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- PDB-1llm: Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA -

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Basic information

Entry
Database: PDB / ID: 1llm
TitleCrystal Structure of a Zif23-GCN4 Chimera Bound to DNA
Components
  • 5'-D(*TP*CP*CP*CP*AP*CP*GP*CP*GP*TP*GP*GP*G)-3'
  • chimera of Zif23-GCN4
KeywordsTRANSCRIPTION/DNA / Dimerization / DNA recognition / leucine zipper / structure-based design / zinc fingers / 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 / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / 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 / TFIID-class transcription factor complex binding / estrous cycle / amino acid biosynthetic process / T cell differentiation / positive regulation of transcription initiation by RNA polymerase II / long-term memory / positive regulation of RNA polymerase II transcription preinitiation complex assembly / RNA polymerase II core promoter sequence-specific DNA binding / BMP signaling pathway / response to glucose / regulation of neuron apoptotic process / positive regulation of chemokine production / cellular response to amino acid starvation / 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 / negative regulation of canonical Wnt signaling pathway / circadian regulation of gene expression / response to insulin / cellular response to gamma radiation / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / 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 / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / response to hypoxia / learning or memory / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / 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 / identical protein binding / 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 / Basic region leucine zipper / Classic Zinc Finger / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily ...Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Basic region leucine zipper / Classic Zinc Finger / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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) / General control transcription factor GCN4 / Early growth response protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsWolfe, S.A. / Grant, R.A. / Pabo, C.O.
Citation
Journal: Biochemistry / Year: 2003
Title: Structure of a designed dimeric zinc finger protein bound to DNA.
Authors: Wolfe, S.A. / Grant, R.A. / Pabo, C.O.
#1: Journal: Structure / Year: 2000
Title: Combining Structure-based Design with Phage Display to Create New Cys(2)His(2) Zinc Finger Dimers
Authors: Wolfe, S.A. / Ramm, E.I. / Pabo, C.O.
History
DepositionApr 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence Residues C 151-159 and D 251-259 are linkers between the ZIF23 and GCN4.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*CP*CP*CP*AP*CP*GP*CP*GP*TP*GP*GP*G)-3'
B: 5'-D(*TP*CP*CP*CP*AP*CP*GP*CP*GP*TP*GP*GP*G)-3'
C: chimera of Zif23-GCN4
D: chimera of Zif23-GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3058
Polymers29,0444
Non-polymers2624
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.398, 87.398, 118.693
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 3968.573 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein chimera of Zif23-GCN4


Mass: 10553.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The Zif23 section of the chimera is residues 2-50 and is derived from Zif268. The GCN4 section is residues 60-88.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Genus: Mus, Saccharomyces / Species: , / Strain: , / Plasmid: Pet21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 PLysS / References: UniProt: P08046, UniProt: P03069
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 72.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: bis-tris propane, magnesium chloride, ammonium acetate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1bis-tris propane11
2MgCl211
3ammonium acetate11
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.9 mMprotein1drop
280 mMBis-Tris propane1droppH8.0
30.056 mMDNA1drop
410 mMBis-Tris propane1droppH8.0
51 mM1dropMgCl2
6600 mM1reservoirNH4OAc

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11331
21331
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.54
SYNCHROTRONNSLS X4A20.9999
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJun 8, 2000
ADSC QUANTUM 42CCDMar 24, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1yale mirrorsSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.99991
ReflectionResolution: 1.5→20 Å / Num. all: 83074 / Num. obs: 77251 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 17.8 Å2 / Rsym value: 0.095
Reflection shellResolution: 1.5→1.59 Å / % possible all: 97.9
Reflection
*PLUS
Num. obs: 83074 / % possible obs: 98.9 % / Num. measured all: 1187929 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 1.5→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: xplor topology files
RfactorNum. reflection% reflectionSelection details
Rfree0.234 7807 10.1 %RANDOM
Rwork0.216 ---
all0.226 83074 --
obs-77251 91.7 %-
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 526 4 312 2323
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.62
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.031.5
X-RAY DIFFRACTIONx_mcangle_it1.72
X-RAY DIFFRACTIONx_scbond_it1.92
X-RAY DIFFRACTIONx_scangle_it32.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 1130 10.2 %
Rwork0.294 9937 -
obs--79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.64
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.62

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