7XVM | pdb_00007xvm

Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment)

PDB DOI: https://doi.org/10.2210/pdb7XVM/pdb
NAKB: 7XVM

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, synthetic construct, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-24 Released: 2023-05-24
Deposition Author(s): Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free:
0.259 (Depositor), 0.259 (DCC)
R-Value Work:
0.200 (Depositor), 0.204 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment)

Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A.

To be published.

Macromolecule Content

Total Structure Weight: 473.13 kDa
Atom Count: 27,693
Modeled Residue Count: 2,417
Deposited Residue Count: 3,068
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E, K, O	138	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F, L, P	105	Homo sapiens	Mutation(s): 0 Gene Names: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G... H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805 GTEx: ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62805
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G, M, Q	132	Homo sapiens	Mutation(s): 0 Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908 Go to UniProtKB: P04908
PHAROS: P04908 GTEx: ENSG00000277075 ENSG00000278463
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04908
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H, N, R	128	Homo sapiens	Mutation(s): 0 Gene Names: H2BC11, H2BFR, HIST1H2BJ
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06899
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H5	U, V	190	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P02259 (Gallus gallus) Explore P02259 Go to UniProtKB: P02259
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02259
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
DNA (169-MER)	I, S	169	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 6
DNA (169-MER)	J, T	169	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain BA [auth I] SDF format, chain CA [auth I] SDF format, chain DA [auth I] SDF format, chain EA [auth I] SDF format, chain FA [auth I] SDF format, chain GA [auth I] SDF format, chain IA [auth J] SDF format, chain JA [auth J] SDF format, chain KA [auth J] SDF format, chain MA [auth S] SDF format, chain NA [auth S] SDF format, chain OA [auth S] SDF format, chain PA [auth S] SDF format, chain QA [auth T] SDF format, chain RA [auth T] SDF format, chain W [auth C] SDF format, chain Z [auth I] MOL2 format, chain AA [auth I] MOL2 format, chain BA [auth I] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth I] MOL2 format, chain EA [auth I] MOL2 format, chain FA [auth I] MOL2 format, chain GA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain JA [auth J] MOL2 format, chain KA [auth J] MOL2 format, chain MA [auth S] MOL2 format, chain NA [auth S] MOL2 format, chain OA [auth S] MOL2 format, chain PA [auth S] MOL2 format, chain QA [auth T] MOL2 format, chain RA [auth T] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth I] mmCIF format, chain AA [auth I] mmCIF format, chain BA [auth I] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth I] mmCIF format, chain EA [auth I] mmCIF format, chain FA [auth I] mmCIF format, chain GA [auth I] mmCIF format, chain IA [auth J] mmCIF format, chain JA [auth J] mmCIF format, chain KA [auth J] mmCIF format, chain MA [auth S] mmCIF format, chain NA [auth S] mmCIF format, chain OA [auth S] mmCIF format, chain PA [auth S] mmCIF format, chain QA [auth T] mmCIF format, chain RA [auth T] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth I]	AA [auth I] BA [auth I] CA [auth I] DA [auth I] EA [auth I] AA [auth I], BA [auth I], CA [auth I], DA [auth I], EA [auth I], FA [auth I], GA [auth I], IA [auth J], JA [auth J], KA [auth J], MA [auth S], NA [auth S], OA [auth S], PA [auth S], QA [auth T], RA [auth T], W [auth C], Z [auth I]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth I] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain MA [auth S] Focus chain NA [auth S] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain QA [auth T] Focus chain RA [auth T] Focus chain W [auth C] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth I] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain MA [auth S] Focus chain NA [auth S] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain QA [auth T] Focus chain RA [auth T] Focus chain W [auth C] Focus chain Z [auth I]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain SA [auth T] SDF format, chain HA [auth I] MOL2 format, chain SA [auth T] MOL2 format, chain HA [auth I] mmCIF format, chain SA [auth T] mmCIF format, chain HA [auth I]	HA [auth I], SA [auth T]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain HA [auth I] Focus chain SA [auth T] Interactions & Density Focus chain HA [auth I] Focus chain SA [auth T]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain LA [auth M] SDF format, chain X [auth C] SDF format, chain Y [auth H] MOL2 format, chain LA [auth M] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth H] mmCIF format, chain LA [auth M] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth H]	LA [auth M], X [auth C], Y [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain LA [auth M] Focus chain X [auth C] Focus chain Y [auth H] Interactions & Density Focus chain LA [auth M] Focus chain X [auth C] Focus chain Y [auth H]