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- PDB-4nw3: Crystal structure of MLL CXXC domain in complex with a CpG DNA -

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Basic information

Entry
Database: PDB / ID: 4nw3
TitleCrystal structure of MLL CXXC domain in complex with a CpG DNA
Components
  • 5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3'
  • Histone-lysine N-methyltransferase 2A
KeywordsDNA BINDING PROTEIN/DNA / Histone-lysine N-methyltransferase / CpG island / CG island / structural genomics consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation / definitive hemopoiesis ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation / definitive hemopoiesis / histone H3K4 methyltransferase activity / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / circadian regulation of gene expression / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / methylation / protein-containing complex assembly / apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. ...KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / 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. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain profile. / SET domain / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.82 Å
AuthorsBian, C. / Tempel, W. / Chao, X. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2018
Title: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Authors: Xu, C. / Liu, K. / Lei, M. / Yang, A. / Li, Y. / Hughes, T.R. / Min, J.
History
DepositionDec 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase 2A
B: 5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3'
C: 5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2635
Polymers16,1323
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-17 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.327, 40.225, 60.959
Angle α, β, γ (deg.)90.000, 93.510, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DC / End label comp-ID: DC / Refine code: _ / Auth seq-ID: 1 - 12 / Label seq-ID: 1 - 12

Dom-IDAuth asym-IDLabel asym-ID
1BB
2CC

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Components

#1: 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: 8805.320 Da / Num. of mol.: 1 / Fragment: CXXC zinc finger domain (UNP residues 1147-1204)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q03164
#2: DNA chain 5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3'


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CpG island
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% PEG3350, 0.05 M sodium tartrate, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28231 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28231 Å / Relative weight: 1
ReflectionResolution: 2.82→40 Å / Num. all: 4229 / Num. obs: 4229 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.066 / Χ2: 1.96 / Net I/av σ(I): 31.989 / Net I/σ(I): 12.2 / Num. measured all: 30008
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.82-2.923.60.9518090.9091100
2.92-3.043.80.6868061.0391100
3.04-3.183.80.48041.1911100
3.18-3.343.80.0848241.701199.9
3.34-3.553.70.0857821.945199.9
3.55-3.833.80.0997812.2131100
3.83-4.213.80.0818162.4621100
4.21-4.823.70.0688052.8941100
4.82-6.073.70.0538132.771100
6.07-403.70.0397922.49198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3QMB AND 3QMG

3qmb

3qmg


Resolution: 2.82→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2828 / WRfactor Rwork: 0.2543 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7519 / SU B: 34.965 / SU ML: 0.313 / SU R Cruickshank DPI: 0.7286 / SU Rfree: 0.3517 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.729 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: AUTHORS NOTE THE SMALL NUMBER OF REFLECTIONS IN THE FREE SET, WHICH REDUCES RELIABILITY OF CROSS VALIDATION. COOT, AUTOBUSTER AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 191 4.6 %RANDOM
Rwork0.2185 3999 --
obs0.2206 4190 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.37 Å2 / Biso mean: 101.494 Å2 / Biso min: 67.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0 Å23.9 Å2
2---4.59 Å20 Å2
3---5.62 Å2
Refinement stepCycle: LAST / Resolution: 2.82→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms355 486 2 0 843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.014910
X-RAY DIFFRACTIONr_bond_other_d0.0050.02599
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.4691322
X-RAY DIFFRACTIONr_angle_other_deg2.4313.0121389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.435550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.51726.15413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3831563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.471152
X-RAY DIFFRACTIONr_chiral_restr0.1130.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021712
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02198
X-RAY DIFFRACTIONr_mcbond_it2.1155.773203
X-RAY DIFFRACTIONr_mcbond_other2.1155.757202
X-RAY DIFFRACTIONr_mcangle_it3.3238.635252
Refine LS restraints NCS

Ens-ID: 1 / Number: 892 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2C
LS refinement shellResolution: 2.82→2.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 14 -
Rwork0.382 303 -
all-317 -
obs--96.65 %
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)
11.51270.0888-1.33631.47550.84579.9494-0.21630.25120.26710.25620.2878-0.26640.12760.1366-0.07150.2348-0.1488-0.01840.3656-0.05170.349219.3136-5.729823.2058
25.72420.2359-1.54837.38252.19575.1878-0.22050.0040.4862-0.32590.00830.2667-0.0178-0.11570.21230.2135-0.2552-0.03290.38110.10010.319815.969-5.9910.5357
37.8321.2730.721710.80131.68811.9459-0.54791.03190.2112-0.59760.6366-0.0769-0.0676-0.2073-0.08880.185-0.3048-0.00670.52460.03570.436715.1049-4.946511.637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1150 - 1200
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION3C1 - 12

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