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- PDB-6mlc: PHD6 domain of MLL3 in complex with histone H4 -

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Basic information

Entry
Database: PDB / ID: 6mlc
TitlePHD6 domain of MLL3 in complex with histone H4
Components
  • Histone H4
  • Histone-lysine N-methyltransferase 2C
KeywordsTRANSFERASE / MLL3 / PHD6 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / acyltransferase activity / histone methyltransferase activity / Formation of WDR5-containing histone-modifying complexes / negative regulation of megakaryocyte differentiation ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / acyltransferase activity / histone methyltransferase activity / Formation of WDR5-containing histone-modifying complexes / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / response to electrical stimulus / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / methylation / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / transcription coactivator activity / protein heterodimerization activity / Amyloid fiber formation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
Histone-lysine N-methyltransferase 2C / KMT2C, ePHD1 / KMT2C, ePHD2 / : / : / : / DHHC domain profile. / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / FY-rich, N-terminal ...Histone-lysine N-methyltransferase 2C / KMT2C, ePHD1 / KMT2C, ePHD2 / : / : / : / DHHC domain profile. / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / 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 / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / PHD-zinc-finger like domain / 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 / Ring finger / Zinc finger PHD-type signature. / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H4 / Histone-lysine N-methyltransferase 2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsDong, A. / Liu, Y. / Qin, S. / Lei, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2019
Title: Structural insights into trans-histone regulation of H3K4 methylation by unique histone H4 binding of MLL3/4.
Authors: Liu, Y. / Qin, S. / Chen, T.Y. / Lei, M. / Dhar, S.S. / Ho, J.C. / Dong, A. / Loppnau, P. / Li, Y. / Lee, M.G. / Min, J.
History
DepositionSep 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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 2C
B: Histone-lysine N-methyltransferase 2C
C: Histone-lysine N-methyltransferase 2C
D: Histone-lysine N-methyltransferase 2C
E: Histone H4
F: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,39032
Polymers46,0146
Non-polymers1,37626
Water2,504139
1
A: Histone-lysine N-methyltransferase 2C
B: Histone-lysine N-methyltransferase 2C
E: Histone H4
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)141,34296
Polymers138,04218
Non-polymers3,30078
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area36720 Å2
ΔGint-813 kcal/mol
Surface area49960 Å2
MethodPISA
2
C: Histone-lysine N-methyltransferase 2C
D: Histone-lysine N-methyltransferase 2C
F: Histone H4
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)142,99996
Polymers138,04218
Non-polymers4,95778
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area42610 Å2
ΔGint-793 kcal/mol
Surface area47990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.939, 85.939, 98.733
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDEF

#1: Protein
Histone-lysine N-methyltransferase 2C / Lysine N-methyltransferase 2C / Homologous to ALR protein / Myeloid/lymphoid or mixed-lineage ...Lysine N-methyltransferase 2C / Homologous to ALR protein / Myeloid/lymphoid or mixed-lineage leukemia protein 3


Mass: 10502.802 Da / Num. of mol.: 4 / Fragment: PHD-type 7 zinc finger, residues 1055-1144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2C, HALR, KIAA1506, MLL3 / Plasmid: pET28GST-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE
References: UniProt: Q8NEZ4, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H4


Mass: 2001.370 Da / Num. of mol.: 2 / Fragment: residues 2-21 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805

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Non-polymers , 4 types, 165 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.37 Å3/Da / Density % sol: 48.1 % / Mosaicity: 0.3 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2 M Na-Form, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→43.01 Å / Num. obs: 38485 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.032 / Rrim(I) all: 0.103 / Net I/σ(I): 18.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.839.21.35722740.6860.4631.43599.5
8.99-42.979.90.0393260.9990.0130.04199.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
HKL-3000data reduction
RefinementResolution: 1.8→43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.697 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1507 3.9 %RANDOM
Rwork0.1944 ---
obs0.1952 36874 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.99 Å2 / Biso mean: 27.893 Å2 / Biso min: 10.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å2-0 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 1.8→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 51 143 2960
Biso mean--31.8 33.82 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132955
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182482
X-RAY DIFFRACTIONr_angle_refined_deg1.351.6414002
X-RAY DIFFRACTIONr_angle_other_deg1.3931.5775780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.365366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69821.327196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1315481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4721533
X-RAY DIFFRACTIONr_chiral_restr0.0790.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023439
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02680
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 95 -
Rwork0.274 2747 -
all-2842 -
obs--99.93 %

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