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- PDB-5f6l: The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbB... -

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Basic information

Entry
Database: PDB / ID: 5f6l
TitleThe crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L
Components
  • Histone-lysine N-methyltransferase 2A
  • Retinoblastoma-binding protein 5
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
KeywordsPROTEIN BINDING/TRANSFERASE / histone methyltransferase / histone methylation / SET domain / protein complex / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex ...negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / definitive hemopoiesis / regulation of short-term neuronal synaptic plasticity / histone H3K4 methyltransferase activity / anterior/posterior pattern specification / embryonic hemopoiesis / T-helper 2 cell differentiation / Formation of WDR5-containing histone-modifying complexes / exploration behavior / histone methyltransferase complex / minor groove of adenine-thymine-rich DNA binding / hemopoiesis / MLL1 complex / membrane depolarization / cellular response to transforming growth factor beta stimulus / negative regulation of fibroblast proliferation / spleen development / homeostasis of number of cells within a tissue / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / Deactivation of the beta-catenin transactivating complex / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / beta-catenin binding / visual learning / protein modification process / PKMTs methylate histone lysines / response to estrogen / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein-containing complex assembly / fibroblast proliferation / histone binding / methylation / transcription cis-regulatory region binding / positive regulation of cell population proliferation / apoptotic process / DNA damage response / chromatin binding / positive regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 ...: / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / SPRY domain / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Beta-clip-like / SET domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Beta Complex / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / WD domain, G-beta repeat / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Trp-Asp (WD) repeats profile. / Jelly Rolls / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase 2A / Retinoblastoma-binding protein 5 / Set1/Ash2 histone methyltransferase complex subunit ASH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Model detailshistone methylation, histone methyltransferase
AuthorsLi, Y. / Lei, M. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08010201 China
CitationJournal: Nature / Year: 2016
Title: Structural basis for activity regulation of MLL family methyltransferases.
Authors: Li, Y. / Han, J. / Zhang, Y. / Cao, F. / Liu, Z. / Li, S. / Wu, J. / Hu, C. / Wang, Y. / Shuai, J. / Chen, J. / Cao, L. / Li, D. / Shi, P. / Tian, C. / Zhang, J. / Dou, Y. / Li, G. / Chen, Y. / Lei, M.
History
DepositionDec 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Retinoblastoma-binding protein 5
B: Set1/Ash2 histone methyltransferase complex subunit ASH2
A: Histone-lysine N-methyltransferase 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5465
Polymers42,0963
Non-polymers4502
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.966, 44.410, 117.792
Angle α, β, γ (deg.)90.000, 106.160, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-4215-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules J

#1: Protein/peptide Retinoblastoma-binding protein 5 / RBBP-5 / Retinoblastoma-binding protein RBQ-3


Mass: 3255.321 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 330-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP5, RBQ3 / Plasmid: pET28b-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q15291

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Protein , 2 types, 2 molecules BA

#2: Protein Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein


Mass: 20597.355 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 380-496, 539-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH2L, ASH2L1 / Plasmid: pET28b-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9UBL3
#3: Protein Histone-lysine N-methyltransferase 2A / Lysine N-methyltransferase 2A / ALL-1 / CXXC-type zinc finger protein 7 / Myeloid/lymphoid or mixed- ...Lysine N-methyltransferase 2A / ALL-1 / CXXC-type zinc finger protein 7 / Myeloid/lymphoid or mixed-lineage leukemia / Myeloid/lymphoid or mixed-lineage leukemia protein 1 / Trithorax-like protein / Zinc finger protein HRX


Mass: 18243.195 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 3813-3969 / Mutation: N3861I, Q3867L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / Plasmid: pET28b-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q03164, histone-lysine N-methyltransferase

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Non-polymers , 3 types, 363 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 200mM NaCl, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 29683 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.14 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.097 / Rrim(I) all: 0.186 / Χ2: 1.225 / Net I/av σ(I): 11.333 / Net I/σ(I): 6.1 / Num. measured all: 106735
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.973.30.54829500.6770.3610.6580.75999.8
1.97-2.053.40.43429250.790.280.5180.86199.8
2.05-2.143.50.38829520.840.2430.4590.91199.7
2.14-2.253.60.3529450.850.2140.4110.99599.8
2.25-2.393.70.29329550.9120.1760.3431.03799.8
2.39-2.583.70.26529690.9290.160.311.1799.7
2.58-2.843.70.20829450.950.1260.2441.45399.8
2.84-3.253.70.1529690.9730.0910.1761.78799.6
3.25-4.093.60.08729880.9860.0530.1021.51899.3
4.09-503.70.07330850.9890.0440.0861.699.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TOJ, 2W5Y

3toj

2w5y


Resolution: 1.9→37.537 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 2975 10.06 %Random
Rwork0.1663 26602 --
obs0.1711 29577 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.99 Å2 / Biso mean: 21.4602 Å2 / Biso min: 4.53 Å2
Refinement stepCycle: final / Resolution: 1.9→37.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 27 361 3192
Biso mean--27.14 29.99 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082900
X-RAY DIFFRACTIONf_angle_d1.0443904
X-RAY DIFFRACTIONf_chiral_restr0.046401
X-RAY DIFFRACTIONf_plane_restr0.005501
X-RAY DIFFRACTIONf_dihedral_angle_d14.491089
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.93120.28881460.213512431389100
1.9312-1.96450.26161320.200812511383100
1.9645-2.00030.25121480.188112491397100
2.0003-2.03870.22491250.177312721397100
2.0387-2.08030.2121480.174812631411100
2.0803-2.12560.25771230.174412551378100
2.1256-2.1750.23871430.170612741417100
2.175-2.22940.25131420.165612531395100
2.2294-2.28970.2161410.162212641405100
2.2897-2.3570.23361260.17512511377100
2.357-2.43310.24581530.181812721425100
2.4331-2.520.24481230.17581268139199
2.52-2.62090.21731500.16712621412100
2.6209-2.74020.19761410.179212891430100
2.7402-2.88460.23091360.172812631399100
2.8846-3.06520.23821360.16912731409100
3.0652-3.30180.22111520.15371244139699
3.3018-3.63380.18821570.15051276143399
3.6338-4.1590.17071460.14211252139899
4.159-5.23770.16181480.13612941442100
5.2377-37.54420.19661590.189813341493100
Refinement TLS params.

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

IDL11 (°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)
18.7674-5.4503-4.98984.19485.45149.67680.04190.612-0.6897-0.2043-0.80420.96780.2246-1.35940.66290.3163-0.0927-0.00880.5314-0.01030.416722.9944-10.895360.6478
25.7515-3.47585.37057.7574-3.5415.0574-0.358-0.79890.34360.50060.03160.344-0.2039-1.03220.2370.2616-0.0188-0.01920.39110.01980.172929.1079-4.1791368.1282
37.3611-3.8810.05144.5517-2.47055.4464-0.12170.2847-0.7098-0.36710.19160.35730.6271-0.3224-0.00650.2069-0.0419-0.03950.1197-0.03290.139143.3211-9.9227373.9243
45.9086-0.3492-0.58085.6572-1.2925.37780.1310.24830.8065-0.3512-0.15390.1402-0.9825-0.44830.22930.22040.04590.02930.06890.03590.179552.101414.7967380.2443
51.10620.82250.14464.46410.62053.00340.0456-0.05190.3209-0.1075-0.25380.3228-0.319-0.4690.13970.08530.0265-0.01440.0944-0.0060.137943.36517.6932381.3926
61.8734-0.29351.31741.61910.36931.5255-0.08510.42310.3886-0.43390.0278-0.2069-0.36350.19990.03840.1239-0.05440.0560.0810.02260.131558.80378.5292378.1155
71.81720.570.4561.64180.30311.7703-0.0377-0.01530.02870.00170.02520.05690.0385-0.05580.01890.0644-0.00810.01290.0411-0.00030.062352.04080.3605386.9335
81.83050.47021.36023.0968-0.27262.24010.05080.2621-0.0185-0.481-0.0554-0.13160.0260.3013-0.00140.13620.00950.040.0949-0.00750.057454.26060.0294371.3592
91.2939-0.3989-0.77081.72170.68583.8169-0.00350.0474-0.1882-0.0185-0.03140.02960.371-0.07660.02610.0785-0.0063-0.00820.05060.00030.093854.0914-9.1957383.33
103.58951.0536-1.3782.1808-0.60123.49930.061-0.0407-0.037-0.16820.002-0.41980.10040.32370.06860.0508-0.00510.00160.1069-0.00690.149765.402-1.2477386.0301
110.23560.1829-0.95762.78671.04325.81650.20220.05170.05620.0040.0969-0.3730.35140.5188-0.14770.08790.06130.0150.1361-0.01610.122862.8976-7.3665388.7532
121.61320.18260.22151.77340.2551.6189-0.0295-0.08380.0319-0.0070.0479-0.1158-0.03970.1775-0.02390.0644-0.0060.01930.0582-0.00540.070359.0824.568386.9206
133.565-0.0291-1.10075.22594.30188.0991-0.1063-0.0168-0.16770.063-0.3610.29810.3824-0.58550.40410.13080.0402-0.03560.13890.01420.15217.6744-0.4224353.943
146.8889-1.77544.22863.1411-1.72765.8315-0.1471-0.24110.4098-0.1138-0.0753-0.0719-0.1029-0.54570.19140.10590.0194-0.01070.1738-0.03740.110818.33613.4788353.2546
152.82630.4381-0.13377.01914.61873.70680.17570.4475-0.6789-0.14640.1874-0.33570.21630.3661-0.35130.19690.0645-0.06930.2279-0.04260.235841.1849-9.2567361.7962
164.8649-0.14650.51294.3969-0.16062.12860.16950.2151-0.3273-0.2179-0.0474-0.0310.33650.1631-0.08680.17520.0351-0.0380.15570.00590.115534.4872-4.6223358.8262
177.6450.8582-0.4295.98211.07255.9061-0.07590.1915-0.1945-0.3491-0.1938-0.47860.32820.46070.19070.13570.0459-0.01130.1517-0.00960.122526.7716-0.8511345.3932
184.70590.30321.17563.69063.53185.7172-0.3638-0.53690.53540.10160.06780.0895-0.24210.1180.17730.11680.0371-0.02270.1971-0.03040.213626.33756.9716359.6287
193.8710.0035-0.2394.14570.47154.0863-0.2130.19520.0051-0.36570.1116-0.73860.22990.64650.06530.2610.01310.03770.34380.03060.221629.89791.9169340.926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'J' and (resid 336 through 340 )J0
2X-RAY DIFFRACTION2chain 'J' and (resid 341 through 345 )J0
3X-RAY DIFFRACTION3chain 'J' and (resid 346 through 354 )J0
4X-RAY DIFFRACTION4chain 'B' and (resid 285 through 294 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 295 through 313 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 314 through 324 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 325 through 347 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 348 through 362 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 363 through 390 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 391 through 451 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 452 through 461 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 462 through 504 )B0
13X-RAY DIFFRACTION13chain 'A' and (resid 3814 through 3845 )A0
14X-RAY DIFFRACTION14chain 'A' and (resid 3846 through 3860 )A0
15X-RAY DIFFRACTION15chain 'A' and (resid 3861 through 3878 )A0
16X-RAY DIFFRACTION16chain 'A' and (resid 3879 through 3900 )A0
17X-RAY DIFFRACTION17chain 'A' and (resid 3901 through 3912 )A0
18X-RAY DIFFRACTION18chain 'A' and (resid 3913 through 3930 )A0
19X-RAY DIFFRACTION19chain 'A' and (resid 3931 through 3969 )A0

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