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- PDB-5svh: Crystal structure of the KIX domain of CBP in complex with a MLL/... -

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Basic information

Entry
Database: PDB / ID: 5svh
TitleCrystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera
Components
  • CREB-binding protein
  • MLL/c-Myb chimera
KeywordsTRANSCRIPTION / CBP / 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 / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity ...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 / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / N-terminal peptidyl-lysine acetylation / regulation of short-term neuronal synaptic plasticity / regulation of smoothened signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / definitive hemopoiesis / MRF binding / histone H3K4 methyltransferase activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / anterior/posterior pattern specification / T-helper 2 cell differentiation / exploration behavior / embryonic hemopoiesis / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / protein-lysine-acetyltransferase activity / embryonic digit morphogenesis / histone methyltransferase complex / protein acetylation / homeostatic process / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / Formation of paraxial mesoderm / histone acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / acetyltransferase activity / FOXO-mediated transcription of cell death genes / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / minor groove of adenine-thymine-rich DNA binding / MLL1 complex / histone acetyltransferase complex / membrane depolarization / canonical NF-kappaB signal transduction / cellular response to nutrient levels / positive regulation of double-strand break repair via homologous recombination / Attenuation phase / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / regulation of cellular response to heat / negative regulation of fibroblast proliferation / histone acetyltransferase / cellular response to transforming growth factor beta stimulus / spleen development / homeostasis of number of cells within a tissue / : / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Transcriptional and post-translational regulation of MITF-M expression and activity / CD209 (DC-SIGN) signaling / transcription initiation-coupled chromatin remodeling / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / : / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / Heme signaling
Similarity search - Function
Coactivator CBP, KIX domain / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 ...Coactivator CBP, KIX domain / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / 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 / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Post-SET domain / Post-SET domain profile. / Coactivator CBP, KIX domain superfamily / Myb-type HTH DNA-binding domain profile. / Serum Albumin; Chain A, Domain 1 / Zinc finger ZZ-type signature. / Myb domain / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / 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 / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Nuclear receptor coactivator, interlocking / 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 / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator Myb / Histone-lysine N-methyltransferase 2A / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLangelaan, D.N. / Smith, S.P. / Allingham, J.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Design of a nanomolar affinity ligand to the KIX domain of CBP
Authors: Langelaan, D.N. / Smith, S.P.
History
DepositionAug 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / Item: _entity.pdbx_fragment
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CREB-binding protein
B: MLL/c-Myb chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,16911
Polymers16,7372
Non-polymers4329
Water1,802100
1
A: CREB-binding protein
hetero molecules

B: MLL/c-Myb chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,16911
Polymers16,7372
Non-polymers4329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
Buried area2270 Å2
ΔGint-46 kcal/mol
Surface area9460 Å2
MethodPISA
2
A: CREB-binding protein
B: MLL/c-Myb chimera
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)103,01666
Polymers100,42212
Non-polymers2,59454
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area35400 Å2
ΔGint-404 kcal/mol
Surface area34990 Å2
MethodPISA
3
A: CREB-binding protein
B: MLL/c-Myb chimera
hetero molecules

A: CREB-binding protein
B: MLL/c-Myb chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,33922
Polymers33,4744
Non-polymers86518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
Buried area10340 Å2
ΔGint-125 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.820, 119.820, 50.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-102-

CL

21A-805-

HOH

31A-827-

HOH

41B-204-

HOH

51B-220-

HOH

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Components

#1: Protein CREB-binding protein


Mass: 10353.856 Da / Num. of mol.: 1 / Fragment: UNP residues 587-673
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793, histone acetyltransferase
#2: Protein MLL/c-Myb chimera / 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 / Proto-oncogene c-Myb


Mass: 6383.193 Da / Num. of mol.: 1
Fragment: UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315,UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Gallus gallus (chicken)
Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1, MYB / Production host: Escherichia coli (E. coli)
References: UniProt: Q03164, UniProt: P01103, histone-lysine N-methyltransferase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.12 Å3/Da / Density % sol: 60.6 % / Description: Large hexagonal prism
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M potassium sulfate 2.3M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→59.9 Å / Num. obs: 13648 / % possible obs: 98.7 % / Redundancy: 27.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 31
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 24.7 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.871 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2agh

2agh


Resolution: 2.05→59.9 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.47
RfactorNum. reflection% reflection
Rfree0.242 693 5.08 %
Rwork0.2063 --
obs0.2082 13646 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→59.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 19 100 1165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071092
X-RAY DIFFRACTIONf_angle_d0.971463
X-RAY DIFFRACTIONf_dihedral_angle_d13.338443
X-RAY DIFFRACTIONf_chiral_restr0.042158
X-RAY DIFFRACTIONf_plane_restr0.005186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.20830.28541260.24362503X-RAY DIFFRACTION97
2.2083-2.43060.26811210.23442542X-RAY DIFFRACTION98
2.4306-2.78230.30191520.23722550X-RAY DIFFRACTION99
2.7823-3.50530.27091330.21582611X-RAY DIFFRACTION99
3.5053-59.93560.20811610.1862747X-RAY DIFFRACTION99

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