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- PDB-2lnk: Solution structure of Ca-bound S100A4 in complex with non-muscle ... -

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Basic information

Entry
Database: PDB / ID: 2lnk
TitleSolution structure of Ca-bound S100A4 in complex with non-muscle myosin IIA
Components
  • Myosin heavy chain, non-muscle IIaMyosin
  • Protein S100-A4
KeywordsCALCIUM BINDING PROTEIN / EF-hand / calcium binding / all alpha / METAL BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / cortical granule exocytosis / cytokinetic process / establishment of meiotic spindle localization / myosin II filament / establishment of T cell polarity / cortical granule / actomyosin contractile ring ...negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / cortical granule exocytosis / cytokinetic process / establishment of meiotic spindle localization / myosin II filament / establishment of T cell polarity / cortical granule / actomyosin contractile ring / positive regulation of protein processing in phagocytic vesicle / regulated exocytosis / uropod / blood vessel endothelial cell migration / actin filament-based movement / meiotic spindle organization / RAGE receptor binding / actomyosin / lysosome localization / myosin filament / plasma membrane repair / myoblast fusion / actomyosin structure organization / myosin II complex / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / CD163 mediating an anti-inflammatory response / microfilament motor activity / platelet formation / phagocytosis, engulfment / leukocyte migration / EPHA-mediated growth cone collapse / endodermal cell differentiation / chemoattractant activity / cell leading edge / RHO GTPases activate PAKs / cleavage furrow / brush border / monocyte differentiation / cytoskeletal motor activity / membrane protein ectodomain proteolysis / transition metal ion binding / immunological synapse / Signaling by ALK fusions and activated point mutants / epithelial to mesenchymal transition / protein-membrane adaptor activity / stress fiber / RHO GTPases activate PKNs / ruffle / integrin-mediated signaling pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / ADP binding / FCGR3A-mediated phagocytosis / adherens junction / neuromuscular junction / cytoplasmic side of plasma membrane / spindle / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / protein transport / integrin binding / actin binding / regulation of cell shape / actin cytoskeleton organization / collagen-containing extracellular matrix / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / nuclear body / calmodulin binding / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
S-100 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / RGS domain superfamily / Myosin tail / Myosin tail / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Myosin N-terminal SH3-like domain ...S-100 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / RGS domain superfamily / Myosin tail / Myosin tail / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein S100-A4 / Myosin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsBarsukov, I.L. / Elliott, P.R.
CitationJournal: Structure / Year: 2012
Title: Asymmetric Mode of Ca(2+)-S100A4 Interaction with Nonmuscle Myosin IIA Generates Nanomolar Affinity Required for Filament Remodeling.
Authors: Elliott, P.R. / Irvine, A.F. / Jung, H.S. / Tozawa, K. / Pastok, M.W. / Picone, R. / Badyal, S.K. / Basran, J. / Rudland, P.S. / Barraclough, R. / Lian, L.Y. / Bagshaw, C.R. / Kriajevska, M. / Barsukov, I.L.
History
DepositionDec 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Myosin heavy chain, non-muscle IIa
A: Protein S100-A4
B: Protein S100-A4


Theoretical massNumber of molelcules
Total (without water)30,8113
Polymers30,8113
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Myosin heavy chain, non-muscle IIa / Myosin / Myosin-9 / Cellular myosin heavy chain / type A / Myosin heavy chain 9 / Myosin heavy chain / non- ...Myosin-9 / Cellular myosin heavy chain / type A / Myosin heavy chain 9 / Myosin heavy chain / non-muscle IIa / Non-muscle myosin heavy chain A / NMMHC-A / Non-muscle myosin heavy chain IIa / NMMHC II-a / NMMHC-IIA


Mass: 4509.135 Da / Num. of mol.: 1 / Fragment: UNP residues 1897-1935 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35579
#2: Protein Protein S100-A4 / / Calvasculin / Metastasin / Placental calcium-binding protein / Protein Mts1 / S100 calcium-binding protein A4


Mass: 13151.065 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A4, CAPL, MTS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: P26447

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY aliphatic
1213D 1H-13C NOESY aromatic
1312D 1H-1H filtered NOESY
1413D 1H-15N NOESY
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D (H)CCH-TOCSY
1813D HNCO
1912D 1H-1H filtered TOCSY

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Sample preparation

DetailsContents: 0.5 mM protein_1, 1 mM [U-100% 13C; U-100% 15N] protein_2, 5 mM CALCIUM ION, 20 mM MES, 20 mM sodium chloride, 4 mM TCEP, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity_1-11
1 mMentity_2-2[U-100% 13C; U-100% 15N]1
5 mMCALCIUM ION-31
20 mMMES-41
20 mMsodium chloride-51
4 mMTCEP-61
Sample conditionsIonic strength: 0.02 / pH: 6.1 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CCPN_Analysis2.1CCPNchemical shift assignment
TopSpin2.1Bruker Biospinprocessing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ProcheckNMRLaskowski and MacArthurgeometry optimization
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 7085 / NOE intraresidue total count: 2709 / NOE long range total count: 2753 / NOE medium range total count: 1600 / NOE sequential total count: 1820 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 182 / Protein psi angle constraints total count: 182
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 1.9 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 8 ° / Maximum upper distance constraint violation: 0.5 Å / Torsion angle constraint violation method: cns
NMR ensemble rmsDistance rms dev: 0.05 Å / Distance rms dev error: 0.004 Å

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