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- PDB-6akm: Crystal structure of SLMAP-SIKE1 complex -

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Basic information

Entry
Database: PDB / ID: 6akm
TitleCrystal structure of SLMAP-SIKE1 complex
Components
  • Sarcolemmal membrane-associated protein
  • Suppressor of IKBKE 1
KeywordsPROTEIN BINDING / Coiled-coil domain / heterotetramer
Function / homology
Function and homology information


regulation of membrane depolarization during cardiac muscle cell action potential / regulation of voltage-gated sodium channel activity / regulation of sodium ion transmembrane transport / TRAF6 mediated IRF7 activation / smooth endoplasmic reticulum / muscle contraction / protein localization to plasma membrane / sarcolemma / small GTPase binding / SARS-CoV-1 activates/modulates innate immune responses ...regulation of membrane depolarization during cardiac muscle cell action potential / regulation of voltage-gated sodium channel activity / regulation of sodium ion transmembrane transport / TRAF6 mediated IRF7 activation / smooth endoplasmic reticulum / muscle contraction / protein localization to plasma membrane / sarcolemma / small GTPase binding / SARS-CoV-1 activates/modulates innate immune responses / TRAF3-dependent IRF activation pathway / centrosome / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / plasma membrane / cytosol
Similarity search - Function
SIKE family / SIKE family / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily
Similarity search - Domain/homology
Sarcolemmal membrane-associated protein / Suppressor of IKBKE 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMa, J. / 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 1.2Nov 22, 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: Suppressor of IKBKE 1
B: Sarcolemmal membrane-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6973
Polymers14,6052
Non-polymers921
Water63135
1
A: Suppressor of IKBKE 1
B: Sarcolemmal membrane-associated protein
hetero molecules

A: Suppressor of IKBKE 1
B: Sarcolemmal membrane-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3956
Polymers29,2114
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area8500 Å2
ΔGint-84 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.763, 66.763, 61.353
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-222-

HOH

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Components

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


Mass: 7184.042 Da / Num. of mol.: 1
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: Protein Sarcolemmal membrane-associated protein / Sarcolemmal-associated protein


Mass: 7421.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLMAP, KIAA1601, SLAP, UNQ1847/PRO3577 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Variant (production host): CodonPlus / References: UniProt: Q14BN4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate, pH 5.5; 15% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 7336 / % possible obs: 100 % / Redundancy: 18.8 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.022 / Rrim(I) all: 0.097 / Net I/σ(I): 21.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 19 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 713 / CC1/2: 0.948 / Rpim(I) all: 0.193 / Rrim(I) all: 0.844 / % 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: MOLECULAR REPLACEMENT
Starting model: 6AKK

6akk


Resolution: 2.3→42.08 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.238 734 10.06 %
Rwork0.204 --
obs0.2074 7294 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 6 35 739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007745
X-RAY DIFFRACTIONf_angle_d0.8861009
X-RAY DIFFRACTIONf_dihedral_angle_d10.271678
X-RAY DIFFRACTIONf_chiral_restr0.055122
X-RAY DIFFRACTIONf_plane_restr0.005131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.47770.29091430.23231289X-RAY DIFFRACTION100
2.4777-2.7270.27481430.21411289X-RAY DIFFRACTION100
2.727-3.12160.27671490.2121306X-RAY DIFFRACTION100
3.1216-3.93280.20951480.18891300X-RAY DIFFRACTION100
3.9328-57.83640.2221510.20181376X-RAY DIFFRACTION99
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)
18.2041.0304-0.70293.0426-1.56234.26240.4224-0.02841.0696-0.08250.29630.3516-0.3839-0.9338-0.25160.19290.0822-0.03250.57590.10140.2654-8.50014.8447.6801
28.8843-0.9176-1.64244.2021-0.61724.39570.45580.1259-0.1738-0.11230.22810.41180.6385-1.2162-0.02060.2051-0.109-0.02370.63670.09030.2855-8.4144-2.58935.1742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 48 )
2X-RAY DIFFRACTION2chain 'B' and (resid 163 through 208 )

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