[English] 日本語
Yorodumi
- PDB-1k8p: Structure of the Human G-quadruplex reveals a novel topology -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k8p
TitleStructure of the Human G-quadruplex reveals a novel topology
Components5'-D(*(BRU)P*AP*GP*GP*GP*(BRU)P*TP*AP*GP*GP*GP*T)-3'
KeywordsDNA / quadruplex DNA / double chain reversal loop / dimeric quadruplex / Human telomere sequence / G(anti).G(anti).G(anti).G(anti) / parallel stranded
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.4 Å
AuthorsParkinson, G.N. / Lee, M.P.H. / Neidle, S.
Citation
Journal: Nature / Year: 2002
Title: Crystal structure of parallel quadruplexes from human telomeric DNA.
Authors: Parkinson, G.N. / Lee, M.P. / Neidle, S.
#1: Journal: PATENT / Year: 2002
Title: Crystal Structure of G-quadruplex
Authors: Parkinson, G.N. / Lee, M.P.H. / Neidle, S.
History
DepositionOct 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues ...pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _citation.country / _citation.pdbx_database_id_patent ..._citation.country / _citation.pdbx_database_id_patent / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.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.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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*(BRU)P*AP*GP*GP*GP*(BRU)P*TP*AP*GP*GP*GP*T)-3'
B: 5'-D(*(BRU)P*AP*GP*GP*GP*(BRU)P*TP*AP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9085
Polymers7,8062
Non-polymers1013
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.607, 56.607, 40.546
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

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


Mass: 3903.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, KCl, LiCl, MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3LiCl11
4MgCl211
5MPD12
Crystal grow
*PLUS
Temperature: 285 K / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 %ammonium sulfate gradient1reservoir
2500 mMammonium sulfate1drop
350 mM1dropNaCl
450 mM1dropKCl
550 mM1dropLi2SO4
60.5 mMDNA1drop
750 mMpotassium cacodylate1droppH6.5

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2001 / Details: Osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→26 Å / Num. all: 3130 / Num. obs: 2870 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 9.6 / Num. unique all: 294 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 3130 / % possible obs: 99.2 % / Num. measured all: 64877

-
Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→10 Å / σ(F): 0 / Stereochemistry target values: Parkinson et al.
RfactorNum. reflectionSelection details
Rfree0.28 286 Random
Rwork0.189 --
all0.197 3029 -
obs0.193 2572 -
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 498 7 50 555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.016
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_from_restr_planes0.012
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor obs: 0.186 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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