Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment
Ma, Z., Davey, C.A.To be published.
Experimental Data Snapshot
Starting Model: experimental
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wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Histone H3.1 | A [auth AAA], E [auth EEE], K [auth KKK], O [auth OOO] | 98 | Homo sapiens | Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB... | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431 | |||||
PHAROS:  P68431 GTEx:  ENSG00000197409  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P68431 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Histone H4 | B [auth BBB], F [auth FFF], L [auth LLL], P [auth PPP] | 79 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for A0A8C1JQV0 (Cyprinus carpio) Explore A0A8C1JQV0  Go to UniProtKB:  A0A8C1JQV0 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A8C1JQV0 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Histone H2A | C [auth CCC], M [auth MMM] | 105 | Homo sapiens | Mutation(s): 0  Gene Names: H2AC8 | ![]() |
UniProt | |||||
Find proteins for H2QSF5 (Pan troglodytes) Explore H2QSF5  Go to UniProtKB:  H2QSF5 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | H2QSF5 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Histone H2B type 1-J | D [auth DDD], N [auth NNN] | 96 | Homo sapiens | Mutation(s): 0  Gene Names: H2BC11 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899 | |||||
PHAROS:  P06899 GTEx:  ENSG00000124635  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P06899 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Histone H2A | G [auth GGG], Q [auth QQQ] | 103 | Homo sapiens | Mutation(s): 0  Gene Names: LOC102977259 | ![]() |
UniProt | |||||
Find proteins for A0A2Y9FT95 (Physeter macrocephalus) Explore A0A2Y9FT95  Go to UniProtKB:  A0A2Y9FT95 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A2Y9FT95 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 6 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Histone H2B type 1-J | H [auth HHH], R [auth RRR] | 97 | Homo sapiens | Mutation(s): 0  Gene Names: H2BC11 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899 | |||||
PHAROS:  P06899 GTEx:  ENSG00000124635  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P06899 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 7 | |||||
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Molecule | Chains | Length | Organism | Image | |
DNA (167-MER) | I [auth III], S [auth SSS] | 167 | synthetic construct | ![]() | |
Sequence AnnotationsExpand | |||||
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Entity ID: 8 | |||||
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Molecule | Chains | Length | Organism | Image | |
DNA (167-MER) | J [auth JJJ], T [auth TTT] | 167 | synthetic construct | ![]() | |
Sequence AnnotationsExpand | |||||
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Ligands 1 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
MN Query on MN | AA [auth III] AB [auth TTT] BA [auth III] CA [auth III] DA [auth III] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |
Length ( Å ) | Angle ( ˚ ) |
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a = 108.437 | α = 90 |
b = 103.722 | β = 93.59 |
c = 185.405 | γ = 90 |
Software Name | Purpose |
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REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |
Funding Organization | Location | Grant Number |
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Ministry of Education (MoE, Singapore) | Singapore | -- |