLo, Y.S. / Tseng, W.H. / Hou, M.H.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats.
Authors: Lo, Y.S. / Tseng, W.H. / Chuang, C.Y. / Hou, M.H.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references / Derived calculations / Source and taxonomy
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 3.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3')
B: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3')
C: ACTINOMYCIN D
D: ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)8,0954
Polymers8,0954
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.936, 86.936, 49.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-161-

HOH

-
Components

#1: DNA chain DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3')


Mass: 2755.823 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein/peptide ACTINOMYCIN D


Type: Polypeptide / Class: Antibiotic / Mass: 1291.446 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (natural) Streptomyces antibioticus (bacteria) / References: NOR: NOR00228, Actinomycin D
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 40mM sodium cacodylate, 3mM magnesium chloride, 5mM calcium chloride, 10mM spermine, 8% MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9062 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2011
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9062 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 4378 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 54.205
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsDiffraction-ID% possible all
2.6-2.6913.84.111100
2.69-2.813.87.191100
2.8-2.9313.89.861100
2.93-3.0813.917.891100
3.08-3.2813.534.211100
3.28-3.5313.659.91100
3.53-3.8813.254.241100
3.88-4.4412.948.81100
4.44-5.5912.464.6199.7
5.59-3011.390.7198.8

-
Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 2.6→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 181 RANDOM
Rwork0.26 --
obs0.26 4378 -
all-6495 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.299 Å21.151 Å20 Å2
2--1.299 Å20 Å2
3----2.598 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms180 366 0 133 679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004705
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_deg1.408
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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 shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDRfactor Rfree error% reflection obs (%)
2.6-2.720.0940.42X-RAY DIFFRACTION0.0457.4
2.72-2.860.307100.349X-RAY DIFFRACTION0.09715.4
2.86-3.040.431120.302X-RAY DIFFRACTION0.12525.6
3.04-3.280.268310.305X-RAY DIFFRACTION0.04844.2
3.28-3.60.299410.279X-RAY DIFFRACTION0.04762.1
3.6-4.120.329530.303X-RAY DIFFRACTION0.04574.8
4.12-5.190.303850.28X-RAY DIFFRACTION0.03387.1
5.19-25.10.419880.437X-RAY DIFFRACTION0.04596

+
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