8QKT

Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment

PDB DOI: https://doi.org/10.2210/pdb8QKT/pdb
NAKB: 8QKT

Classification: DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-17 Released: 2023-10-18
Deposition Author(s): Ma, Z., Davey, C.A.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.26 Å
R-Value Free: 0.321
R-Value Work: 0.269

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment

Ma, Z., Davey, C.A.

To be published.

Macromolecule Content

Total Structure Weight: 378.68 kDa
Atom Count: 25,695
Modelled Residue Count: 2,176
Deposited Residue Count: 2,178
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
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... H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
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
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Reference Sequence

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Entity ID: 3
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
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Reference Sequence

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Entity ID: 4
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
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Reference Sequence

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Entity ID: 5
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
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Reference Sequence

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Entity ID: 6
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 Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (167-MER)	I [auth III], S [auth SSS]	167	synthetic construct
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (167-MER)	J [auth JJJ], T [auth TTT]	167	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth III] SDF format, chain AB [auth TTT] SDF format, chain BA [auth III] SDF format, chain CA [auth III] SDF format, chain DA [auth III] SDF format, chain EA [auth III] SDF format, chain FA [auth JJJ] SDF format, chain GA [auth JJJ] SDF format, chain HA [auth JJJ] SDF format, chain IA [auth JJJ] SDF format, chain JA [auth JJJ] SDF format, chain KA [auth JJJ] SDF format, chain LA [auth JJJ] SDF format, chain MA [auth JJJ] SDF format, chain NA [auth SSS] SDF format, chain OA [auth SSS] SDF format, chain PA [auth SSS] SDF format, chain QA [auth SSS] SDF format, chain RA [auth SSS] SDF format, chain SA [auth SSS] SDF format, chain TA [auth TTT] SDF format, chain U [auth III] SDF format, chain UA [auth TTT] SDF format, chain V [auth III] SDF format, chain VA [auth TTT] SDF format, chain W [auth III] SDF format, chain WA [auth TTT] SDF format, chain X [auth III] SDF format, chain XA [auth TTT] SDF format, chain Y [auth III] SDF format, chain YA [auth TTT] SDF format, chain Z [auth III] SDF format, chain ZA [auth TTT] MOL2 format, chain AA [auth III] MOL2 format, chain AB [auth TTT] MOL2 format, chain BA [auth III] MOL2 format, chain CA [auth III] MOL2 format, chain DA [auth III] MOL2 format, chain EA [auth III] MOL2 format, chain FA [auth JJJ] MOL2 format, chain GA [auth JJJ] MOL2 format, chain HA [auth JJJ] MOL2 format, chain IA [auth JJJ] MOL2 format, chain JA [auth JJJ] MOL2 format, chain KA [auth JJJ] MOL2 format, chain LA [auth JJJ] MOL2 format, chain MA [auth JJJ] MOL2 format, chain NA [auth SSS] MOL2 format, chain OA [auth SSS] MOL2 format, chain PA [auth SSS] MOL2 format, chain QA [auth SSS] MOL2 format, chain RA [auth SSS] MOL2 format, chain SA [auth SSS] MOL2 format, chain TA [auth TTT] MOL2 format, chain U [auth III] MOL2 format, chain UA [auth TTT] MOL2 format, chain V [auth III] MOL2 format, chain VA [auth TTT] MOL2 format, chain W [auth III] MOL2 format, chain WA [auth TTT] MOL2 format, chain X [auth III] MOL2 format, chain XA [auth TTT] MOL2 format, chain Y [auth III] MOL2 format, chain YA [auth TTT] MOL2 format, chain Z [auth III] MOL2 format, chain ZA [auth TTT]	AA [auth III] AB [auth TTT] BA [auth III] CA [auth III] DA [auth III] AA [auth III], AB [auth TTT], BA [auth III], CA [auth III], DA [auth III], EA [auth III], FA [auth JJJ], GA [auth JJJ], HA [auth JJJ], IA [auth JJJ], JA [auth JJJ], KA [auth JJJ], LA [auth JJJ], MA [auth JJJ], NA [auth SSS], OA [auth SSS], PA [auth SSS], QA [auth SSS], RA [auth SSS], SA [auth SSS], TA [auth TTT], U [auth III], UA [auth TTT], V [auth III], VA [auth TTT], W [auth III], WA [auth TTT], X [auth III], XA [auth TTT], Y [auth III], YA [auth TTT], Z [auth III], ZA [auth TTT]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth III] Focus chain AB [auth TTT] Focus chain BA [auth III] Focus chain CA [auth III] Focus chain DA [auth III] Focus chain EA [auth III] Focus chain FA [auth JJJ] Focus chain GA [auth JJJ] Focus chain HA [auth JJJ] Focus chain IA [auth JJJ] Focus chain JA [auth JJJ] Focus chain KA [auth JJJ] Focus chain LA [auth JJJ] Focus chain MA [auth JJJ] Focus chain NA [auth SSS] Focus chain OA [auth SSS] Focus chain PA [auth SSS] Focus chain QA [auth SSS] Focus chain RA [auth SSS] Focus chain SA [auth SSS] Focus chain TA [auth TTT] Focus chain U [auth III] Focus chain UA [auth TTT] Focus chain V [auth III] Focus chain VA [auth TTT] Focus chain W [auth III] Focus chain WA [auth TTT] Focus chain X [auth III] Focus chain XA [auth TTT] Focus chain Y [auth III] Focus chain YA [auth TTT] Focus chain Z [auth III] Focus chain ZA [auth TTT] Interactions & Density Focus chain AA [auth III] Focus chain AB [auth TTT] Focus chain BA [auth III] Focus chain CA [auth III] Focus chain DA [auth III] Focus chain EA [auth III] Focus chain FA [auth JJJ] Focus chain GA [auth JJJ] Focus chain HA [auth JJJ] Focus chain IA [auth JJJ] Focus chain JA [auth JJJ] Focus chain KA [auth JJJ] Focus chain LA [auth JJJ] Focus chain MA [auth JJJ] Focus chain NA [auth SSS] Focus chain OA [auth SSS] Focus chain PA [auth SSS] Focus chain QA [auth SSS] Focus chain RA [auth SSS] Focus chain SA [auth SSS] Focus chain TA [auth TTT] Focus chain U [auth III] Focus chain UA [auth TTT] Focus chain V [auth III] Focus chain VA [auth TTT] Focus chain W [auth III] Focus chain WA [auth TTT] Focus chain X [auth III] Focus chain XA [auth TTT] Focus chain Y [auth III] Focus chain YA [auth TTT] Focus chain Z [auth III] Focus chain ZA [auth TTT]