3u88

Crystal structure of human menin in complex with MLL1 and LEDGF

Method: X-RAY DIFFRACTION

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

Menin

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Histone-lysine N-methyltransferase 2A × 1 （Q03164） Lens epithelium-derived growth factor × 1 （O75475） CHOLIC ACID × 1 L-CANAVANINE × 4 (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLYOXYLIC ACID × 4 SULFATE ION × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Histone-lysine N-methyltransferase 2A × 1 （Q03164） Lens epithelium-derived growth factor × 1 （O75475） CHOLIC ACID × 1 L-CANAVANINE × 1 (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLYOXYLIC ACID × 2 SULFATE ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MEN1_HUMAN
Isoform	O00255-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–459； UniProt 2–459 Author chain A； PDBConstruct 460–550； UniProt 520–610 Author chain B； PDBConstruct 2–459； UniProt 2–459 Author chain B； PDBConstruct 460–550； UniProt 520–610

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 3	Menin × 1 （O00255） Lens epithelium-derived growth factor × 1 （O75475） CHOLIC ACID × 1 L-CANAVANINE × 4 (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLYOXYLIC ACID × 4 SULFATE ION × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Menin × 1 （O00255） Lens epithelium-derived growth factor × 1 （O75475） CHOLIC ACID × 1 L-CANAVANINE × 1 (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLYOXYLIC ACID × 2 SULFATE ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KMT2A_HUMAN
Isoform	Q03164-2
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 25–75； UniProt 103–153 Author chain N； PDBConstruct 25–75； UniProt 103–153

Lens epithelium-derived growth factor

Homo sapiens

UniProt O75475

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Menin × 1 （O00255） Histone-lysine N-methyltransferase 2A × 1 （Q03164） CHOLIC ACID × 1 L-CANAVANINE × 4 (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLYOXYLIC ACID × 4 SULFATE ION × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Menin × 1 （O00255） Histone-lysine N-methyltransferase 2A × 1 （Q03164） CHOLIC ACID × 1 L-CANAVANINE × 1 (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLYOXYLIC ACID × 2 SULFATE ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSIP1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–89； UniProt 347–435 Author chain D； PDBConstruct 1–89； UniProt 347–435

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	3u88
Deposition date deposition_date	2011-10-16
Structure title title	Crystal structure of human menin in complex with MLL1 and LEDGF
Keywords keywords	menin, MEN1, MLL, JunD, LEDGF, TPR, TRANSCRIPTION; TRANSCRIPTION
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.

3u88__assembly_1__model_1

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

Download this curve (.dat)

3u88__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3u88__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.00 Å
Rg (electron density)	28.51 Å
Total Rg	29.28 Å
Atom count	5011
Residues	615
Excluded volume	89292 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3u88__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3u88__assembly_2__model_1`	trimeric （3）	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 (8)

Entity 1 Entity 1 polymer

Description description	Menin
Molecular weight formula_weight	61061.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9881

SGLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVIPTNVPELTFQPSPAPDPPGGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDVIPNLLKEAASLLEAGEERPGEQSQGTQSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSGTVAGTARGPEGGSTAQVPAPTASPPPEGPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQVQMKKQKVSTPSDYTLSFLKRQRKGL

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	7782.7 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N

SRWRFPARPGTGRRGLGGAPRQRVPALLRVGPGFDAALQVSAAIGTNLRRFRAVFGESGGGGGSGEDEQFLGFGS

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	Lens epithelium-derived growth factor
Molecular weight formula_weight	10346.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVGEGDSV

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 non-polymer

Description description	CHOLIC ACID
Molecular weight formula_weight	408.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	L-CANAVANINE
Molecular weight formula_weight	176.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	(4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol
Molecular weight formula_weight	326.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYOXYLIC ACID
Molecular weight formula_weight	74.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3u88a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.389 — Menin N-terminal domain-like
Superfamily Superfamily superfamily	d.389.1 — Menin N-terminal domain-like
Family Family family	d.389.1.1 — Menin N-terminal domain-like

Domain ID domain_id	d3u88a2
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.1 — Tetratricopeptide repeat (TPR)

Domain ID domain_id	d3u88b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.389 — Menin N-terminal domain-like
Superfamily Superfamily superfamily	d.389.1 — Menin N-terminal domain-like
Family Family family	d.389.1.1 — Menin N-terminal domain-like

Domain ID domain_id	d3u88b2
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.1 — Tetratricopeptide repeat (TPR)

Domain ID domain_id	d3u88c_
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

Domain ID domain_id	d3u88d_
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

CATH v4.4 (4 domains)

Domain ID domain_id	3u88C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	10 — Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

Domain ID domain_id	3u88D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	10 — Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

Domain ID domain_id	3u88M00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2390 —

Domain ID domain_id	3u88N00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2390 —

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Unit-cell length a length_a	187.990 Å
Unit-cell length b length_b	187.990 Å
Unit-cell length c length_c	238.417 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	48.650 Å
R factor r_factor	0.2050
R_work r_work	0.2020
R_free r_free	0.2330

Crystal structure of human menin in complex with MLL1 and LEDGF

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

Menin

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

Lens epithelium-derived growth factor

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

3u88__assembly_1__model_1

3u88__assembly_1__model_1 | I(q)

3u88__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of human menin in complex with MLL1 and LEDGF

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

Menin

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

Lens epithelium-derived growth factor

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

3u88__assembly_1__model_1

3u88__assembly_1__model_1 | I(q)

3u88__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)