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- PDB-4pzi: Zinc finger region of MLL2 in complex with CpG DNA -

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Basic information

Entry
Database: PDB / ID: 4pzi
TitleZinc finger region of MLL2 in complex with CpG DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3')
  • Histone-lysine N-methyltransferase 2B
KeywordsTRANSCRIPTION/DNA / zinc finger / dna-binding / Structural Genomics / Structural Genomics Consortium / SGC / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / MLL1/2 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / MLL1/2 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / methylation / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
KMT2B, ePHD domain / 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 ...KMT2B, ePHD domain / 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-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone-lysine N-methyltransferase 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsChao, X. / Tempel, W. / Liu, K. / Dong, A. / 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
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Aug 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 1.3Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,0236
Polymers14,8923
Non-polymers1313
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-21 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.736, 41.005, 55.508
Angle α, β, γ (deg.)90.000, 99.240, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit has not been determined

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Components

#1: Protein Histone-lysine N-methyltransferase 2B / Lysine N-methyltransferase 2B / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / Trithorax ...Lysine N-methyltransferase 2B / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / Trithorax homolog 2 / WW domain-binding protein 7 / WBP-7


Mass: 7563.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2B, HRX2, KIAA0304, MLL2, MLL4, TRX2, WBP7 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2
References: UniProt: Q9UMN6, histone-lysine N-methyltransferase
#2: DNA chain DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3')


Mass: 3664.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic dna
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.8 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 25% PEG-3350, 0.2 M ammonium sulfate, 0.1 M TRIS, pH 8.5, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→35.36 Å / Num. obs: 8659 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.15-2.223.71.131.42711729100
8.87-35.363.20.02452.641413095

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.14data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.13data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure of isomorphous crystal was solved by molecular replacement using currently unpublished models of same protein and DNA, respectively.

Resolution: 2.15→34.91 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2545 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7123 / SU B: 15.511 / SU ML: 0.204 / SU R Cruickshank DPI: 0.2259 / SU Rfree: 0.2013 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: coot was used for interactive model building. Model geometry was assessed with molprobity. I note the poor side chain fit of His-957 to electron density. I attempted modeling an alternate ...Details: coot was used for interactive model building. Model geometry was assessed with molprobity. I note the poor side chain fit of His-957 to electron density. I attempted modeling an alternate conformation in which N-terminal extension of main chain and this side chain are switched, but abandoned the attempt after failing to fit a good rotamer to the density.
RfactorNum. reflection% reflectionSelection details
Rfree0.2728 398 4.6 %RANDOM
Rwork0.2258 ---
obs0.228 8658 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.63 Å2 / Biso mean: 61.8311 Å2 / Biso min: 30.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20.68 Å2
2---2.17 Å2-0 Å2
3---2.55 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms441 486 3 8 938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0151001
X-RAY DIFFRACTIONr_bond_other_d0.0020.02697
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.4991441
X-RAY DIFFRACTIONr_angle_other_deg1.2613.011605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.20621.76517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0051582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.299155
X-RAY DIFFRACTIONr_chiral_restr0.0810.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02810
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_mcbond_it2.7943.106245
X-RAY DIFFRACTIONr_mcbond_other2.7793.107244
X-RAY DIFFRACTIONr_mcangle_it3.9624.656305
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 28 -
Rwork0.343 582 -
all-610 -
obs--99.84 %
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)
12.6491-0.87430.25447.2098-0.23967.0875-0.00270.4103-0.0876-0.1508-0.06790.13140.3874-0.04850.07060.1359-0.0387-0.05340.0763-0.01470.194983.187133.014217.1601
27.24953.270.74846.71470.15715.2408-0.0972-0.14820.0808-0.08630.0367-0.1079-0.21770.17820.06050.1412-0.0295-0.0030.25010.03920.17783.171841.529310.8417
37.98643.37431.23897.40870.00936.0651-0.21910.26830.8885-0.35050.22440.0801-0.36460.0102-0.00530.1165-0.026-0.10090.16940.01920.264781.92642.680511.0556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A956 - 1016
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION3C1 - 12

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