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- PDB-4eto: Structure of S100A4 in complex with non-muscle myosin-IIA peptide -

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Basic information

Entry
Database: PDB / ID: 4eto
TitleStructure of S100A4 in complex with non-muscle myosin-IIA peptide
Components
  • Myosin-9
  • Protein S100-A4
KeywordsMETAL BINDING PROTEIN / CALCIUM-BINDING PROTEIN / EF-hand / Structural Genomics / PSI-Biology / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN
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 / actin filament-based movement / blood vessel endothelial cell migration / meiotic spindle organization / RAGE receptor binding / actomyosin / plasma membrane repair / lysosome localization / myosin filament / 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 / cytoskeletal motor activity / monocyte differentiation / brush border / membrane protein ectodomain proteolysis / transition metal ion binding / Signaling by ALK fusions and activated point mutants / immunological synapse / epithelial to mesenchymal transition / stress fiber / protein-membrane adaptor activity / 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 / integrin binding / protein transport / actin binding / regulation of cell shape / actin cytoskeleton organization / angiogenesis / collagen-containing extracellular matrix / 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 / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Myosin tail / Myosin tail / 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 / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Myosin tail / Myosin tail / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsRamagopal, U.A. / Dulyaninova, N.G. / Kumar, P.R. / Almo, S.C. / Bresnick, A.R. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: To be Published
Title: Structure of S100A4 with bound peptide P
Authors: Ramagopal, U.A. / Dulyaninova, N.G. / Kumar, P.R. / Almo, S.C. / Bresnick, A.R.
History
DepositionApr 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references / Structure summary
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A4
B: Protein S100-A4
P: Myosin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6097
Polymers23,4493
Non-polymers1604
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-99 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.279, 91.989, 32.864
Angle α, β, γ (deg.)90.000, 112.600, 90.000
Int Tables number4
Space group name H-MP1211
Detailsdimer bound to a peptide

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Components

#1: Protein Protein S100-A4 / / Calvasculin / Metastasin / Placental calcium-binding protein / Protein Mts1 / S100 calcium-binding protein A4


Mass: 10763.358 Da / Num. of mol.: 2 / Fragment: UNP residues 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPL, MTS1, S100A4 / Plasmid: PET23A) / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3) / References: UniProt: P26447
#2: Protein/peptide Myosin-9 / / Cellular myosin heavy chain / type A / Myosin heavy chain 9 / Myosin heavy chain / non-muscle IIa / ...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: 1922.239 Da / Num. of mol.: 1 / Fragment: Coiled coil region residues 1908-1923
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYH9 / References: UniProt: P35579
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.8 Å3/Da / Density % sol: 31.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.0, 30% (v/v) Jeffamine ED-2001, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 24461 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Χ2: 1.734 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.54-1.573.50.49612141.3961100
1.57-1.63.60.45512421.3681100
1.6-1.633.60.39911931.3881100
1.63-1.663.60.33812371.4371100
1.66-1.693.60.32412141.4241100
1.69-1.733.60.26512301.4061100
1.73-1.783.60.22312371.4221100
1.78-1.833.60.19412191.4711100
1.83-1.883.60.16612091.557199.9
1.88-1.943.60.13212381.6061100
1.94-2.013.60.11812091.681199.8
2.01-2.093.60.09512321.651100
2.09-2.193.60.08112431.872199.5
2.19-2.33.60.07211952.052199.3
2.3-2.443.60.06312071.943199.2
2.44-2.633.60.05912312.05199.2
2.63-2.93.60.05212212.119198.9
2.9-3.323.50.04712352.197199.1
3.32-4.183.50.0412212.287199.3
4.18-503.40.03912342.445197.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q91

2q91


Resolution: 1.54→45.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2494 / WRfactor Rwork: 0.2093 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8274 / SU B: 1.913 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1053 / SU Rfree: 0.1066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1247 5.1 %RANDOM
Rwork0.2089 ---
obs0.2111 24415 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.68 Å2 / Biso mean: 20.1365 Å2 / Biso min: 6.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0.77 Å2
2---0.4 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.54→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 4 86 1620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221633
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9752195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2315207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56725.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52315316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.365156
X-RAY DIFFRACTIONr_chiral_restr0.1290.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021238
X-RAY DIFFRACTIONr_mcbond_it1.2321.51012
X-RAY DIFFRACTIONr_mcangle_it2.13321625
X-RAY DIFFRACTIONr_scbond_it3.5453621
X-RAY DIFFRACTIONr_scangle_it5.2784.5570
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 102 -
Rwork0.304 1697 -
all-1799 -
obs--99.56 %

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