[English] 日本語
Yorodumi
- PDB-6ksf: Crystal Structure of ALKBH1 bound to 21-mer DNA bulge -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ksf
TitleCrystal Structure of ALKBH1 bound to 21-mer DNA bulge
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 1
  • DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DCP*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3')
  • DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DTP*DCP*DAP*DGP*DC)-3')
KeywordsGENE REGULATION / DNA methylation / complex / demethylase
Function / homology
Function and homology information


regulation of translational initiation by tRNA modification / positive regulation of gene expression, epigenetic / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA wobble cytosine modification / tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase ...regulation of translational initiation by tRNA modification / positive regulation of gene expression, epigenetic / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA wobble cytosine modification / tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / RNA repair / 2-oxoglutarate-dependent dioxygenase activity / regulation of translational initiation / chemoattractant activity / developmental growth / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / placenta development / neuron migration / euchromatin / ferrous iron binding / neuron projection development / regulation of gene expression / in utero embryonic development / negative regulation of neuron apoptotic process / tRNA binding / cell differentiation / DNA repair / endoplasmic reticulum / mitochondrion / nucleoplasm
Similarity search - Function
Alkylated DNA repair protein AlkB / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
SUCCINIC ACID / propane-1-thiol / DNA / DNA (> 10) / Nucleic acid dioxygenase ALKBH1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, H. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31725014 China
CitationJournal: Cell Res. / Year: 2020
Title: Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA.
Authors: Zhang, M. / Yang, S. / Nelakanti, R. / Zhao, W. / Liu, G. / Li, Z. / Liu, X. / Wu, T. / Xiao, A. / Li, H.
History
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 1
B: DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DCP*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3')
C: DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DTP*DCP*DAP*DGP*DC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1097
Polymers51,8443
Non-polymers2654
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-39 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.482, 67.482, 263.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-402-

CL

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 1


Mass: 38087.344 Da / Num. of mol.: 1 / Fragment: BRD4-Bromo2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ALKBH1 / Plasmid: pRSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CB42*PLUS

-
DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DCP*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3')


Mass: 7378.727 Da / Num. of mol.: 1 / Fragment: histone H2A.Z peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DTP*DCP*DAP*DGP*DC)-3')


Mass: 6378.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 67 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Chemical ChemComp-XL3 / propane-1-thiol


Mass: 76.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M NaCl, 0.1 M phosphate citrate, pH 4.2,10% PEG3000

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2019 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24642 / % possible obs: 98.8 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.027 / Rrim(I) all: 0.084 / Χ2: 0.779 / Net I/σ(I): 7.1 / Num. measured all: 202846
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.448.60.71611830.8960.2360.7560.43397.8
2.44-2.498.40.63811920.8750.2110.6740.4698.3
2.49-2.538.40.611880.9040.20.6350.43898.3
2.53-2.598.20.52612010.9090.1770.5570.4598.5
2.59-2.648.20.42112020.9420.1430.4470.46698.4
2.64-2.77.70.32612040.9590.1140.3460.47998.9
2.7-2.778.40.31411890.9690.1060.3320.48798.8
2.77-2.858.60.25511990.9740.0840.270.49697.6
2.85-2.938.40.20612310.980.0690.2180.5199.4
2.93-3.028.50.15711990.9880.0530.1660.57899.3
3.02-3.138.30.1312230.9910.0440.1380.61799.3
3.13-3.267.90.09312340.9960.0320.0990.77699.4
3.26-3.418.20.07612290.9970.0250.080.9498.8
3.41-3.588.50.07412320.9960.0250.0780.99899.5
3.58-3.818.50.06712350.9970.0230.0721.00599.3
3.81-4.180.06112460.9970.0220.0661.18999.3
4.1-4.528.30.05712770.9980.020.061.28999.4
4.52-5.178.30.05212730.9980.0180.0551.28999.3
5.17-6.5180.05212950.9980.0190.0561.19298.8
6.51-507.30.04714100.9980.0180.0511.497.1

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IMC

6imc


Resolution: 2.4→32.888 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 1203 4.9 %0
Rwork0.2281 ---
obs0.2302 24541 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.33 Å2 / Biso mean: 57.3443 Å2 / Biso min: 24.68 Å2
Refinement stepCycle: final / Resolution: 2.4→32.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 912 14 63 3661
Biso mean--51.28 48.28 -
Num. residues----380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.4980.30841350.2885250598
2.498-2.61170.36791510.2882249698
2.6117-2.74930.30741340.2739252099
2.7493-2.92140.33651280.2949255699
2.9214-3.14680.31481280.2687256799
3.1468-3.46320.25991260.2373259499
3.4632-3.96360.26741380.2281263499
3.9636-4.99090.241090.1943267299
4.9909-32.8880.24431540.199279498

+
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