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- PDB-4cfq: Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100... -

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Basic information

Entry
Database: PDB / ID: 4cfq
TitleCa-bound truncated (delta13C) and C3S, C81S and C86S mutated S100A4 complexed with non-muscle myosin IIA
Components
  • MYOSIN-9
  • PROTEIN S100-A4
KeywordsCA-BINDING PROTEIN/MOTOR PROTEIN / CA-BINDING PROTEIN-MOTOR PROTEIN COMPLEX / S100A4 PROTEINS / EF-HAND
Function / homology
Function and homology information


negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / establishment of meiotic spindle localization / cytokinetic process / myosin II filament / cortical granule exocytosis / establishment of T cell polarity / cortical granule / blood vessel endothelial cell migration ...negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / establishment of meiotic spindle localization / cytokinetic process / myosin II filament / cortical granule exocytosis / establishment of T cell polarity / cortical granule / blood vessel endothelial cell migration / actomyosin contractile ring / positive regulation of protein processing in phagocytic vesicle / uropod / regulated exocytosis / actin filament-based movement / RAGE receptor binding / meiotic spindle organization / lysosome localization / plasma membrane repair / actomyosin / myosin filament / myoblast fusion / RHO GTPases activate CIT / RHO GTPases Activate ROCKs / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / myosin II complex / Sensory processing of sound by outer hair cells of the cochlea / platelet formation / CD163 mediating an anti-inflammatory response / Sensory processing of sound by inner hair cells of the cochlea / leukocyte migration / phagocytosis, engulfment / EPHA-mediated growth cone collapse / microfilament motor activity / chemoattractant activity / endodermal cell differentiation / cell leading edge / RHO GTPases activate PAKs / cleavage furrow / brush border / membrane protein ectodomain proteolysis / cytoskeletal motor activity / monocyte differentiation / transition metal ion binding / immunological synapse / epithelial to mesenchymal transition / RHO GTPases activate PKNs / stress fiber / ruffle / protein-membrane adaptor activity / integrin-mediated signaling pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / adherens junction / neuromuscular junction / ADP binding / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / spindle / cytoplasmic side of plasma membrane / integrin binding / calcium-dependent protein binding / actin filament binding / Signaling by ALK fusions and activated point mutants / protein transport / regulation of cell shape / actin cytoskeleton / : / virus receptor activity / actin binding / actin cytoskeleton organization / angiogenesis / in utero embryonic development / calmodulin binding / positive regulation of canonical NF-kappaB signal transduction / nuclear body / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / symbiont entry into host cell / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
S-100 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / RGS domain superfamily / 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 / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / RGS domain superfamily / 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. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / 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: 1.37 Å
AuthorsDuelli, A. / Kiss, B. / Lundholm, I. / Bodor, A. / Radnai, L. / Petoukhov, M. / Svergun, D. / Nyitray, L. / Katona, G.
CitationJournal: Plos One / Year: 2014
Title: The C-Terminal Random Coil Region Tunes the Ca2+-Binding Affinity of S100A4 Through Conformational Activation.
Authors: Duelli, A. / Kiss, B. / Lundholm, I. / Bodor, A. / Radnai, L. / Petoukhov, M. / Svergun, D. / Nyitray, L. / Katona, G.
History
DepositionNov 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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.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_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_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_conn.ptnr2_label_seq_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
C: PROTEIN S100-A4
D: PROTEIN S100-A4
Q: MYOSIN-9
R: MYOSIN-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,51614
Polymers52,1956
Non-polymers3218
Water5,729318
1
C: PROTEIN S100-A4
D: PROTEIN S100-A4
R: MYOSIN-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2587
Polymers26,0983
Non-polymers1604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-94.7 kcal/mol
Surface area9740 Å2
MethodPISA
2
A: PROTEIN S100-A4
B: PROTEIN S100-A4
Q: MYOSIN-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2587
Polymers26,0983
Non-polymers1604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-86.5 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.720, 38.790, 71.430
Angle α, β, γ (deg.)88.65, 75.54, 72.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PROTEIN S100-A4 / CALVASCULIN / METASTASIN / PLACENTAL CALCIUM-BINDING PROTEIN / PROTEIN MTS1 / S100 CALCIUM-BINDING ...CALVASCULIN / METASTASIN / PLACENTAL CALCIUM-BINDING PROTEIN / PROTEIN MTS1 / S100 CALCIUM-BINDING PROTEIN A4 / S100A4


Mass: 10369.749 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-88 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HEK / Plasmid: PBH4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(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: 5358.213 Da / Num. of mol.: 2 / Fragment: RESIDUES 1893-1937 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HEK / Plasmid: PBH4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35579
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 3

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Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 34.97 % / Description: NONE
Crystal growpH: 4.6 / Details: 0.1 M MIB, PH 4, 25% W/V PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0722
DetectorDetector: CCD / Date: Sep 11, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 1.37→31.8 Å / Num. obs: 79285 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 1.37→1.44 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZWH

3zwh


Resolution: 1.37→31.772 Å / SU ML: 0.13 / σ(F): 2 / Phase error: 18.92 / Stereochemistry target values: ML
Details: CHAIN A ONLY DEFINED UNTIL RES 87, CHAIN B DEFINED UNTIL RES 84, CHAIN Q ONLY DEFINED FROM RES 1902-RES 1928. CHAIN C DEFINED FROM RES 2, CHAIN D DEFINED UNTIL RES 84 AND CHAIN R DEFINED FROM 1902-1930
RfactorNum. reflection% reflection
Rfree0.1928 2376 3 %
Rwork0.1611 --
obs0.162 79280 98.59 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.64 Å2
Refinement stepCycle: LAST / Resolution: 1.37→31.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 8 318 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0353251
X-RAY DIFFRACTIONf_angle_d1.8734444
X-RAY DIFFRACTIONf_dihedral_angle_d14.7791238
X-RAY DIFFRACTIONf_chiral_restr0.084476
X-RAY DIFFRACTIONf_plane_restr0.006552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.3980.26761350.23084296X-RAY DIFFRACTION94
1.398-1.42840.22461330.20334405X-RAY DIFFRACTION95
1.4284-1.46160.27381190.18434361X-RAY DIFFRACTION96
1.4616-1.49810.23331580.16594518X-RAY DIFFRACTION98
1.4981-1.53860.19111400.14884583X-RAY DIFFRACTION99
1.5386-1.58390.181260.14064571X-RAY DIFFRACTION100
1.5839-1.6350.18681490.13314571X-RAY DIFFRACTION100
1.635-1.69350.18591360.13264608X-RAY DIFFRACTION100
1.6935-1.76130.19181460.1334602X-RAY DIFFRACTION100
1.7613-1.84140.17091510.13194553X-RAY DIFFRACTION100
1.8414-1.93850.19291320.13744591X-RAY DIFFRACTION100
1.9385-2.05990.18471540.14164555X-RAY DIFFRACTION100
2.0599-2.21890.17961370.14014551X-RAY DIFFRACTION100
2.2189-2.44220.17961400.14554553X-RAY DIFFRACTION99
2.4422-2.79540.18491580.16324508X-RAY DIFFRACTION99
2.7954-3.52120.18091360.17894568X-RAY DIFFRACTION99
3.5212-31.78050.20741260.19174510X-RAY DIFFRACTION98

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