PDB-1liq: Non-native Solution Structure of a fragment of the CH1 domain of CBP

Basic information

• Entry: Database: PDB / ID: 1liq
• Title: Non-native Solution Structure of a fragment of the CH1 domain of CBP
• Components: CREB Binding ProteinCREB-binding protein
• Keywords: PROTEIN BINDING / zinc finger / protein design

Function / homology

Function:

NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / histone H3K27 acetyltransferase activity / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / MRF binding / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / negative regulation of transcription by RNA polymerase I / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / peptide-lysine-N-acetyltransferase activity / NFE2L2 regulating anti-oxidant/detoxification enzymes / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / embryonic digit morphogenesis / homeostatic process / Notch-HLH transcription pathway / protein acetylation / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / Attenuation phase / regulation of cellular response to heat / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Formation of the beta-catenin:TCF transactivating complex / protein destabilization / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein localization to nucleus / transcription corepressor activity / cellular response to UV / rhythmic process / Circadian Clock / p53 binding / TRAF3-dependent IRF activation pathway / HATs acetylate histones / protein-containing complex assembly / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / response to hypoxia / nuclear body / chromatin binding / chromatin / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm

Domain/homology:

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 / 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 / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / 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. / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type

Component:

CREB-binding protein

• Method: SOLUTION NMR / distance geometry simulated annealing, molecular dynamics
• Authors: Sharpe, B.K. / Matthews, J.M. / Kwan, A.H.Y. / Newton, A. / Gell, D.A. / Crossley, M. / Mackay, J.P.
• Citation: Journal: Structure / Year: 2002; Title: A New Zinc Binding Fold Underlines the Versatility of Zinc Binding Modules in Protein Evolution; Authors: Sharpe, B.K. / Matthews, J.M. / Kwan, A.H.Y. / Newton, A. / Gell, D.A. / Crossley, M. / Mackay, J.P.

History

Deposition	Apr 18, 2002	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	May 29, 2002	Provider: repository / Type: Initial release
Revision 1.1	Apr 28, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 23, 2022	Group: Data collection / Database references / Derived calculations Category: database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: CREB Binding Protein

hetero molecules

Summary:

• 3.14 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	3,138	2
Polymers	3,073	1
Non-polymers	65	1
Water	0

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	20 / 50	structures with the lowest energy
Representative	Model #1	lowest energy

Components

#1: Protein/peptide

A CREB Binding Protein / CREB-binding protein

Details:

Mass: 3072.656 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-27 / Source method: obtained synthetically / Details: this sequence occurs naturally in humans / References: UniProt: Q92793

#2: Chemical

A-28 ChemComp-ZN / ZINC ION

Details:

Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

Experimental details

Experiment

• Experiment: Method: SOLUTION NMR

NMR experiment

Conditions-ID	Experiment-ID	Solution-ID	Type
1	1	1	DQF-COSY
1	2	1	2D TOCSY
1	3	1	2D NOESY
1	4	2	E-COSY

• NMR details: Text: This structure was determined using standard 2D homonuclear techniques

Sample preparation

Details

Solution-ID	Contents	Solvent system
1	0.4mM CBP(376-402), 0.6mM TCEP, 0.6mM ZnSO4, 95% H2O, 10% D2O	95% H2O, 10% D2O
2	0.4mM CBP(376-402), 0.6mM TCEP, 0.6mM ZnSO4, 100% D2O	100% D2O

• Sample conditions: pH: 6.5 / Pressure: ambient / Temperature: 275 K
• Crystal grow: Method: other / Details: NMR

NMR measurement

• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
• Radiation wavelength: Relative weight: 1
• NMR spectrometer: Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

Processing

NMR software

Name	Version	Developer	Classification
XwinNMR	2.5	Bruker	processing
XEASY	1.3.13	Bartels et al	data analysis
DYANA	1.5	Guntert et al	data analysis
CNS	1	Brunger et al	refinement

• Refinement: Method: distance geometry simulated annealing, molecular dynamics; Software ordinal: 1 ; Details: the structures are based on 275 umambiguous NOE-derived distance constraints, 31 sets of ambiguous NOE-derived distance constraints and 110 dihedral angle restraints.
• NMR representative: Selection criteria: lowest energy
• NMR ensemble: Conformer selection criteria: structures with the lowest energy; Conformers calculated total number: 50 / Conformers submitted total number: 20