PDB-3re2: Crystal structure of menin reveals the binding site for Mixed Lin...

ID or keywords:

Entry

Database: PDB / ID: 3re2

Title

Crystal structure of menin reveals the binding site for Mixed Lineage Leukemia (MLL) protein

Components

Predicted protein

Keywords

UNKNOWN FUNCTION / menin / Multiple Endocrine Neoplasia 1 / Tumor suppressor / Mixed Lineage Leukemia

Function / homology

Function and homology information

Y-form DNA binding / histone methyltransferase complex / negative regulation of cell cycle / chromatin organization / transcription cis-regulatory region binding / negative regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin
Similarity search - Function

Biological species

Nematostella vectensis (starlet sea anemone)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 Å

Authors

Murai, M.J. / Chruszcz, M. / Reddy, G. / Grembecka, J. / Cierpicki, T.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Menin Reveals Binding Site for Mixed Lineage Leukemia (MLL) Protein.
Authors: Murai, M.J. / Chruszcz, M. / Reddy, G. / Grembecka, J. / Cierpicki, T.

History

Deposition	Apr 2, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 13, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 21, 2011	Group: Database references
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3re2.cif.gz	195.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3re2.ent.gz	157 KB	Display	PDB format
PDBx/mmJSON format	3re2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/re/3re2 ftp://data.pdbj.org/pub/pdb/validation_reports/re/3re2	HTTPS FTP

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Related structure data

Similar structure data	3mo4-2 1twd-d 1ud5-d 2d3l-d 1x8c-d 1x7i-d 6gxv-2 3bh4-2 3mo4-1 1wp6-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#31 - Jul 2002 p53 Tumor Suppressor similarity (1) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Predicted protein

hetero molecules

53.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	89.881, 89.881, 115.601
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-487- GOL

#1: Protein	Predicted protein Mass: 52997.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nematostella vectensis (starlet sea anemone) Gene: v1g241841 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: A7RZU9
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.16 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 3350, 0.1 M Bis-Tris pH 6.0, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F	1	0.9787
SYNCHROTRON	APS	19-BM	2	0.9791

Detector

Type	ID	Detector	Date	Details
MARMOSAIC 225 mm CCD	1	CCD	Mar 17, 2011	mirrors
ADSC QUANTUM 210r	2	CCD	Mar 17, 2011	mirrors

Radiation

Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9787	1
2	0.9791	1

Reflection

Resolution: 1.95→50 Å / Num. all: 35267 / Num. obs: 35267 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.8 % / R_merge(I) obs: 0.091 / R_sym value: 0.091 / Net I/σ(I): 34.8

Reflection shell

Resolution: 1.95→1.98 Å / Redundancy: 13.5 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1725 / R_sym value: 0.78 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
MD2		data collection
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		model building
RESOLVE		model building
ARP/wARP		model building
CCP4		model building
REFMAC	5.5.0109	refinement
Coot		model building
HKL-2000		data reduction
HKL-2000		data scaling
DM		phasing
RESOLVE		phasing
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.95→50 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.939 / SU B: 5.995 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21145	1767	5 %	RANDOM
R_work	0.16107	-	-	-
all	0.16349	33400	-	-
obs	0.16349	33400	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 34.498 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.61 Å²	0 Å²	0 Å²
2-	-	0.61 Å²	0 Å²
3-	-	-	-1.22 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3468	0	6	339	3813

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	3645
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2439
X-RAY DIFFRACTION	r_angle_refined_deg	1.602	1.95	4950
X-RAY DIFFRACTION	r_angle_other_deg	1.001	3	5959
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.894	5	448
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.129	24.593	172
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.712	15	615
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.842	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	539
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	4059
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	740
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.986	1.5	2220
X-RAY DIFFRACTION	r_mcbond_other	0.297	1.5	891
X-RAY DIFFRACTION	r_mcangle_it	1.731	2	3581
X-RAY DIFFRACTION	r_scbond_it	2.621	3	1425
X-RAY DIFFRACTION	r_scangle_it	4.012	4.5	1366
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.265	115	-
R_work	0.191	2448	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	6.5784	3.0471	0.7139	5.2852	0.9793	3.5553	0.0731	0.5278	-0.4058	-0.2288	0.067	0.0397	0.4295	-0.1627	-0.1401	0.1452	-0.0215	-0.0275	0.1395	-0.024	0.0769	15.212	31.002	1.918
2	2.0289	1.7199	-0.6778	5.3191	-1.7955	3.028	-0.0857	0.0626	-0.2216	-0.0946	0.1217	0.1995	0.2275	-0.314	-0.036	0.0496	-0.0297	0.0018	0.0812	0.0011	0.0717	12.465	33.967	12.029
3	2.9436	2.4757	0.3945	7.1954	-0.0599	1.8942	-0.1124	0.1326	0.0858	0.0316	0.1636	0.4854	-0.1695	-0.398	-0.0512	0.0829	-0.0049	-0.0398	0.1523	0.0594	0.0905	6.633	45.336	9.053
4	1.6302	0.2745	-0.1474	2.3433	-1.0078	2.4754	-0.0558	-0.0685	0.0931	0.1718	0.0957	0.1124	-0.2018	-0.1898	-0.0399	0.0489	0.0129	0.0136	0.0419	0.0103	0.0326	12.888	45.564	20.893
5	2.827	-0.8832	1.4943	2.7006	-0.8702	2.1074	-0.19	-0.2205	0.2995	0.2699	0.1481	-0.1269	-0.3795	0.2226	0.0419	0.1445	-0.0296	-0.0059	0.1308	-0.035	0.1362	26.943	49.364	26.123
6	1.6379	-0.6072	-0.3793	2.6857	0.0883	1.6948	-0.0761	0.0349	-0.1197	0.0655	0.0531	0.1421	0.2907	0.0128	0.023	0.0851	-0.0095	0.0152	0.059	-0.0093	0.0412	22.747	29.109	14.141
7	0.9218	0.5463	0.2635	3.661	1.109	2.2187	0.0084	0.0252	-0.0396	-0.0265	0.0548	-0.3264	0.2354	0.2089	-0.0632	0.0631	0.0378	0.012	0.0926	-0.0129	0.0775	34.934	27.109	17.148
8	1.8464	-0.6574	-0.27	2.6939	-0.4964	1.7098	-0.0752	-0.3188	-0.2384	0.2456	0.0529	-0.0683	0.2172	0.0591	0.0223	0.108	0.044	-0.04	0.1761	0.0216	0.1183	35.577	26.338	34.223
9	2.8741	-1.65	-0.0605	2.15	-0.3086	1.9302	-0.3378	-0.5673	-0.1173	0.4334	0.1911	-0.2421	-0.0163	0.3423	0.1467	0.1868	0.0799	-0.0993	0.391	0.0776	0.1688	44.345	27.218	45.468
10	22.2674	-22.1332	1.41	45.6762	-14.6196	16.182	-0.4361	-1.2063	0.3884	1.3603	0.1207	-1.2475	0.257	0.4166	0.3154	0.4783	0.0741	-0.1383	0.6126	0.0279	0.0618	39.857	29.464	56.078

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 30
2	X-RAY DIFFRACTION	2	A	31 - 47
3	X-RAY DIFFRACTION	3	A	58 - 88
4	X-RAY DIFFRACTION	4	A	89 - 149
5	X-RAY DIFFRACTION	5	A	150 - 208
6	X-RAY DIFFRACTION	6	A	209 - 252
7	X-RAY DIFFRACTION	7	A	253 - 292
8	X-RAY DIFFRACTION	8	A	293 - 358
9	X-RAY DIFFRACTION	9	A	370 - 445
10	X-RAY DIFFRACTION	10	A	451 - 459

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