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- PDB-3zwh: Ca2+-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with ... -

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Basic information

Entry
Database: PDB / ID: 3zwh
TitleCa2+-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with myosin IIA
Components
  • MYOSIN-9
  • PROTEIN S100-A4
KeywordsCA-BINDING PROTEIN/MOTOR PROTEIN / CA-BINDING PROTEIN-MOTOR PROTEIN COMPLEX / S100 PROTEINS / EF-HAND
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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2420 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2420 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / Helix non-globular / EF-hand, calcium binding motif / Special / 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
ACETATE ION / AZIDE ION / Protein S100-A4 / Myosin-9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKiss, B. / Duelli, A. / Radnai, L. / Kekesi, A.K. / Katona, G. / Nyitray, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal Structure of the S100A4-Nonmuscle Myosin Iia Tail Fragment Complex Reveals an Asymmetric Target Binding Mechanism.
Authors: Kiss, B. / Duelli, A. / Radnai, L. / Kekesi, K.A. / Katona, G. / Nyitray, L.
History
DepositionJul 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Nov 27, 2013Group: Database references / Structure summary
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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
Q: MYOSIN-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,75811
Polymers29,3963
Non-polymers3628
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-112.1 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.972, 63.972, 138.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2044-

HOH

21A-2046-

HOH

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABQ

#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: 12018.653 Da / Num. of mol.: 2 / 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.: 1 / 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

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Non-polymers , 4 types, 209 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 3 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 45 TO TRP ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, CYS 3 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 45 TO TRP ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 86 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 3 TO SER ENGINEERED RESIDUE IN CHAIN B, PHE 45 TO TRP ENGINEERED RESIDUE IN CHAIN B, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 86 TO SER ENGINEERED RESIDUE IN CHAIN Q, ARG 1893 TO TYR

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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: 2.37 Å3/Da / Density % sol: 48.13 % / Description: NONE
Crystal growpH: 5.6
Details: 30% PEG 4000, 0.2 M NA-ACETATE PH 5.6, 0.1 M NA-CITRATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 10, 2011 / Details: KB MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→19.4 Å / Num. obs: 22196 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 20.12 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 18.44
Reflection shellResolution: 1.9→2.1 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 3.54 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C1V

3c1v


Resolution: 1.94→19.936 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 17.55 / Stereochemistry target values: ML
Details: CHAIN A RES MET-1 AND RES ASP95- -LYS101, CHAIN B RES LYS100-LYS101 AND CHAIN Q ARG1936- -LYS1937, COULD NOT BE MODELLED DUE TO MISSING ELECTRON DENSITY
RfactorNum. reflection% reflection
Rfree0.2064 1129 5.1 %
Rwork0.1753 --
obs0.1768 22109 99.93 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.329 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 24.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.143 Å20 Å20 Å2
2--0.143 Å20 Å2
3----0.2861 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 18 201 2126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071966
X-RAY DIFFRACTIONf_angle_d0.6712615
X-RAY DIFFRACTIONf_dihedral_angle_d12.497758
X-RAY DIFFRACTIONf_chiral_restr0.051275
X-RAY DIFFRACTIONf_plane_restr0.003342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9401-2.02830.25811260.22362561X-RAY DIFFRACTION100
2.0283-2.13510.22441440.18952567X-RAY DIFFRACTION100
2.1351-2.26870.21471660.17492541X-RAY DIFFRACTION100
2.2687-2.44360.23131460.17232584X-RAY DIFFRACTION100
2.4436-2.6890.21851510.18052591X-RAY DIFFRACTION100
2.689-3.07680.24211310.18192627X-RAY DIFFRACTION100
3.0768-3.87180.16811450.16492660X-RAY DIFFRACTION100
3.8718-19.93740.18121200.16472849X-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)
10.28160.46890.10581.0058-0.23160.6905-0.0219-0.06770.0045-0.07870.03740.06830.0518-0.01620.00770.06610.00990.00070.08050.02430.070919.40542.388711.539
20.5451-0.28540.00810.4651-0.34750.9598-0.0472-0.2828-0.0148-0.0015-0.1169-0.2986-0.03070.3666-0.04040.0567-0.0269-0.03060.24080.01820.154639.507210.38915.3482
30.2502-0.0365-0.29040.1478-0.05090.2369-0.0309-0.0115-0.1725-0.08490.0544-0.10010.22650.0504-0.00610.1114-0.02430.03040.0879-0.00370.102127.83137.5467-0.2418
40.03960.0356-0.0530.04210.00190.04690.0772-0.0201-0.1194-0.0393-0.05490.53150.0083-0.280800.11940.0090.00640.12780.01370.139416.023-2.142924.528
50.05770.0934-0.00890.1475-0.0212-0.002-0.1159-0.28050.06560.35240.04890.4245-0.00170.0406-0.00120.31430.03890.010.1747-0.00370.103517.817511.734720.0613
60.10310.040.0085-0.0018-0.01430.03740.08350.08220.24370.09170.0312-0.0738-0.27320.04940.00010.1132-0.02710.0030.13090.00110.130430.498520.2187.7556
70.21750.08180.21180.21360.22350.3346-0.13370.05230.0307-0.1821-0.3508-0.1961-0.18480.1865-0.03160.2282-0.03140.02980.13290.05410.153236.152612.4065-3.339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:94)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 1:74)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 75:99)
4X-RAY DIFFRACTION4(CHAIN Q AND RESID 1893:1902)
5X-RAY DIFFRACTION5(CHAIN Q AND RESID 1903:1908)
6X-RAY DIFFRACTION6(CHAIN Q AND RESID 1909:1930)
7X-RAY DIFFRACTION7(CHAIN Q AND RESID 1931:1935)

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