9DWM image
Deposition Date 2024-10-09
Release Date 2025-01-15
Last Version Date 2025-05-14
Entry Detail
PDB ID:
9DWM
Keywords:
DNA BINDING PROTEIN/DNA/TRANSFERASE
Title:
DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9DWM validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Gene (Uniprot):H3C15, H3C14, H3C13
Chain IDs:A, E
Chain Length:135
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:Q71DI3 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:B, F
Chain Length:102
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62805 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1
Gene (Uniprot):H2AC11, H2AC13, H2AC15, H2AC16, H2AC17
Chain IDs:C, G
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P0C0S8 Pfam ID:PF00125, PF16211
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-C/E/F/G/I
Gene (Uniprot):H2BC4, H2BC6, H2BC7, H2BC8, H2BC10
Chain IDs:D, H
Chain Length:125
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62807 Pfam ID:PF00125
Polymer Type:polydeoxyribonucleotide
Molecule:601 I strand (damaged strand 1)
Chain IDs:I
Chain Length:127
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:601 J strand (non-damaged strand)
Chain IDs:J
Chain Length:147
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:601 K strand (damaged strand 2)
Chain IDs:K
Chain Length:19
Number of Molecules:1
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase beta
Gene (Uniprot):POLB
Chain IDs:L
Chain Length:335
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P06746 Pfam ID:PF14716, PF10391, PF14792, PF14791 EC:2.7.7.7
Ligand Molecules
NA
Primary Citation
DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5
To Be Published ? ? ? (?)
Primary Citation of related structures
9DWM