[English] 日本語
Yorodumi
- PDB-2wbu: CRYSTAL STRUCTURE OF THE ZINC FINGER DOMAIN OF KLF4 BOUND TO ITS ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wbu
TitleCRYSTAL STRUCTURE OF THE ZINC FINGER DOMAIN OF KLF4 BOUND TO ITS TARGET DNA
Components
  • 5'-D(*DGP*DAP*DGP*DGP*DCP*DGP*DTP* DGP*DGP*DC)-3'
  • 5'-D(*DGP*DCP*DCP*DAP*DCP*DGP*DCP* DCP*DTP*DC)-3'
  • KRUEPPEL-LIKE FACTOR 4
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / NUCLEUS / ACTIVATOR / DNA-BINDING / ZINC-FINGER / TRANSCRIPTION / METAL-BINDING / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


negative regulation of leukocyte adhesion to arterial endothelial cell / regulation of blastocyst development / cellular response to cycloheximide / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of response to cytokine stimulus / post-embryonic camera-type eye development / positive regulation of hemoglobin biosynthetic process / negative regulation of muscle hyperplasia / epidermal cell differentiation ...negative regulation of leukocyte adhesion to arterial endothelial cell / regulation of blastocyst development / cellular response to cycloheximide / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of response to cytokine stimulus / post-embryonic camera-type eye development / positive regulation of hemoglobin biosynthetic process / negative regulation of muscle hyperplasia / epidermal cell differentiation / negative regulation of heterotypic cell-cell adhesion / epidermis morphogenesis / cellular response to peptide / phosphatidylinositol 3-kinase regulator activity / cellular response to laminar fluid shear stress / negative regulation of interleukin-8 production / regulation of axon regeneration / post-embryonic hemopoiesis / negative regulation of cell migration involved in sprouting angiogenesis / defense response to tumor cell / stem cell population maintenance / negative regulation of G1/S transition of mitotic cell cycle / lncRNA binding / positive regulation of sprouting angiogenesis / fat cell differentiation / positive regulation of telomere maintenance / regulation of cell differentiation / somatic stem cell population maintenance / epidermis development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / establishment of skin barrier / canonical Wnt signaling pathway / response to retinoic acid / cellular response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / epithelial cell differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of cell migration / negative regulation of angiogenesis / transcription coregulator binding / cellular response to leukemia inhibitory factor / negative regulation of smooth muscle cell proliferation / promoter-specific chromatin binding / euchromatin / negative regulation of ERK1 and ERK2 cascade / beta-catenin binding / cellular response to growth factor stimulus / chromatin DNA binding / positive regulation of miRNA transcription / histone deacetylase binding / cellular response to hydrogen peroxide / positive regulation of nitric oxide biosynthetic process / regulation of cell population proliferation / microtubule cytoskeleton / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / gene expression / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Krueppel-like factor 4
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSchuetz, A. / Zocher, G. / Carstanjen, D. / Heinemann, U.
CitationJournal: Cell.Mol.Life Sci. / Year: 2011
Title: The Structure of the Klf4 DNA-Binding Domain Links to Self-Renewal and Macrophage Differentiation.
Authors: Schuetz, A. / Nana, D. / Rose, C. / Zocher, G. / Milanovic, M. / Koenigsmann, J. / Blasig, R. / Heinemann, U. / Carstanjen, D.
History
DepositionMar 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 5, 2011Group: Database references / Source and taxonomy / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KRUEPPEL-LIKE FACTOR 4
B: 5'-D(*DGP*DAP*DGP*DGP*DCP*DGP*DTP* DGP*DGP*DC)-3'
C: 5'-D(*DGP*DCP*DCP*DAP*DCP*DGP*DCP* DCP*DTP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8616
Polymers16,6653
Non-polymers1963
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-13 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.275, 50.275, 131.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein KRUEPPEL-LIKE FACTOR 4 / GUT-ENRICHED KRUEPPEL-LIKE FACTOR / EPITHELIAL ZINC FINGER PROTEIN EZF


Mass: 10572.937 Da / Num. of mol.: 1 / Fragment: RESIDUES 396-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PQLINKH / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q60793
#2: DNA chain 5'-D(*DGP*DAP*DGP*DGP*DCP*DGP*DTP* DGP*DGP*DC)-3'


Mass: 3126.040 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*DGP*DCP*DCP*DAP*DCP*DGP*DCP* DCP*DTP*DC)-3'


Mass: 2965.945 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.49 Å3/Da / Density % sol: 55.98 % / Description: NONE
Crystal growpH: 8.5
Details: 27 % PEG 3350, 0.2 M NAACETATE, 0.1 M TRIS-HCL PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.5→46.93 Å / Num. obs: 6277 / % possible obs: 99.5 % / Observed criterion σ(I): 4.2 / Redundancy: 8.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.4
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 4.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WBS

2wbs


Resolution: 2.5→46.93 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 21.518 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 503 8 %RANDOM
Rwork0.214 ---
obs0.22 5773 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.05 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å20 Å2
2--2.22 Å20 Å2
3----4.45 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms708 404 3 21 1136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211184
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3552.3461676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.698584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39920.51339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.0515123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.21158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02784
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.551.5421
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.082670
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93763
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6634.51006
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 36 -
Rwork0.304 410 -
obs--100 %
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)
15.1011-2.27542.779313.42051.58768.05360.08670.02-0.5257-0.3828-0.05830.45650.0138-0.5908-0.02840.0491-0.03690.03770.1102-0.02880.2204-25.85-13.9381.297
24.05130.4908-1.02592.78162.51295.14360.1585-0.2357-0.09830.2245-0.0161-0.53960.09490.2879-0.14240.0724-0.0121-0.01060.0626-0.02490.324-9.431-3.18610.501
35.3605-4.9505-2.90410.04314.99194.1332-0.3096-0.37940.56470.38530.4469-0.4012-0.04770.0219-0.13730.0980.06690.00210.1468-0.06610.2251-22.38812.39621.356
42.5304-0.07821.37223.1149-2.20310.72150.018-0.0191-0.12540.00030.10910.06910.0542-0.3137-0.12720.00880.00560.00270.0243-0.00850.0354-24.477-1.44910.083
52.010.0281-3.93940.7135-0.349812.159-0.01950.06760.011-0.0228-0.14660.119-0.0004-0.30750.16610.0172-0.0104-0.01370.0678-0.02280.0463-24.692-0.07910.644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A399 - 424
2X-RAY DIFFRACTION2A425 - 455
3X-RAY DIFFRACTION3A456 - 483
4X-RAY DIFFRACTION4B1 - 10
5X-RAY DIFFRACTION5C1 - 10

+
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