8YTI | pdb_00008yti

Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment)

PDB DOI: https://doi.org/10.2210/pdb8YTI/pdb
Entry: 8YTI supersedes: 7XX7
NAKB: 8YTI

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

Deposited: 2024-03-26 Released: 2024-04-03
Deposition Author(s): Adhireksan, Z., Qiuye, B., Padavattan, S., Davey, C.A.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.267 (Depositor), 0.268 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Linker Histones Associate Heterogeneously with Nucleosomes in the Condensed State

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

To be published.

Macromolecule Content

Total Structure Weight: 476.17 kDa
Atom Count: 28,083
Modeled Residue Count: 2,439
Deposited Residue Count: 3,082
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E, K, O	136	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD... HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
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
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F, L, P	103	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D... HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, 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	130	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
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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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H, N, R	126	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H2BJ, H2BFR
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 H1x	U, V	213	Homo sapiens	Mutation(s): 0 Gene Names: H1FX
UniProt & NIH Common Fund Data Resources
Find proteins for Q92522 (Homo sapiens) Explore Q92522 Go to UniProtKB: Q92522
PHAROS: Q92522 GTEx: ENSG00000184897
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92522
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Reference Sequence

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(by identity cutoff)

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

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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 ZB [auth S] SDF format, chain ZA [auth J] SDF format, chain Z [auth C] SDF format, chain YB [auth S] SDF format, chain YA [auth J] SDF format, chain Y [auth C] SDF format, chain XB [auth S] SDF format, chain XA [auth J] SDF format, chain X [auth C] SDF format, chain WB [auth S] SDF format, chain WA [auth J] SDF format, chain VB [auth S] SDF format, chain VA [auth J] SDF format, chain UB [auth S] SDF format, chain UA [auth J] SDF format, chain TB [auth S] SDF format, chain TA [auth J] SDF format, chain SB [auth S] SDF format, chain SA [auth J] SDF format, chain RB [auth S] SDF format, chain RA [auth J] SDF format, chain QB [auth S] SDF format, chain PB [auth S] SDF format, chain OB [auth S] SDF format, chain OA [auth I] SDF format, chain NB [auth S] SDF format, chain NA [auth I] SDF format, chain MB [auth S] SDF format, chain MA [auth I] SDF format, chain LB [auth S] SDF format, chain LA [auth I] SDF format, chain KC [auth T] SDF format, chain KA [auth I] SDF format, chain JC [auth T] SDF format, chain JB [auth R] SDF format, chain JA [auth I] SDF format, chain IC [auth T] SDF format, chain IB [auth Q] SDF format, chain IA [auth I] SDF format, chain HC [auth T] SDF format, chain HB [auth Q] SDF format, chain HA [auth I] SDF format, chain GC [auth T] SDF format, chain GB [auth Q] SDF format, chain FC [auth T] SDF format, chain FA [auth G] SDF format, chain EB [auth N] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain CC [auth S] SDF format, chain BC [auth S] SDF format, chain AC [auth S] MOL2 format, chain ZB [auth S] MOL2 format, chain ZA [auth J] MOL2 format, chain Z [auth C] MOL2 format, chain YB [auth S] MOL2 format, chain YA [auth J] MOL2 format, chain Y [auth C] MOL2 format, chain XB [auth S] MOL2 format, chain XA [auth J] MOL2 format, chain X [auth C] MOL2 format, chain WB [auth S] MOL2 format, chain WA [auth J] MOL2 format, chain VB [auth S] MOL2 format, chain VA [auth J] MOL2 format, chain UB [auth S] MOL2 format, chain UA [auth J] MOL2 format, chain TB [auth S] MOL2 format, chain TA [auth J] MOL2 format, chain SB [auth S] MOL2 format, chain SA [auth J] MOL2 format, chain RB [auth S] MOL2 format, chain RA [auth J] MOL2 format, chain QB [auth S] MOL2 format, chain PB [auth S] MOL2 format, chain OB [auth S] MOL2 format, chain OA [auth I] MOL2 format, chain NB [auth S] MOL2 format, chain NA [auth I] MOL2 format, chain MB [auth S] MOL2 format, chain MA [auth I] MOL2 format, chain LB [auth S] MOL2 format, chain LA [auth I] MOL2 format, chain KC [auth T] MOL2 format, chain KA [auth I] MOL2 format, chain JC [auth T] MOL2 format, chain JB [auth R] MOL2 format, chain JA [auth I] MOL2 format, chain IC [auth T] MOL2 format, chain IB [auth Q] MOL2 format, chain IA [auth I] MOL2 format, chain HC [auth T] MOL2 format, chain HB [auth Q] MOL2 format, chain HA [auth I] MOL2 format, chain GC [auth T] MOL2 format, chain GB [auth Q] MOL2 format, chain FC [auth T] MOL2 format, chain FA [auth G] MOL2 format, chain EB [auth N] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain CC [auth S] MOL2 format, chain BC [auth S] MOL2 format, chain AC [auth S] mmCIF format, chain ZB [auth S] mmCIF format, chain ZA [auth J] mmCIF format, chain Z [auth C] mmCIF format, chain YB [auth S] mmCIF format, chain YA [auth J] mmCIF format, chain Y [auth C] mmCIF format, chain XB [auth S] mmCIF format, chain XA [auth J] mmCIF format, chain X [auth C] mmCIF format, chain WB [auth S] mmCIF format, chain WA [auth J] mmCIF format, chain VB [auth S] mmCIF format, chain VA [auth J] mmCIF format, chain UB [auth S] mmCIF format, chain UA [auth J] mmCIF format, chain TB [auth S] mmCIF format, chain TA [auth J] mmCIF format, chain SB [auth S] mmCIF format, chain SA [auth J] mmCIF format, chain RB [auth S] mmCIF format, chain RA [auth J] mmCIF format, chain QB [auth S] mmCIF format, chain PB [auth S] mmCIF format, chain OB [auth S] mmCIF format, chain OA [auth I] mmCIF format, chain NB [auth S] mmCIF format, chain NA [auth I] mmCIF format, chain MB [auth S] mmCIF format, chain MA [auth I] mmCIF format, chain LB [auth S] mmCIF format, chain LA [auth I] mmCIF format, chain KC [auth T] mmCIF format, chain KA [auth I] mmCIF format, chain JC [auth T] mmCIF format, chain JB [auth R] mmCIF format, chain JA [auth I] mmCIF format, chain IC [auth T] mmCIF format, chain IB [auth Q] mmCIF format, chain IA [auth I] mmCIF format, chain HC [auth T] mmCIF format, chain HB [auth Q] mmCIF format, chain HA [auth I] mmCIF format, chain GC [auth T] mmCIF format, chain GB [auth Q] mmCIF format, chain FC [auth T] mmCIF format, chain FA [auth G] mmCIF format, chain EB [auth N] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain CC [auth S] mmCIF format, chain BC [auth S] mmCIF format, chain AC [auth S]	AC [auth S] BC [auth S] CC [auth S] DA [auth G] EA [auth G] AC [auth S], BC [auth S], CC [auth S], DA [auth G], EA [auth G], EB [auth N], FA [auth G], FC [auth T], GB [auth Q], GC [auth T], HA [auth I], HB [auth Q], HC [auth T], IA [auth I], IB [auth Q], IC [auth T], JA [auth I], JB [auth R], JC [auth T], KA [auth I], KC [auth T], LA [auth I], LB [auth S], MA [auth I], MB [auth S], NA [auth I], NB [auth S], OA [auth I], OB [auth S], PB [auth S], QB [auth S], RA [auth J], RB [auth S], SA [auth J], SB [auth S], TA [auth J], TB [auth S], UA [auth J], UB [auth S], VA [auth J], VB [auth S], WA [auth J], WB [auth S], X [auth C], XA [auth J], XB [auth S], Y [auth C], YA [auth J], YB [auth S], Z [auth C], ZA [auth J], ZB [auth S]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AC [auth S] Focus chain BC [auth S] Focus chain CC [auth S] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain EB [auth N] Focus chain FA [auth G] Focus chain FC [auth T] Focus chain GB [auth Q] Focus chain GC [auth T] Focus chain HA [auth I] Focus chain HB [auth Q] Focus chain HC [auth T] Focus chain IA [auth I] Focus chain IB [auth Q] Focus chain IC [auth T] Focus chain JA [auth I] Focus chain JB [auth R] Focus chain JC [auth T] Focus chain KA [auth I] Focus chain KC [auth T] Focus chain LA [auth I] Focus chain LB [auth S] Focus chain MA [auth I] Focus chain MB [auth S] Focus chain NA [auth I] Focus chain NB [auth S] Focus chain OA [auth I] Focus chain OB [auth S] Focus chain PB [auth S] Focus chain QB [auth S] Focus chain RA [auth J] Focus chain RB [auth S] Focus chain SA [auth J] Focus chain SB [auth S] Focus chain TA [auth J] Focus chain TB [auth S] Focus chain UA [auth J] Focus chain UB [auth S] Focus chain VA [auth J] Focus chain VB [auth S] Focus chain WA [auth J] Focus chain WB [auth S] Focus chain X [auth C] Focus chain XA [auth J] Focus chain XB [auth S] Focus chain Y [auth C] Focus chain YA [auth J] Focus chain YB [auth S] Focus chain Z [auth C] Focus chain ZA [auth J] Focus chain ZB [auth S] Interactions & Density Focus chain AC [auth S] Focus chain BC [auth S] Focus chain CC [auth S] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain EB [auth N] Focus chain FA [auth G] Focus chain FC [auth T] Focus chain GB [auth Q] Focus chain GC [auth T] Focus chain HA [auth I] Focus chain HB [auth Q] Focus chain HC [auth T] Focus chain IA [auth I] Focus chain IB [auth Q] Focus chain IC [auth T] Focus chain JA [auth I] Focus chain JB [auth R] Focus chain JC [auth T] Focus chain KA [auth I] Focus chain KC [auth T] Focus chain LA [auth I] Focus chain LB [auth S] Focus chain MA [auth I] Focus chain MB [auth S] Focus chain NA [auth I] Focus chain NB [auth S] Focus chain OA [auth I] Focus chain OB [auth S] Focus chain PB [auth S] Focus chain QB [auth S] Focus chain RA [auth J] Focus chain RB [auth S] Focus chain SA [auth J] Focus chain SB [auth S] Focus chain TA [auth J] Focus chain TB [auth S] Focus chain UA [auth J] Focus chain UB [auth S] Focus chain VA [auth J] Focus chain VB [auth S] Focus chain WA [auth J] Focus chain WB [auth S] Focus chain X [auth C] Focus chain XA [auth J] Focus chain XB [auth S] Focus chain Y [auth C] Focus chain YA [auth J] Focus chain YB [auth S] Focus chain Z [auth C] Focus chain ZA [auth J] Focus chain ZB [auth S]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain QA [auth I] SDF format, chain PA [auth I] SDF format, chain LC [auth T] SDF format, chain EC [auth S] SDF format, chain DC [auth S] SDF format, chain DB [auth M] SDF format, chain BA [auth C] SDF format, chain AB [auth J] MOL2 format, chain QA [auth I] MOL2 format, chain PA [auth I] MOL2 format, chain LC [auth T] MOL2 format, chain EC [auth S] MOL2 format, chain DC [auth S] MOL2 format, chain DB [auth M] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth J] mmCIF format, chain QA [auth I] mmCIF format, chain PA [auth I] mmCIF format, chain LC [auth T] mmCIF format, chain EC [auth S] mmCIF format, chain DC [auth S] mmCIF format, chain DB [auth M] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth J]	AB [auth J] BA [auth C] DB [auth M] DC [auth S] EC [auth S] AB [auth J], BA [auth C], DB [auth M], DC [auth S], EC [auth S], LC [auth T], PA [auth I], QA [auth I]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain BA [auth C] Focus chain DB [auth M] Focus chain DC [auth S] Focus chain EC [auth S] Focus chain LC [auth T] Focus chain PA [auth I] Focus chain QA [auth I] Interactions & Density Focus chain AB [auth J] Focus chain BA [auth C] Focus chain DB [auth M] Focus chain DC [auth S] Focus chain EC [auth S] Focus chain LC [auth T] Focus chain PA [auth I] Focus chain QA [auth I]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain KB [auth R] SDF format, chain GA [auth G] SDF format, chain FB [auth O] SDF format, chain CB [auth M] SDF format, chain CA [auth E] SDF format, chain BB [auth K] SDF format, chain AA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain KB [auth R] MOL2 format, chain GA [auth G] MOL2 format, chain FB [auth O] MOL2 format, chain CB [auth M] MOL2 format, chain CA [auth E] MOL2 format, chain BB [auth K] MOL2 format, chain AA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain KB [auth R] mmCIF format, chain GA [auth G] mmCIF format, chain FB [auth O] mmCIF format, chain CB [auth M] mmCIF format, chain CA [auth E] mmCIF format, chain BB [auth K] mmCIF format, chain AA [auth C]	AA [auth C] BB [auth K] CA [auth E] CB [auth M] FB [auth O] AA [auth C], BB [auth K], CA [auth E], CB [auth M], FB [auth O], GA [auth G], KB [auth R], W [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain CB [auth M] Focus chain FB [auth O] Focus chain GA [auth G] Focus chain KB [auth R] Focus chain W [auth A] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain CB [auth M] Focus chain FB [auth O] Focus chain GA [auth G] Focus chain KB [auth R] Focus chain W [auth A]