[English] 日本語
Yorodumi
- PDB-7eof: Structure of CCDC25-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eof
TitleStructure of CCDC25-DNA complex
Components
  • Coiled-coil domain-containing protein 25
  • DNA (5'-D(*CP*AP*GP*AP*TP*CP*AP*CP*TP*AP*GP*TP*AP*GP*AP*T)-3')
  • DNA (5'-D(*GP*AP*TP*CP*TP*AP*CP*TP*AP*GP*TP*GP*AP*TP*CP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / CCDC25 / NETs / NET-DNA binding / nucleosome binding / cancer / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of cell motility / plasma membrane => GO:0005886 / endomembrane system / DNA binding
Similarity search - Function
Jlp2/Ccd25 / NFACT, RNA-binding domain / NFACT protein RNA binding domain
Similarity search - Domain/homology
DNA / DNA (> 10) / Coiled-coil domain-containing protein 25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.733 Å
AuthorsLiu, Y.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of CCDC25-DNA complex
Authors: Liu, Y.R.
History
DepositionApr 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(*GP*AP*TP*CP*TP*AP*CP*TP*AP*GP*TP*GP*AP*TP*CP*T)-3')
D: DNA (5'-D(*CP*AP*GP*AP*TP*CP*AP*CP*TP*AP*GP*TP*AP*GP*AP*T)-3')
B: Coiled-coil domain-containing protein 25
A: Coiled-coil domain-containing protein 25


Theoretical massNumber of molelcules
Total (without water)57,8794
Polymers57,8794
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.028, 74.795, 103.618
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 4888.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*CP*AP*GP*AP*TP*CP*AP*CP*TP*AP*GP*TP*AP*GP*AP*T)-3')


Mass: 4906.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Coiled-coil domain-containing protein 25


Mass: 24042.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WR0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M MES, 10% isopropanol, pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.73→40 Å / Num. obs: 13026 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 45.19 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 19.9
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.987 / Num. unique obs: 1182

-
Processing

Software
NameVersionClassification
PHENIX1.10-2155refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: de novo predition

Resolution: 2.733→35.177 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 663 5.09 %
Rwork0.2294 12363 -
obs0.2312 13026 82.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.94 Å2 / Biso mean: 62.5144 Å2 / Biso min: 19.32 Å2
Refinement stepCycle: final / Resolution: 2.733→35.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 650 0 0 3611
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033741
X-RAY DIFFRACTIONf_angle_d0.5435157
X-RAY DIFFRACTIONf_chiral_restr0.04557
X-RAY DIFFRACTIONf_plane_restr0.003549
X-RAY DIFFRACTIONf_dihedral_angle_d20.8342187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.733-2.94360.3994370.339282128
2.9436-3.23960.36581390.2921247184
3.2396-3.7080.28541470.24312969100
3.708-4.66990.21891870.20222970100
4.6699-35.1770.23991530.21313132100
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)
12.55660.4955-0.3931.56770.78424.20270.81830.5317-0.11830.74220.03120.22310.28851.1207-0.41.3274-0.14410.22811.09440.00990.325620.829236.746952.2327
21.7256-0.0887-0.18350.77711.82865.00960.67410.6396-0.22360.5244-0.37770.16080.47380.8278-0.16841.0344-0.0271-0.0280.960.08160.392518.209937.051549.4003
34.73480.68210.00433.7991-1.77261.8323-0.00170.014-0.1472-0.18440.35740.5549-0.0912-0.2611-0.28290.2009-0.03420.00420.33520.09320.3024-21.672750.588834.8058
42.69990.0071-0.99591.50570.43193.5324-0.03840.0867-1.01640.00350.2601-0.03320.49240.0769-0.09970.3047-0.0349-0.07870.26390.03630.8278-11.876227.712931.5061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 1 through 16)C1 - 16
2X-RAY DIFFRACTION2(chain 'D' and resid 1 through 16)D1 - 16
3X-RAY DIFFRACTION3(chain 'B' and resid 1 through 181)B1 - 181
4X-RAY DIFFRACTION4(chain 'A' and resid 1 through 180)A1 - 180

+
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://pdbjlvh1.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