7BWD

Structure of Dot1L-H2BK34ub Nucleosome Complex

PDB DOI: https://doi.org/10.2210/pdb7BWD/pdb
NAKB: 7BWD
EM Map EMD-30232: EMDB EMDataResource

Classification: TRANSLATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-04-14 Released: 2021-04-14
Deposition Author(s): Lou, Z.Y., Liu, L., Cao, L., Ai, H.S., Sun, Z.X.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the Dot1L-H2BK34ub Nucleosome Complex Reveals an Unprecedented Crosstalk Activation Mechanism through Nucleosome Shape Distortion

Liu, L., Lou, Z.Y., Ai, H.S., Cao, L.

To be published.

Macromolecule Content

Total Structure Weight: 264.05 kDa
Atom Count: 16,042
Modelled Residue Count: 1,548
Deposited Residue Count: 1,842
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-lysine N-methyltransferase, H3 lysine-79 specific	A [auth K]	416	Homo sapiens	Mutation(s): 0 Gene Names: DOT1L, KIAA1814, KMT4 EC: 2.1.1.360
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEK3 (Homo sapiens) Explore Q8TEK3 Go to UniProtKB: Q8TEK3
PHAROS: Q8TEK3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TEK3
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B [auth F], I [auth B]	102	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, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805
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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 [auth G], H [auth C]	129	Homo sapiens	Mutation(s): 0 Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
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Find proteins for P04908 (Homo sapiens) Explore P04908 Go to UniProtKB: P04908
PHAROS: P04908
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-K	D [auth H], G [auth D]	125	Homo sapiens	Mutation(s): 0 Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
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Find proteins for O60814 (Homo sapiens) Explore O60814 Go to UniProtKB: O60814
PHAROS: O60814
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UniProt Group	O60814
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	E, F [auth A]	135	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, H3C1, H3C2, H3C3, H3FC HIST1H3C, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12
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Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431
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UniProt Group	P68431
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	L, M	76	Homo sapiens	Mutation(s): 1 Gene Names: RPS27A, UBA80, UBCEP1
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Find proteins for P62979 (Homo sapiens) Explore P62979 Go to UniProtKB: P62979
PHAROS: P62979
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UniProt Group	P62979
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	J [auth I]	146	Homo sapiens
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	K [auth J]	146	Homo sapiens
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain N [auth K] MOL2 format, chain N [auth K]	N [auth K]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2021-04-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2017YFA0505200
National Natural Science Foundation of China (NSFC)	China	21532004
National Natural Science Foundation of China (NSFC)	China	91753205
National Natural Science Foundation of China (NSFC)	China	81621002