[English] 日本語
Yorodumi
- PDB-1p47: Crystal Structure of tandem Zif268 molecules complexed to DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p47
TitleCrystal Structure of tandem Zif268 molecules complexed to DNA
Components
  • 5'-D(*CP*AP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*A)-3'
  • 5'-D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3'
  • Early growth response protein 1
KeywordsTranscription/DNA / ZINC FINGER / DNA-BINDING PROTEIN / COMPLEX (ZINC FINGER-DNA) / Transcription-DNA COMPLEX
Function / homology
Function and homology information


glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to mycophenolic acid / cellular response to heparin / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to mycophenolic acid / cellular response to heparin / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / cellular response to organic substance / positive regulation of smooth muscle cell migration / skeletal muscle cell differentiation / locomotor rhythm / estrous cycle / T cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / BMP signaling pathway / response to glucose / long-term memory / regulation of neuron apoptotic process / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / regulation of long-term neuronal synaptic plasticity / positive regulation of smooth muscle cell proliferation / circadian regulation of gene expression / response to insulin / cellular response to gamma radiation / negative regulation of canonical Wnt signaling pathway / positive regulation of miRNA transcription / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / sequence-specific DNA binding / response to hypoxia / learning or memory / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / 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 / cytoplasm
Similarity search - Function
Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / 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 / DNA (> 10) / Early growth response protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPeisach, E. / Pabo, C.O.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Constraints for Zinc Finger Linker Design as Inferred from X-ray Crystal Structure of Tandem Zif268-DNA Complexes
Authors: Peisach, E. / Pabo, C.O.
#1: Journal: Structure / Year: 1996
Title: Zif268 protein-DNA complex refined at 1.6A: implications for understanding zinc finger DNA recognition
Authors: Elrod-Erickson, M. / Rould, M.A. / Nekludova, L. / Pabo, C.O.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants.
Authors: Kim, J.S. / Pabo, C.O.
History
DepositionApr 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3'
D: 5'-D(*CP*AP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*A)-3'
A: Early growth response protein 1
B: Early growth response protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,85910
Polymers34,4674
Non-polymers3926
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.629, 70.629, 99.608
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

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


Mass: 6937.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED DNA OLIGO / Keywords: GONUCLEOTIDE BINDING SITE
#2: DNA chain 5'-D(*CP*AP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*A)-3'


Mass: 6573.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED DNA OLIGO / Keywords: GONUCLEOTIDE BINDING SITE
#3: Protein Early growth response protein 1 / EGR-1 / Krox-24 protein / ZIF268 / Nerve growth factor-induced protein A / NGFI-A


Mass: 10478.034 Da / Num. of mol.: 2 / Fragment: residues 333-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: EGR1 OR EGR-1 OR KROX-24 / Plasmid: PZIF89 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: ZINC FINGERS / References: UniProt: P08046
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 4.21 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: bis-tris propane-HCl, sodium chloride, zinc cloride, ammonium acetate, PEG 400, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1bis-tris propane-HCl11
2sodium chloride11
3zinc cloride11
4ammonium acetate11
5PEG 40011
6H2O11
7PEG 40012
8ammonium acetate12
9zinc cloride12
10sodium chloride12
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMBTP1droppH8.0
21.4 mM1dropZnCl2
34-15 %(w/v)PEG4001reservoir
40-200 mM1reservoir
5100 mMBTP1reservoirpH7.0
60.56 mMDNA1drop
7100 mMBTP1droppH8.0
8400 mM1dropNaCl
91
101

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 25748 / Num. obs: 24823 / % possible obs: 90.4 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 4.4 % / Rsym value: 0.047 / Net I/σ(I): 27.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.12 % / Num. unique all: 1243 / Rsym value: 0.405 / % possible all: 43
Reflection
*PLUS
Num. obs: 25748 / Num. measured all: 113508 / Rmerge(I) obs: 0.047

-
Processing

Software
NameVersionClassification
REFMAC5.1.22refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AAY

1aay


Resolution: 2.2→60.86 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.785 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.21 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26743 2429 9.8 %RANDOM
Rwork0.21394 ---
all0.2192 22393 --
obs0.2192 22393 90.4 %-
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 mean: 62.044 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 896 6 100 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0450.0212493
X-RAY DIFFRACTIONr_bond_other_d0.0030.021723
X-RAY DIFFRACTIONr_angle_refined_deg4.4332.3963514
X-RAY DIFFRACTIONr_angle_other_deg1.61634076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9075169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.2150.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.022080
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02367
X-RAY DIFFRACTIONr_nbd_refined0.2440.2518
X-RAY DIFFRACTIONr_nbd_other0.2960.22119
X-RAY DIFFRACTIONr_nbtor_other0.1180.21077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8831.5857
X-RAY DIFFRACTIONr_mcangle_it3.23921392
X-RAY DIFFRACTIONr_scbond_it5.24531636
X-RAY DIFFRACTIONr_scangle_it7.144.52122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.253 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.46 67
Rwork0.376 626
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 60.9 Å / Num. reflection obs: 19964 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.046
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg4.309
X-RAY DIFFRACTIONr_plane_restr0.025

+
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