6J99

Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome

PDB DOI: https://doi.org/10.2210/pdb6J99/pdb
EM Map EMD-9783: EMDB EMDataResource
NAKB: 6J99

Classification: TRANSCRIPTION
Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-01-22 Released: 2019-02-27
Deposition Author(s): Yao, T., Huang, J.
Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis of the crosstalk between histone H2B monoubiquitination and H3 lysine 79 methylation on nucleosome.

Yao, T., Jing, W., Hu, Z., Tan, M., Cao, M., Wang, Q., Li, Y., Yuan, G., Lei, M., Huang, J.

(2019) Cell Res 29: 330-333

PubMed: 30770869 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-019-0146-7
Primary Citation of Related Structures:
6J99

Organizational Affiliation

State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201210, China.

Macromolecule Content

Total Structure Weight: 256.4 kDa
Atom Count: 15,266
Modelled Residue Count: 1,452
Deposited Residue Count: 1,770
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	A, E	136	Xenopus laevis	Mutation(s): 0 Gene Names: XELAEV_18002543mg
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis) Explore A0A310TTQ1 Go to UniProtKB: A0A310TTQ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A310TTQ1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62799
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	130	Xenopus laevis	Mutation(s): 0 Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8 Go to UniProtKB: Q6AZJ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6AZJ8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	123	Xenopus laevis	Mutation(s): 2
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02281
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	K [auth L]	76	Homo sapiens	Mutation(s): 1 Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens) Explore P62979 Go to UniProtKB: P62979
PHAROS: P62979 GTEx: ENSG00000143947
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62979
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase, H3 lysine-79 specific	L [auth K]	416	Homo sapiens	Mutation(s): 0 Gene Names: DOT1L, KIAA1814, KMT4 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEK3 (Homo sapiens) Explore Q8TEK3 Go to UniProtKB: Q8TEK3
PHAROS: Q8TEK3 GTEx: ENSG00000104885
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TEK3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (144-MER)	I	147	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	J	147	synthetic construct
Sequence Annotations Expand
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 M [auth K] MOL2 format, chain M [auth K] mmCIF format, chain M [auth K]	M [auth K]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain M [auth K] Interactions & Density Focus chain M [auth K]

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB: 6J99	Ki: min: 160, max: 270 (nM) from 2 assay(s)
		Kd: min: 150, max: 360 (nM) from 2 assay(s)
		IC50: min: 140, max: 600 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-02-27

Deposition Author(s):

Yao, T.

Huang, J.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2016YFA0501803
National Natural Science Foundation of China	China	31570766
National Natural Science Foundation of China	China	U1632130