[English] 日本語
Yorodumi
- PDB-3qmc: Structural Basis of Selective Binding of Nonmethylated CpG Island... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qmc
TitleStructural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of CFP1
Components
  • 5'-D(*GP*CP*CP*AP*CP*CP*GP*CP*TP*GP*GP*C)-3'
  • 5'-D(*GP*CP*CP*AP*GP*CP*GP*GP*TP*GP*GP*C)-3'
  • CpG-binding protein
KeywordsDNA BINDING PROTEIN/DNA / Structural Genomics Consortium / SGC / CXXC-type Zn finger / DNA binding / unmethylated CpG motifs / nucleus speckle / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


unmethylated CpG binding / XBP1(S) activates chaperone genes / Set1C/COMPASS complex / histone H3K4me3 reader activity / Formation of WDR5-containing histone-modifying complexes / : / histone methyltransferase complex / cis-regulatory region sequence-specific DNA binding / nuclear matrix / nuclear speck ...unmethylated CpG binding / XBP1(S) activates chaperone genes / Set1C/COMPASS complex / histone H3K4me3 reader activity / Formation of WDR5-containing histone-modifying complexes / : / histone methyltransferase complex / cis-regulatory region sequence-specific DNA binding / nuclear matrix / nuclear speck / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
CpG binding protein, C-terminal / CpG binding protein C-terminal domain / Spp1/CFP1 / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...CpG binding protein, C-terminal / CpG binding protein C-terminal domain / Spp1/CFP1 / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / CXXC-type zinc finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLam, R. / Xu, C. / Bian, C.B. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2011
Title: The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain.
Authors: Xu, C. / Bian, C. / Lam, R. / Dong, A. / Min, J.
History
DepositionFeb 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CpG-binding protein
B: 5'-D(*GP*CP*CP*AP*CP*CP*GP*CP*TP*GP*GP*C)-3'
C: 5'-D(*GP*CP*CP*AP*GP*CP*GP*GP*TP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9885
Polymers16,8573
Non-polymers1312
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-13 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.545, 75.016, 126.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein CpG-binding protein / CXXC-type zinc finger protein 1 / PHD finger and CXXC domain-containing protein 1


Mass: 9527.962 Da / Num. of mol.: 1 / Fragment: CXXC-type Zn finger, residues 161-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXXC1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q9P0U4
#2: DNA chain 5'-D(*GP*CP*CP*AP*CP*CP*GP*CP*TP*GP*GP*C)-3'


Mass: 3624.356 Da / Num. of mol.: 1 / Fragment: DNA (Nonmethylated CpG Island) / Source method: obtained synthetically
Details: DNA was purchased from Integrated DNA Technologies, Inc.
#3: DNA chain 5'-D(*GP*CP*CP*AP*GP*CP*GP*GP*TP*GP*GP*C)-3'


Mass: 3704.404 Da / Num. of mol.: 1 / Fragment: DNA (Nonmethylated CpG Island) / Source method: obtained synthetically
Details: DNA was purchased from Integrated DNA Technologies, Inc.
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2M CaCl2, 28% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2010
Details: Rosenbaum-Rock high-resolution double-crystal monochromator
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 8874 / % possible obs: 100 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.067 / Χ2: 1.089 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.188.50.4938670.944100
2.18-2.268.90.4238630.949100
2.26-2.378.90.318820.962100
2.37-2.498.90.228500.968100
2.49-2.658.90.1448791.013100
2.65-2.858.90.1098701.064100
2.85-3.148.80.0739071.102100
3.14-3.598.80.0458701.039100
3.59-4.528.60.059171.088100
4.52-5080.049691.76499.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.11 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å28.29 Å
Translation3.5 Å28.29 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
EPICS-basedbeamline controldata collection
dataacquisition systemsdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3QMB

3qmb


Resolution: 2.1→37.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 11.738 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 418 4.7 %RANDOM
Rwork0.2142 ---
obs0.2159 8842 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 125.73 Å2 / Biso mean: 53.3165 Å2 / Biso min: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms412 486 2 22 922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021969
X-RAY DIFFRACTIONr_angle_refined_deg1.6052.5771398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.341554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12319.56523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.461583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2181510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02582
X-RAY DIFFRACTIONr_mcbond_it0.5481.5264
X-RAY DIFFRACTIONr_mcangle_it0.9812413
X-RAY DIFFRACTIONr_scbond_it1.6443705
X-RAY DIFFRACTIONr_scangle_it2.614.5984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1540.275250.24257863594.961
2.154-2.2130.292460.231581627100
2.213-2.2770.267260.23587613100
2.277-2.3460.28320.236560592100
2.346-2.4230.342250.22853456099.821
2.423-2.5080.293220.254554576100
2.508-2.6020.265200.244500520100
2.602-2.7080.327190.245517536100
2.708-2.8270.282200.273473493100
2.827-2.9650.386200.288448468100
2.965-3.1240.203200.244457477100
3.124-3.3120.273210.189406427100
3.312-3.5390.203250.198374399100
3.539-3.8190.18170.183374391100
3.819-4.1790.189260.172325351100
4.179-4.6660.22590.166315324100
4.666-5.3730.333180.181282300100
5.373-6.5480.121130.196236249100
6.548-9.1220.32880.222192200100
9.122-37.5080.24960.242131137100
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)
14.13150.18261.16191.641.41556.24650.0664-0.0727-0.06770.06350.1555-0.02320.2242-0.0727-0.22190.0843-0.042-0.02480.2360.03010.0621-4.294-11.05221.881
26.47157.0417-0.128723.53953.3867.60450.7173-0.4545-0.318-0.0375-1.0693-0.20210.4846-0.26680.3520.4755-0.158-0.08670.30440.05390.1713-4.777-11.9188.643
33.79453.8902-0.664310.8017-1.7294.22950.0106-0.3801-0.3964-0.929-0.2203-0.50040.0408-0.23540.20970.2735-0.1088-0.01490.18910.03720.1754-3.767-12.6467.784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999

+
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