[English] 日本語
Yorodumi
- PDB-2i13: Aart, a six finger zinc finger designed to recognize ANN triplets -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i13
TitleAart, a six finger zinc finger designed to recognize ANN triplets
Components
  • 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3'
  • 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3'
  • Aart
KeywordsDNA BINDING PROTEIN/DNA / DNA binding / zinc finger / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


Generic Transcription Pathway / multicellular organism development / spermatogenesis / regulation of gene expression / cell differentiation / DNA binding / nucleus / metal ion binding
Similarity search - Function
SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. ...SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / 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) / Zinc finger and SCAN domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 Å
AuthorsHorton, N.C. / Segal, D.J. / Bhakta, M. / Crotty, J.W. / Barbas III, C.F.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of Aart, a Designed Six-finger Zinc Finger Peptide, Bound to DNA.
Authors: Segal, D.J. / Crotty, J.W. / Bhakta, M.S. / Barbas, C.F. / Horton, N.C.
History
DepositionAug 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / 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_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 999SEQUENCE The protein is a genetically engineered peptide based on mouse transcription factor Zif268

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3'
D: 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3'
E: 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3'
F: 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3'
A: Aart
B: Aart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,07721
Polymers69,9906
Non-polymers1,08815
Water7,512417
1
C: 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3'
D: 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3'
A: Aart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,57111
Polymers34,9953
Non-polymers5778
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3'
F: 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3'
B: Aart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,50610
Polymers34,9953
Non-polymers5117
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.586, 72.054, 74.212
Angle α, β, γ (deg.)75.53, 83.80, 72.67
Int Tables number1
Space group name H-MP1

-
Components

-
DNA chain , 2 types, 4 molecules CEDF

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


Mass: 6875.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid phase synthesis by phosphoramidite chemistry
#2: DNA chain 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3'


Mass: 6630.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid phase synthesis by phosphoramidite chemistry

-
Protein , 1 types, 2 molecules AB

#3: Protein Aart


Mass: 21489.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pMAL fusion / Production host: Escherichia coli (E. coli) / References: UniProt: Q07230

-
Non-polymers , 3 types, 432 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 4000, 400mM NaCl, 100mM Ammonium Acetate, 100mM citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NaCl11
3Ammonium Acetate11
4citrate11
5HOH11
6PEG 400012
7NaCl12
8Ammonium Acetate12
9citrate12
10HOH12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.38, 1.2834, 1.2830, 1.2574
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.381
21.28341
31.2831
41.25741
ReflectionResolution: 1.96→50 Å / Num. all: 51971 / Num. obs: 51971 / % possible obs: 90.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 64.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 37
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3674 / % possible all: 91.3

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.96→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2609 4.6 %Random 5%
Rwork0.203 ---
all0.203 51911 --
obs0.203 51911 90.8 %-
Solvent computationBsol: 48.732 Å2
Displacement parametersBiso mean: 49.346 Å2
Baniso -1Baniso -2Baniso -3
1-0.561 Å20.909 Å23.458 Å2
2--6.672 Å2-0.329 Å2
3----7.233 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 1.96→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 1792 35 417 4534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.015
X-RAY DIFFRACTIONr_angle_refined_deg1.713
X-RAY DIFFRACTIONr_mcbond_it2.4953.5
X-RAY DIFFRACTIONr_scbond_it2.8974
X-RAY DIFFRACTIONr_mcangle_it3.3514
X-RAY DIFFRACTIONr_scangle_it4.0324.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_plus_finger.paramprotein_plus_finger.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5gol.pargol.par

+
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://pdbjlvh1.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