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- PDB-6ar2: Structure of human SLMAP FHA domain in complex with pMST2 -

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Basic information

Entry
Database: PDB / ID: 6ar2
TitleStructure of human SLMAP FHA domain in complex with pMST2
Components
  • ASP-GLY-TPO-MET-LYS-ARG
  • Sarcolemmal membrane-associated protein
KeywordsMEMBRANE PROTEIN / Hippo / SLMAP / FHA / phospho-MST2
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 cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of hippo signaling / endocardium development / negative regulation of organ growth ...regulation of membrane depolarization during cardiac muscle cell action potential / regulation of voltage-gated sodium channel activity / regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of hippo signaling / endocardium development / negative regulation of organ growth / FAR/SIN/STRIPAK complex / hippo signaling / regulation of sodium ion transmembrane transport / transcription regulator activator activity / Signaling by Hippo / protein localization to centrosome / M band / organ growth / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / negative regulation of hippo signaling / smooth endoplasmic reticulum / JNK cascade / muscle contraction / protein serine/threonine kinase activator activity / central nervous system development / epithelial cell proliferation / protein localization to plasma membrane / protein tetramerization / positive regulation of JNK cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of canonical Wnt signaling pathway / sarcolemma / mitochondrial membrane / Z disc / negative regulation of epithelial cell proliferation / protein import into nucleus / protein-macromolecule adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / protein stabilization / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / endoplasmic reticulum membrane / magnesium ion binding / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / : / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain ...: / : / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / : / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / p53-like tetramerisation domain superfamily / SMAD/FHA domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase 3 / Sarcolemmal membrane-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOsinski, A. / Ni, L. / Luo, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107415 United States
Welch FoundationI-1932 United States
CitationJournal: Elife / Year: 2017
Title: SAV1 promotes Hippo kinase activation through antagonizing the PP2A phosphatase STRIPAK.
Authors: Bae, S.J. / Ni, L. / Osinski, A. / Tomchick, D.R. / Brautigam, C.A. / Luo, X.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sarcolemmal membrane-associated protein
B: Sarcolemmal membrane-associated protein
C: ASP-GLY-TPO-MET-LYS-ARG
D: ASP-GLY-TPO-MET-LYS-ARG


Theoretical massNumber of molelcules
Total (without water)34,1604
Polymers34,1604
Non-polymers00
Water3,657203
1
A: Sarcolemmal membrane-associated protein
C: ASP-GLY-TPO-MET-LYS-ARG


Theoretical massNumber of molelcules
Total (without water)17,0802
Polymers17,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-6 kcal/mol
Surface area7610 Å2
MethodPISA
2
B: Sarcolemmal membrane-associated protein
D: ASP-GLY-TPO-MET-LYS-ARG


Theoretical massNumber of molelcules
Total (without water)17,0802
Polymers17,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-5 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.758, 70.534, 91.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sarcolemmal membrane-associated protein / Sarcolemmal-associated protein


Mass: 15789.931 Da / Num. of mol.: 2 / Fragment: UNP residues 1-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLMAP, KIAA1601, SLAP, UNQ1847/PRO3577 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14BN4
#2: Protein/peptide ASP-GLY-TPO-MET-LYS-ARG


Mass: 1290.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13188*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.82 Å3/Da / Density % sol: 32.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM KSCN, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.55→38.24 Å / Num. obs: 36933 / % possible obs: 99.8 % / Redundancy: 12.5 % / Rpim(I) all: 0.029 / Net I/σ(I): 39.4
Reflection shellResolution: 1.55→1.59 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2719 / Rpim(I) all: 0.318 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AR0

6ar0


Resolution: 1.55→38.239 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.62
RfactorNum. reflection% reflection
Rfree0.1877 1846 5 %
Rwork0.1614 --
obs0.1627 36924 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→38.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 0 203 2413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092256
X-RAY DIFFRACTIONf_angle_d1.0053046
X-RAY DIFFRACTIONf_dihedral_angle_d16.8281366
X-RAY DIFFRACTIONf_chiral_restr0.063334
X-RAY DIFFRACTIONf_plane_restr0.007396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.59190.30281360.27482583X-RAY DIFFRACTION97
1.5919-1.63870.31961400.23122660X-RAY DIFFRACTION100
1.6387-1.69160.26361410.20552669X-RAY DIFFRACTION100
1.6916-1.75210.23141400.18312652X-RAY DIFFRACTION100
1.7521-1.82220.24511380.1742665X-RAY DIFFRACTION100
1.8222-1.90520.25451420.1662685X-RAY DIFFRACTION100
1.9052-2.00560.1921400.15862676X-RAY DIFFRACTION100
2.0056-2.13120.17451430.14992700X-RAY DIFFRACTION100
2.1312-2.29580.19551420.15062704X-RAY DIFFRACTION100
2.2958-2.52680.181430.16012701X-RAY DIFFRACTION100
2.5268-2.89230.20341430.16142730X-RAY DIFFRACTION100
2.8923-3.64350.1751450.15132758X-RAY DIFFRACTION100
3.6435-38.2510.16051530.15772895X-RAY DIFFRACTION100
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)
13.5618-1.5821-0.44933.29680.15142.9911-0.0412-0.27150.01050.2886-0.11330.1485-0.17480.06520.15590.2377-0.04920.03050.276-0.03140.25067.8517156.6078120.0852
24.482-1.7329-0.34573.74330.47165.67480.2439-0.2033-0.06750.0035-0.0341-0.03160.51240.312-0.11420.2406-0.00940.00970.24130.0150.23499.9693146.493114.7527
37.3961-2.78734.77313.9101-3.81656.36370.2226-0.4128-0.4118-0.04750.07270.43520.2321-0.5714-0.22840.2446-0.02310.00880.3218-0.00350.2858-1.9086150.1394114.3928
44.3171-0.61291.47211.14070.44762.08350.12820.1612-0.205-0.0241-0.05970.00440.08060.1843-0.090.17770.00690.01250.1937-0.00350.197513.3758150.6264106.7184
53.29020.40731.27031.93570.10893.1335-0.04110.21330.3971-0.1595-0.06170.1383-0.28310.06910.10010.2458-0.0068-0.00720.23440.01060.2557.795160.8095105.2739
67.73722.08221.6290.66440.70181.073-0.38350.10991.1302-0.1848-0.00870.1078-0.2086-0.330.26140.39470.0312-0.0750.4841-0.09740.5871-11.2799166.5626110.9897
75.3726-3.10520.96852.1795-0.31320.329-0.0755-0.0327-0.10730.1302-0.08760.019-0.14460.08830.17910.222-0.04140.00020.27650.01530.258612.7543157.3242117.7616
83.9193-1.8331-1.43062.00780.59074.22970.3659-0.2744-0.02461.0126-0.404-1.40740.02711.16440.18310.36210.0018-0.06860.62010.06940.41824.4685149.9259119.4139
95.10560.8188-4.59343.3603-1.16748.612-0.2352-0.1066-0.4519-0.36060.16390.02460.45710.0059-0.07940.29510.0182-0.00210.21550.03120.2323-4.8176129.707191.4299
104.29310.4513-1.19825.2791-0.6753.20390.0136-0.5533-0.20210.1248-0.0290.46710.03690.190.02210.19630.04250.01780.23980.05530.2326-7.5861134.6214101.61
112.29391.62712.8391.97812.09393.53820.6115-0.9586-0.60591.2527-0.5021-0.4847-0.01781.1742-0.31640.35330.0226-0.06810.55890.07470.3367.6288135.7403101.1036
122.48330.13-0.94791.77280.46081.9824-0.1191-0.3996-0.1194-0.07350.1579-0.11340.13060.4329-0.02350.22830.02890.00120.2941-0.00780.2008-1.6572138.718396.8907
133.4789-0.1454-0.71391.5030.41611.5551-0.02240.21990.1011-0.27820.08560.0208-0.1952-0.0071-0.06250.2763-0.0238-0.01490.24230.00710.2185-7.6966144.25790.0839
143.1817-0.78261.70141.77790.56412.1930.02040.42920.21950.10620.2379-0.3382-0.28780.5796-0.19720.333-0.07650.05350.5514-0.16520.445814.0947139.865881.6351
159.45622.4833-6.97830.7709-2.00115.4059-0.30170.1892-0.1298-0.38620.24340.1450.23180.01240.1120.3508-0.03960.00170.2150.0270.322-9.8394131.903790.4452
164.22930.5106-0.12675.3595-0.57241.9527-0.20570.3354-0.83370.13790.09641.50280.7948-1.88990.27970.3751-0.05520.09180.43450.00420.7262-21.6337129.425697.589
175.7053.02040.52599.60580.60194.8334-0.64870.06171.160.39250.37960.9225-0.3464-0.31310.3020.25050.0306-0.07720.3144-0.04080.4127-5.9234159.071103.7407
187.1215-0.9285-1.90588.71021.60046.50180.21350.5120.3749-0.75050.1145-0.8182-0.34541.2091-0.35740.3795-0.09880.08050.5598-0.04960.43118.8609146.733689.9029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 50 )
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 120 )
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 128 )
8X-RAY DIFFRACTION8chain 'A' and (resid 129 through 135 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 19 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 30 )
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 40 )
12X-RAY DIFFRACTION12chain 'B' and (resid 41 through 61 )
13X-RAY DIFFRACTION13chain 'B' and (resid 62 through 111 )
14X-RAY DIFFRACTION14chain 'B' and (resid 112 through 120 )
15X-RAY DIFFRACTION15chain 'B' and (resid 121 through 128 )
16X-RAY DIFFRACTION16chain 'B' and (resid 129 through 135 )
17X-RAY DIFFRACTION17chain 'C' and (resid 376 through 381 )
18X-RAY DIFFRACTION18chain 'D' and (resid 376 through 381 )

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