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- PDB-3s9g: Structure of human Hexim1 (delta stammer) coiled coil domain -

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Basic information

Entry
Database: PDB / ID: 3s9g
TitleStructure of human Hexim1 (delta stammer) coiled coil domain
ComponentsProtein HEXIM1
KeywordsTRANSCRIPTION / Cyclin T-binding domain (TBD) / Cyclin T1/P-TEFb/7SK snRNA / nucleus
Function / homology
Function and homology information


7SK snRNP / 7SK snRNA binding / snRNA binding / negative regulation of viral transcription / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / protein kinase inhibitor activity / negative regulation of transcription elongation by RNA polymerase II / positive regulation of signal transduction by p53 class mediator / P-TEFb complex binding ...7SK snRNP / 7SK snRNA binding / snRNA binding / negative regulation of viral transcription / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / protein kinase inhibitor activity / negative regulation of transcription elongation by RNA polymerase II / positive regulation of signal transduction by p53 class mediator / P-TEFb complex binding / activation of innate immune response / heart development / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
HEXIM / Hexamethylene bis-acetamide-inducible protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBigalke, J.M. / Blankenfeldt, W. / Geyer, M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure and Dynamics of a Stabilized Coiled-Coil Domain in the P-TEFb Regulator Hexim1.
Authors: Bigalke, J.M. / Dames, S.A. / Blankenfeldt, W. / Grzesiek, S. / Geyer, M.
History
DepositionJun 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein HEXIM1
B: Protein HEXIM1


Theoretical massNumber of molelcules
Total (without water)24,8422
Polymers24,8422
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-36 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.770, 70.770, 90.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Protein HEXIM1 / Cardiac lineage protein 1 / Estrogen down-regulated gene 1 protein / Hexamethylene bis-acetamide- ...Cardiac lineage protein 1 / Estrogen down-regulated gene 1 protein / Hexamethylene bis-acetamide-inducible protein 1 / Menage a quatre protein 1


Mass: 12420.767 Da / Num. of mol.: 2 / Fragment: Cyclin T-binding domain / Mutation: C297S, delta(316-318)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLP1, EDG1, HEXIM1, HIS1, MAQ1 / Plasmid: pProEx-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94992
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium cacodylate, 0.1 M calcium acetate, 4% PEG 8000, 5 mM magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97943 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2007
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.1→45.5 Å / Num. obs: 13117 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.55 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→45.5 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 17.536 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 629 4.8 %RANDOM
Rwork0.23617 ---
obs0.23904 12487 99.99 %-
all-13115 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.557 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å20 Å2
2---2.83 Å20 Å2
3---5.65 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 0 51 1321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211275
X-RAY DIFFRACTIONr_bond_other_d0.0010.02876
X-RAY DIFFRACTIONr_angle_refined_deg2.0312.0011711
X-RAY DIFFRACTIONr_angle_other_deg1.13532136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0685156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18125.13972
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.22815258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1941514
X-RAY DIFFRACTIONr_chiral_restr0.1130.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02236
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_it7.13610788
X-RAY DIFFRACTIONr_mcbond_other3.70710314
X-RAY DIFFRACTIONr_mcangle_it8.442101242
X-RAY DIFFRACTIONr_scbond_it9.13710487
X-RAY DIFFRACTIONr_scangle_it11.03710469
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 41 -
Rwork0.301 920 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7351-3.4931-0.55832.78780.51050.62-0.1242-0.2487-0.1795-0.11320.16720.2382-0.0520.1255-0.0430.2388-0.0136-0.05320.147-0.05270.1297-0.7247.261167.3465
25.3962-3.3196-0.55932.21290.25910.16210.075-0.03260.1758-0.18340.0093-0.04480.0185-0.0418-0.08430.1320.0318-0.02680.1348-0.0330.07133.201144.22666.4223
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B272 - 350
2X-RAY DIFFRACTION2A266 - 350

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