[English] 日本語
Yorodumi
- PDB-8woh: human dsDNA sensor CCDC25 complexed with 18bp DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8woh
Titlehuman dsDNA sensor CCDC25 complexed with 18bp DNA
Components
  • (18bp DNA) x 2
  • Coiled-coil domain-containing protein 25
KeywordsDNA BINDING PROTEIN / dsDNA / sensor / complex / NET DNA
Function / homology
Function and homology information


positive regulation of cell motility / endomembrane system / DNA binding / plasma membrane
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWen, Y. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: human dsDNA sensor CCDC25 complexed with 18bp DNA
Authors: Wen, Y. / Wu, B.X.
History
DepositionOct 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 18bp DNA
D: 18bp DNA
B: Coiled-coil domain-containing protein 25
A: Coiled-coil domain-containing protein 25


Theoretical massNumber of molelcules
Total (without water)57,5854
Polymers57,5854
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.660, 77.964, 99.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid -4 through 176)
d_1ens_2(chain "C" and (resid 1 through 4 or resid 6 through 15))
d_2ens_2(chain "D" and ((resid 2 and (name O5" or name...

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1HISHISLYSLYSAD-4 - 1765 - 185
d_2ens_1HISHISLYSLYSBC-4 - 1765 - 185
d_1ens_2DGDGDCDCCA1 - 43 - 6
d_2ens_2DGDGDCDCDB2 - 54 - 7

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.93138678649, -0.0499627181067, -0.360586162729), (0.009053451923, -0.993409437331, 0.114261650744), (-0.363918519672, 0.103157242217, 0.925700758571)28.0942769596, -3.95591218101, 5.32701816273
2given(-0.824626175586, -0.564060364869, 0.0427501499786), (-0.564824544424, 0.816877345875, -0.11698134814), (0.0310629128644, -0.120612215717, -0.992213580266)-34.1157498335, -9.45650339731, 2.76575437304

-
Components

#1: DNA chain 18bp DNA


Mass: 5827.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain 18bp DNA


Mass: 5818.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Coiled-coil domain-containing protein 25


Mass: 22969.258 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 BL21(DE3) (bacteria) / References: UniProt: Q86WR0
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 5.0, 10% MPD pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 9651 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 130.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 15.4
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.274 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1376 / CC1/2: 0.595 / Rpim(I) all: 0.498 / Rrim(I) all: 1.37 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 3.2→28.2 Å / SU ML: 0.4167 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.6506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2912 473 4.92 %
Rwork0.2299 9141 -
obs0.233 9614 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 131.98 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 650 0 0 3686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113824
X-RAY DIFFRACTIONf_angle_d1.28645267
X-RAY DIFFRACTIONf_chiral_restr0.0663562
X-RAY DIFFRACTIONf_plane_restr0.0148563
X-RAY DIFFRACTIONf_dihedral_angle_d25.8946707
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DAX-RAY DIFFRACTIONTorsion NCS2.44179135855
ens_2d_2ACX-RAY DIFFRACTIONTorsion NCS2.22460808388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.660.36591520.30092982X-RAY DIFFRACTION99.94
3.66-4.610.33811450.28763031X-RAY DIFFRACTION99.97
4.61-28.20.2641760.1953128X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: 10.8226707652 Å / Origin y: -2.18187519225 Å / Origin z: -14.3332652664 Å
111213212223313233
T0.638039715788 Å2-0.0876610122999 Å2-0.0183158710932 Å2-0.592898468724 Å20.0460075476615 Å2--0.596144656769 Å2
L2.90362601912 °2-0.6475538572 °2-0.737993350264 °2-2.64093325334 °20.956864308097 °2--2.33438299044 °2
S0.0246891948845 Å °0.0591541604963 Å °0.599490426847 Å °-0.0015627522576 Å °0.133620752324 Å °-0.0635143911895 Å °-0.203553584772 Å °0.0235414404513 Å °-0.148909933137 Å °
Refinement TLS groupSelection details: all

+
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