7w67

The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Set1/Ash2 histone methyltransferase complex subunit ASH2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone-lysine N-methyltransferase 2A × 1 （Q03164） Retinoblastoma-binding protein 5 × 1 （Q15291） Histone H3.3C × 1 （Q6NXT2） S-ADENOSYL-L-HOMOCYSTEINE × 1 ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASH2L_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–118； UniProt 380–496 Author chain A； PDBConstruct 125–184； UniProt 539–598

Histone-lysine N-methyltransferase 2A

Homo sapiens

UniProt Q03164

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Retinoblastoma-binding protein 5 × 1 （Q15291） Histone H3.3C × 1 （Q6NXT2） S-ADENOSYL-L-HOMOCYSTEINE × 1 ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KMT2A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–158； UniProt 3813–3969

Retinoblastoma-binding protein 5

Homo sapiens

UniProt Q15291

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Histone H3.3C × 1 （Q6NXT2） S-ADENOSYL-L-HOMOCYSTEINE × 1 ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBBP5_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–27； UniProt 330–356

Histone H3.3C

OrganismNot specified

UniProt Q6NXT2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Retinoblastoma-binding protein 5 × 1 （Q15291） S-ADENOSYL-L-HOMOCYSTEINE × 1 ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H3C_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain M； PDBConstruct 1–9； UniProt 2–10

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7w67
Deposition date deposition_date	2021-12-01
Structure title title	The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide
Keywords keywords	MLL family methyltransferases, product specificity, F/Y switch, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7w67__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7w67__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7w67__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.30 Å
Rg (electron density)	24.47 Å
Total Rg	25.43 Å
Atom count	2909
Residues	360
Excluded volume	51748 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7w67__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Set1/Ash2 histone methyltransferase complex subunit ASH2
Molecular weight formula_weight	20597.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3037

SRVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTISGRGSSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPMSDMG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone-lysine N-methyltransferase 2A
Molecular weight formula_weight	18227.1 kDa
EC 编号 ec_number	2.1.1.364,2.1.1.-
Mutation mutation	N3861I,Q3867L,C3882SS
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DLPMPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGIVIRSILTDKREKYYDSKGIGSSYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Retinoblastoma-binding protein 5
Molecular weight formula_weight	3255.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

SAFAPDFKELDENVEYEERESEFDIED

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H3.3C
Molecular weight formula_weight	1063.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

ARTKQTARK

Entity 5 Entity 5 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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Unit-cell length a length_a	76.150 Å
Unit-cell length b length_b	44.571 Å
Unit-cell length c length_c	121.333 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.194 Å
Low-resolution limit resolution_low	31.889 Å
R factor r_factor	0.1772
R_work r_work	0.1750
R_free r_free	0.2219

The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

Set1/Ash2 histone methyltransferase complex subunit ASH2

State in the Current Structure

Other States of the Same Protein in the Database

Histone-lysine N-methyltransferase 2A

State in the Current Structure

Other States of the Same Protein in the Database

Retinoblastoma-binding protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Histone H3.3C

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7w67__assembly_1__model_1

7w67__assembly_1__model_1 | I(q)

7w67__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

Set1/Ash2 histone methyltransferase complex subunit ASH2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone-lysine N-methyltransferase 2A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Retinoblastoma-binding protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H3.3C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7w67__assembly_1__model_1

7w67__assembly_1__model_1 | I(q)

7w67__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)