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- PDB-4cy1: Crystal structure of the KANSL1-WDR5 complex. -

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Basic information

Entry
Database: PDB / ID: 4cy1
TitleCrystal structure of the KANSL1-WDR5 complex.
Components
  • KAT8 REGULATORY NSL COMPLEX SUBUNIT 1
  • WD REPEAT-CONTAINING PROTEIN 5
KeywordsTRANSCRIPTION / EPIGENETIC REGULATOR / HISTONE ACETYLATION / CHROMATIN
Function / homology
Function and homology information


: / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation ...: / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / histone acetyltransferase binding / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / kinetochore / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / chromatin organization / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
KAT8 regulatory NSL complex subunit 1 / PEHE domain / PEHE domain / PEHE / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...KAT8 regulatory NSL complex subunit 1 / PEHE domain / PEHE domain / PEHE / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5 / KAT8 regulatory NSL complex subunit 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDias, J. / Brettschneider, J. / Cusack, S. / Kadlec, J.
CitationJournal: Genes Dev. / Year: 2014
Title: Structural Analysis of the Kansl1/Wdr5/Kansl2 Complex Reveals that Wdr5 is Required for Efficient Assembly and Chromatin Targeting of the Nsl Complex.
Authors: Dias, J. / Van Nguyen, N. / Georgiev, P. / Gaub, A. / Brettschneider, J. / Cusack, S. / Kadlec, J. / Akhtar, A.
History
DepositionApr 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD REPEAT-CONTAINING PROTEIN 5
B: WD REPEAT-CONTAINING PROTEIN 5
C: KAT8 REGULATORY NSL COMPLEX SUBUNIT 1
D: KAT8 REGULATORY NSL COMPLEX SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7397
Polymers72,4624
Non-polymers2763
Water5,783321
1
A: WD REPEAT-CONTAINING PROTEIN 5
D: KAT8 REGULATORY NSL COMPLEX SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4154
Polymers36,2312
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-8.8 kcal/mol
Surface area12260 Å2
MethodPISA
2
B: WD REPEAT-CONTAINING PROTEIN 5
C: KAT8 REGULATORY NSL COMPLEX SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3233
Polymers36,2312
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-8 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.760, 92.450, 81.170
Angle α, β, γ (deg.)90.00, 90.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99994, 0.0076, -0.0078), (-0.0076, -0.99997, -0.00091), (-0.00781, -0.00085, 0.99997)11.55323, -22.66982, -40.55124
2given(-0.99989, -0.00911, 0.01185), (0.00912, -0.99996, 0.00102), (0.01184, 0.00113, 0.99993)12.44732, -22.64658, 40.65837

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Components

#1: Protein WD REPEAT-CONTAINING PROTEIN 5 / BMP2-INDUCED 3-KB GENE PROTEIN


Mass: 34620.289 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P61964
#2: Protein/peptide KAT8 REGULATORY NSL COMPLEX SUBUNIT 1 / KANSL1 / MLL1/MLL COMPLEX SUBUNIT KANSL1 / MSL1 HOMOLOG 1 / HMSL1V1 / NSL COMPLEX PROTEIN NSL1 / ...KANSL1 / MLL1/MLL COMPLEX SUBUNIT KANSL1 / MSL1 HOMOLOG 1 / HMSL1V1 / NSL COMPLEX PROTEIN NSL1 / NON-SPECIFIC LETHAL 1 HOMOLOG


Mass: 1610.834 Da / Num. of mol.: 2 / Fragment: RESIDUES 585-598 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q7Z3B3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.07 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 6.5
Details: 26% (W/V) PEG 3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS, PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.793
11-h,-k,l20.207
ReflectionResolution: 1.5→100 Å / Num. obs: 90649 / % possible obs: 96.7 % / Observed criterion σ(I): 2.38 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.4 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G99

2g99


Resolution: 1.5→40.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.82 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18344 4494 5 %RANDOM
Rwork0.16989 ---
obs0.17057 86154 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.934 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20.74 Å2
2--4.49 Å20 Å2
3----3.32 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4891 0 18 321 5230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195022
X-RAY DIFFRACTIONr_bond_other_d0.0010.024762
X-RAY DIFFRACTIONr_angle_refined_deg1.0071.9456807
X-RAY DIFFRACTIONr_angle_other_deg0.665311021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66324.815189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5615863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9871510
X-RAY DIFFRACTIONr_chiral_restr0.060.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021109
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4437.1962524
X-RAY DIFFRACTIONr_mcbond_other0.44360.3932523
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.541.1982498
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.5535001
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded2.65754890
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 306 -
Rwork0.246 5563 -
obs--84.34 %

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