7XX6

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

PDB DOI: https://doi.org/10.2210/pdb7XX6/pdb
NAKB: 7XX6

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

Deposited: 2022-05-28 Released: 2023-05-31
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: 3.39 Å
R-Value Free: 0.296
R-Value Work: 0.227
R-Value Observed: 0.229

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: 905.44 kDa
Atom Count: 53,518
Modelled Residue Count: 4,598
Deposited Residue Count: 5,766
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 EA [auth e] IA [auth i] K A, E, EA [auth e], IA [auth i], K, O, U, Y	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68431
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B F FA [auth f] JA [auth j] L B, F, FA [auth f], JA [auth j], L, P, V, Z	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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	AA [auth a] C G GA [auth g] KA [auth k] AA [auth a], C, G, GA [auth g], KA [auth k], M, Q, W	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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	BA [auth b] D H HA [auth h] LA [auth l] BA [auth b], D, H, HA [auth h], LA [auth l], N, R, X	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06899
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H1.0	OA [auth o], PA [auth p]	195	Homo sapiens	Mutation(s): 0 Gene Names: H1-0, H1F0, H1FV
UniProt & NIH Common Fund Data Resources
Find proteins for P07305 (Homo sapiens) Explore P07305 Go to UniProtKB: P07305
PHAROS: P07305 GTEx: ENSG00000189060
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07305
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (169-MER)	CA [auth c], I, MA [auth m], S	169	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (169-MER)	DA [auth d], J, NA [auth n], T	169	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AC [auth d] SDF format, chain BB [auth J] SDF format, chain BC [auth d] SDF format, chain CB [auth J] SDF format, chain CC [auth d] SDF format, chain DB [auth J] SDF format, chain DC [auth d] SDF format, chain EB [auth J] SDF format, chain EC [auth d] SDF format, chain FB [auth O] SDF format, chain FC [auth d] SDF format, chain GB [auth O] SDF format, chain GC [auth d] SDF format, chain HB [auth S] SDF format, chain HC [auth d] SDF format, chain IB [auth T] SDF format, chain JB [auth T] SDF format, chain JC [auth i] SDF format, chain KB [auth T] SDF format, chain KC [auth j] SDF format, chain LC [auth m] SDF format, chain MC [auth m] SDF format, chain NC [auth n] SDF format, chain OB [auth W] SDF format, chain OC [auth n] SDF format, chain PB [auth Y] SDF format, chain PC [auth o] SDF format, chain QA [auth C] SDF format, chain QB [auth a] SDF format, chain QC [auth p] SDF format, chain RA [auth G] SDF format, chain RB [auth a] SDF format, chain SA [auth I] SDF format, chain SB [auth c] SDF format, chain TA [auth I] SDF format, chain TB [auth c] SDF format, chain UA [auth I] SDF format, chain UB [auth c] SDF format, chain VA [auth I] SDF format, chain VB [auth c] SDF format, chain WA [auth I] SDF format, chain WB [auth c] SDF format, chain XA [auth I] SDF format, chain XB [auth c] SDF format, chain YA [auth I] SDF format, chain YB [auth c] SDF format, chain ZA [auth I] MOL2 format, chain AC [auth d] MOL2 format, chain BB [auth J] MOL2 format, chain BC [auth d] MOL2 format, chain CB [auth J] MOL2 format, chain CC [auth d] MOL2 format, chain DB [auth J] MOL2 format, chain DC [auth d] MOL2 format, chain EB [auth J] MOL2 format, chain EC [auth d] MOL2 format, chain FB [auth O] MOL2 format, chain FC [auth d] MOL2 format, chain GB [auth O] MOL2 format, chain GC [auth d] MOL2 format, chain HB [auth S] MOL2 format, chain HC [auth d] MOL2 format, chain IB [auth T] MOL2 format, chain JB [auth T] MOL2 format, chain JC [auth i] MOL2 format, chain KB [auth T] MOL2 format, chain KC [auth j] MOL2 format, chain LC [auth m] MOL2 format, chain MC [auth m] MOL2 format, chain NC [auth n] MOL2 format, chain OB [auth W] MOL2 format, chain OC [auth n] MOL2 format, chain PB [auth Y] MOL2 format, chain PC [auth o] MOL2 format, chain QA [auth C] MOL2 format, chain QB [auth a] MOL2 format, chain QC [auth p] MOL2 format, chain RA [auth G] MOL2 format, chain RB [auth a] MOL2 format, chain SA [auth I] MOL2 format, chain SB [auth c] MOL2 format, chain TA [auth I] MOL2 format, chain TB [auth c] MOL2 format, chain UA [auth I] MOL2 format, chain UB [auth c] MOL2 format, chain VA [auth I] MOL2 format, chain VB [auth c] MOL2 format, chain WA [auth I] MOL2 format, chain WB [auth c] MOL2 format, chain XA [auth I] MOL2 format, chain XB [auth c] MOL2 format, chain YA [auth I] MOL2 format, chain YB [auth c] MOL2 format, chain ZA [auth I]	AC [auth d] BB [auth J] BC [auth d] CB [auth J] CC [auth d] AC [auth d], BB [auth J], BC [auth d], CB [auth J], CC [auth d], DB [auth J], DC [auth d], EB [auth J], EC [auth d], FB [auth O], FC [auth d], GB [auth O], GC [auth d], HB [auth S], HC [auth d], IB [auth T], JB [auth T], JC [auth i], KB [auth T], KC [auth j], LC [auth m], MC [auth m], NC [auth n], OB [auth W], OC [auth n], PB [auth Y], PC [auth o], QA [auth C], QB [auth a], QC [auth p], RA [auth G], RB [auth a], SA [auth I], SB [auth c], TA [auth I], TB [auth c], UA [auth I], UB [auth c], VA [auth I], VB [auth c], WA [auth I], WB [auth c], XA [auth I], XB [auth c], YA [auth I], YB [auth c], ZA [auth I]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AC [auth d] Focus chain BB [auth J] Focus chain BC [auth d] Focus chain CB [auth J] Focus chain CC [auth d] Focus chain DB [auth J] Focus chain DC [auth d] Focus chain EB [auth J] Focus chain EC [auth d] Focus chain FB [auth O] Focus chain FC [auth d] Focus chain GB [auth O] Focus chain GC [auth d] Focus chain HB [auth S] Focus chain HC [auth d] Focus chain IB [auth T] Focus chain JB [auth T] Focus chain JC [auth i] Focus chain KB [auth T] Focus chain KC [auth j] Focus chain LC [auth m] Focus chain MC [auth m] Focus chain NC [auth n] Focus chain OB [auth W] Focus chain OC [auth n] Focus chain PB [auth Y] Focus chain PC [auth o] Focus chain QA [auth C] Focus chain QB [auth a] Focus chain QC [auth p] Focus chain RA [auth G] Focus chain RB [auth a] Focus chain SA [auth I] Focus chain SB [auth c] Focus chain TA [auth I] Focus chain TB [auth c] Focus chain UA [auth I] Focus chain UB [auth c] Focus chain VA [auth I] Focus chain VB [auth c] Focus chain WA [auth I] Focus chain WB [auth c] Focus chain XA [auth I] Focus chain XB [auth c] Focus chain YA [auth I] Focus chain YB [auth c] Focus chain ZA [auth I] Interactions & Density Focus chain AC [auth d] Focus chain BB [auth J] Focus chain BC [auth d] Focus chain CB [auth J] Focus chain CC [auth d] Focus chain DB [auth J] Focus chain DC [auth d] Focus chain EB [auth J] Focus chain EC [auth d] Focus chain FB [auth O] Focus chain FC [auth d] Focus chain GB [auth O] Focus chain GC [auth d] Focus chain HB [auth S] Focus chain HC [auth d] Focus chain IB [auth T] Focus chain JB [auth T] Focus chain JC [auth i] Focus chain KB [auth T] Focus chain KC [auth j] Focus chain LC [auth m] Focus chain MC [auth m] Focus chain NC [auth n] Focus chain OB [auth W] Focus chain OC [auth n] Focus chain PB [auth Y] Focus chain PC [auth o] Focus chain QA [auth C] Focus chain QB [auth a] Focus chain QC [auth p] Focus chain RA [auth G] Focus chain RB [auth a] Focus chain SA [auth I] Focus chain SB [auth c] Focus chain TA [auth I] Focus chain TB [auth c] Focus chain UA [auth I] Focus chain UB [auth c] Focus chain VA [auth I] Focus chain VB [auth c] Focus chain WA [auth I] Focus chain WB [auth c] Focus chain XA [auth I] Focus chain XB [auth c] Focus chain YA [auth I] Focus chain YB [auth c] Focus chain ZA [auth I]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain IC [auth d] SDF format, chain LB [auth T] SDF format, chain MB [auth T] SDF format, chain NB [auth T] SDF format, chain ZB [auth c] MOL2 format, chain AB [auth I] MOL2 format, chain IC [auth d] MOL2 format, chain LB [auth T] MOL2 format, chain MB [auth T] MOL2 format, chain NB [auth T] MOL2 format, chain ZB [auth c]	AB [auth I] IC [auth d] LB [auth T] MB [auth T] NB [auth T] AB [auth I], IC [auth d], LB [auth T], MB [auth T], NB [auth T], ZB [auth c]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain IC [auth d] Focus chain LB [auth T] Focus chain MB [auth T] Focus chain NB [auth T] Focus chain ZB [auth c] Interactions & Density Focus chain AB [auth I] Focus chain IC [auth d] Focus chain LB [auth T] Focus chain MB [auth T] Focus chain NB [auth T] Focus chain ZB [auth c]