[English] 日本語
Yorodumi
- PDB-6es2: Structure of CDX2-DNA(CAA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6es2
TitleStructure of CDX2-DNA(CAA)
Components
  • DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')
  • Homeobox protein CDX-2
KeywordsTRANSCRIPTION / homeodomain transcription factor / CDX2-DNA complex
Function / homology
Function and homology information


intestinal epithelial cell differentiation / regulation of somitogenesis / trophectodermal cell differentiation / labyrinthine layer development / establishment or maintenance of epithelial cell apical/basal polarity / methyl-CpG binding / anterior/posterior axis specification / endosome to lysosome transport / blood vessel development / somatic stem cell population maintenance ...intestinal epithelial cell differentiation / regulation of somitogenesis / trophectodermal cell differentiation / labyrinthine layer development / establishment or maintenance of epithelial cell apical/basal polarity / methyl-CpG binding / anterior/posterior axis specification / endosome to lysosome transport / blood vessel development / somatic stem cell population maintenance / transcription repressor complex / condensed nuclear chromosome / stem cell differentiation / positive regulation of cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Caudal-like activation domain / : / Caudal like protein activation region / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...Caudal-like activation domain / : / Caudal like protein activation region / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein CDX-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMorgunova, E. / Yin, Y. / Jolma, A. / Popov, A. / Taipale, J.
CitationJournal: Elife / Year: 2018
Title: Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.
Authors: Morgunova, E. / Yin, Y. / Das, P.K. / Jolma, A. / Zhu, F. / Popov, A. / Xu, Y. / Nilsson, L. / Taipale, J.
History
DepositionOct 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')
K: Homeobox protein CDX-2
B: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')
L: Homeobox protein CDX-2
D: DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
E: DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)39,8536
Polymers39,8536
Non-polymers00
Water18010
1
A: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')
K: Homeobox protein CDX-2
D: DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)19,9263
Polymers19,9263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-25 kcal/mol
Surface area11260 Å2
MethodPISA
2
B: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')
L: Homeobox protein CDX-2
E: DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)19,9263
Polymers19,9263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-24 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.248, 46.695, 128.634
Angle α, β, γ (deg.)90.000, 101.400, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12K
22L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 36
2010B1 - 36
1020K187 - 254
2020L187 - 254

NCS ensembles :
ID
1
2

-
Components

#1: DNA chain DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')


Mass: 5454.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Homeobox protein CDX-2 / / CDX-3 / Caudal-type homeobox protein 2


Mass: 8896.251 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDX2, CDX3 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / References: UniProt: Q99626
#3: DNA chain DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Mass: 5575.672 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 27 % PME 5000, 0.15M potassium chloride, 0.1M magnesium chloride, 8% PEG 400, 0.05M TRIS buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.95→66.19 Å / Num. obs: 8494 / % possible obs: 96.6 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.051 / Rrim(I) all: 0.093 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.95-3.133.20.8312640.6110.5390.99390.5
8.86-55.962.80.0383410.9980.0270.04797.4

-
Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTY

5lty


Resolution: 2.95→66.19 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 53.863 / SU ML: 0.427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.431
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 418 4.9 %RANDOM
Rwork0.2085 ---
obs0.2103 8076 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 204.74 Å2 / Biso mean: 98.684 Å2 / Biso min: 57.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-3.27 Å2
2--0.01 Å20 Å2
3---0.63 Å2
Refinement stepCycle: final / Resolution: 2.95→66.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 1476 0 10 2722
Biso mean---69.9 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0142915
X-RAY DIFFRACTIONr_bond_other_d0.0030.022045
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.4844220
X-RAY DIFFRACTIONr_angle_other_deg1.48834781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21722.63276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.91515277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0841519
X-RAY DIFFRACTIONr_chiral_restr0.1180.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02631
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A7114
12B7114
21K4658
22L4658
LS refinement shellResolution: 2.953→3.029 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.594 30 -
Rwork0.447 469 -
all-499 -
obs--80.23 %
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)
15.0269-3.3912-1.1452.74910.36451.72330.16710.83080.3599-0.3666-0.3174-0.2572-0.1052-0.40620.15030.70570.1852-0.08520.4404-0.03150.771-16.5746-20.3249-20.5073
21.921.0674-1.04223.75-0.22634.55020.2044-0.1166-0.0796-0.1674-0.3160.06410.3293-0.05780.11160.26670.1741-0.09340.3015-0.07080.6783-14.4199-24.5005-8.6993
35.3952.56130.00261.3731-0.18541.60780.0893-0.7146-0.28240.303-0.2761-0.08870.1248-0.41390.18680.7414-0.20420.08770.4143-0.0170.7842-17.1787-21.894419.9231
42.2356-1.7871-0.32881.70230.58081.48350.02910.2182-0.11530.1497-0.28160.1651-0.19560.06190.25260.2421-0.15360.01050.1316-0.09220.5415-15.1249-17.37838.3954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION1D19 - 36
3X-RAY DIFFRACTION2K187 - 256
4X-RAY DIFFRACTION3B1 - 18
5X-RAY DIFFRACTION3E19 - 36
6X-RAY DIFFRACTION4L186 - 255

+
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