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- PDB-6hw2: The Crystal Structure of CaV beta4c in complex with HP1gamma chro... -

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Basic information

Entry
Database: PDB / ID: 6hw2
TitleThe Crystal Structure of CaV beta4c in complex with HP1gamma chromo shadow domains
Components
  • Chromobox protein homolog 3
  • Voltage-dependent L-type calcium channel subunit beta-4
KeywordsTRANSPORT PROTEIN / Complex
Function / homology
Function and homology information


senescence-associated heterochromatin focus / voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / positive regulation of protein localization to nucleolus / Presynaptic depolarization and calcium channel opening / chromatin lock complex / gamma-aminobutyric acid secretion / detection of light stimulus involved in visual perception / high voltage-gated calcium channel activity / cAMP metabolic process / histone methyltransferase binding ...senescence-associated heterochromatin focus / voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / positive regulation of protein localization to nucleolus / Presynaptic depolarization and calcium channel opening / chromatin lock complex / gamma-aminobutyric acid secretion / detection of light stimulus involved in visual perception / high voltage-gated calcium channel activity / cAMP metabolic process / histone methyltransferase binding / Peyer's patch development / condensed chromosome, centromeric region / muscle cell development / neuronal action potential propagation / nervous system process / nuclear inner membrane / adult walking behavior / voltage-gated calcium channel complex / gamma-aminobutyric acid signaling pathway / neuromuscular junction development / regulation of synaptic vesicle exocytosis / negative regulation of G1/S transition of mitotic cell cycle / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / voltage-gated calcium channel activity / heterochromatin / pericentric heterochromatin / spleen development / : / cellular response to dexamethasone stimulus / cellular response to leukemia inhibitory factor / thymus development / transcription coregulator binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / regulation of membrane potential / synaptic transmission, glutamatergic / RNA Polymerase I Promoter Escape / euchromatin / spindle / RNA polymerase II transcription regulator complex / calcium ion transport / rhythmic process / nuclear envelope / heterochromatin formation / presynapse / T cell receptor signaling pathway / chemical synaptic transmission / chromosome, telomeric region / nuclear speck / chromatin remodeling / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein kinase binding / chromatin / glutamatergic synapse / enzyme binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Chromobox protein homologue 3 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Chromo domain, conserved site ...Chromobox protein homologue 3 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SH3 Domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / Voltage-dependent L-type calcium channel subunit beta-4 / Chromobox protein homolog 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å
AuthorsTanner, N. / Tripathy, D.R. / Hirsch, J.A.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation1201/04 Israel
Israel Science Foundation1500/16 Israel
CitationJournal: To Be Published
Title: The Crystal Structure of CaV beta4c in complex with HP1gamma chromo shadow domains
Authors: Tanner, N. / Tripathy, D.R. / Hirsch, J.A.
History
DepositionOct 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Voltage-dependent L-type calcium channel subunit beta-4
B: Chromobox protein homolog 3
C: Chromobox protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,17114
Polymers34,4693
Non-polymers70211
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-67 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.026, 58.036, 57.546
Angle α, β, γ (deg.)90.000, 109.700, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Voltage-dependent L-type calcium channel subunit beta-4


Mass: 17531.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacnb4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D4A055*PLUS
#2: Protein Chromobox protein homolog 3 / HECH / Heterochromatin protein 1 homolog gamma / HP1 gamma / Modifier 2 protein


Mass: 8468.519 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q13185

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Non-polymers , 5 types, 213 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.15 M NaCl, 12-14% PEG 3350 , pH 5.0, calcium acetate, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.941→33.12 Å / Num. obs: 26484 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.8
Reflection shellResolution: 1.941→2.01 Å / Rmerge(I) obs: 0.404 / Num. unique obs: 2518

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYV

1vyv


Resolution: 1.941→33.12 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2095 --
Rwork0.1775 --
obs0.1792 26484 99.8 %
Refinement stepCycle: LAST / Resolution: 1.941→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 34 202 2279
LS refinement shellResolution: 1.941→2.0104 Å
RfactorNum. reflection% reflection
Rfree0.2774 134 -
Rwork0.2339 2471 -
obs--99 %

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