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- PDB-6akk: Crystal structure of the second Coiled-coil domain of SIKE1 -

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Basic information

Entry
Database: PDB / ID: 6akk
TitleCrystal structure of the second Coiled-coil domain of SIKE1
ComponentsSuppressor of IKBKE 1
KeywordsPROTEIN BINDING / homotetramer / Coiled-coil
Function / homology
Function and homology information


TRAF6 mediated IRF7 activation / small GTPase binding / SARS-CoV-1 activates/modulates innate immune responses / TRAF3-dependent IRF activation pathway / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cytosol
Similarity search - Function
SIKE family / SIKE family
Similarity search - Domain/homology
Suppressor of IKBKE 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhou, L. / Chen, M. / Zhou, Z.C.
CitationJournal: Cell Discov / Year: 2019
Title: Architecture, substructures, and dynamic assembly of STRIPAK complexes in Hippo signaling.
Authors: Tang, Y. / Chen, M. / Zhou, L. / Ma, J. / Li, Y. / Zhang, H. / Shi, Z. / Xu, Q. / Zhang, X. / Gao, Z. / Zhao, Y. / Cheng, Y. / Jiao, S. / Zhou, Z.
History
DepositionSep 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Suppressor of IKBKE 1
B: Suppressor of IKBKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9453
Polymers12,8532
Non-polymers921
Water1,78399
1
A: Suppressor of IKBKE 1
B: Suppressor of IKBKE 1
hetero molecules

A: Suppressor of IKBKE 1
B: Suppressor of IKBKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8906
Polymers25,7064
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6750 Å2
ΔGint-76 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.797, 110.871, 46.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-87-

ASN

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Components

#1: Protein Suppressor of IKBKE 1 / Suppressor of IKK-epsilon


Mass: 6426.421 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIKE1, SIKE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Variant (production host): CodonPlus / References: UniProt: Q9BRV8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.0 M (NH4)2HPO4 (ammonium dibasic phosphate); 0.1 M acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 17636 / % possible obs: 97.6 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.026 / Rrim(I) all: 0.095 / Net I/σ(I): 32.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 873 / CC1/2: 0.994 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→35.598 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 1638 9.97 %
Rwork0.2461 --
obs0.2483 16427 90.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→35.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 6 99 895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005816
X-RAY DIFFRACTIONf_angle_d0.7571095
X-RAY DIFFRACTIONf_dihedral_angle_d2.846616
X-RAY DIFFRACTIONf_chiral_restr0.036125
X-RAY DIFFRACTIONf_plane_restr0.004140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54420.311310.26171180X-RAY DIFFRACTION89
1.5442-1.5940.29711350.23021239X-RAY DIFFRACTION92
1.594-1.6510.24441310.2361250X-RAY DIFFRACTION93
1.651-1.71710.26261400.23391259X-RAY DIFFRACTION94
1.7171-1.79520.31311430.25021293X-RAY DIFFRACTION96
1.7952-1.88980.31261270.26931104X-RAY DIFFRACTION84
1.8898-2.00820.41161120.3391055X-RAY DIFFRACTION78
2.0082-2.16330.25781530.23641343X-RAY DIFFRACTION99
2.1633-2.38090.34441320.29061181X-RAY DIFFRACTION87
2.3809-2.72540.23491520.21951366X-RAY DIFFRACTION100
2.7254-3.43320.22961540.22341375X-RAY DIFFRACTION99
3.4332-35.60820.23361280.23631144X-RAY DIFFRACTION78
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)
10.87730.09910.25233.6763-2.18241.22080.081-0.04360.15680.2476-0.13540.23930.02010.02350.01030.12590.00350.02090.1613-0.00670.100216.184313.272615.4177
21.67880.45040.02287.428-0.51190.22560.0715-0.0658-0.2719-0.3118-0.0730.0708-0.0137-0.0141-0.00610.1412-0.004-0.00710.13990.00120.056116.3852-9.16897.6396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 71 through 119 )
2X-RAY DIFFRACTION2chain 'B' and (resid 72 through 118 )

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