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- PDB-4cfr: Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with no... -

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Basic information

Entry
Database: PDB / ID: 4cfr
TitleCa-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with non- muscle myosin IIA
Components
  • MYOSIN-9
  • PROTEIN S100-A4
KeywordsCA-BINDING PROTEIN/MOTOR PROTEIN / CA-BINDING PROTEIN-MOTOR PROTEIN COMPLEX / CA-BINDING / 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 inner hair cells of the cochlea / Sensory processing of sound by outer 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 / brush border / monocyte differentiation / cleavage furrow / 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 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / integrin-mediated signaling pathway / 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 / protein transport / actin filament binding / actin cytoskeleton / 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 / nucleus / identical protein binding / 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
Protein S100-A4 / Myosin-9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
Q: MYOSIN-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5567
Polymers29,3963
Non-polymers1604
Water4,558253
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-110.1 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.140, 64.140, 138.220
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-2061-

HOH

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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: 12018.653 Da / Num. of mol.: 2 / Fragment: RESDIUES 1-101 / 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-I IA / MYOSIN HEAVY CHAIN / NON MUSCLE MYOSIN IIA


Mass: 5358.213 Da / Num. of mol.: 1 / Fragment: RESIDUES 1893-1935 / 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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.42 Å3/Da / Density % sol: 49.31 % / Description: NONE
Crystal growpH: 4.6
Details: 0.2 M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH4.6, 30% W/V PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0722
DetectorType: ADSC CCD / Detector: 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: 1.4→29.1 Å / Num. obs: 57504 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

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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
Resolution: 1.4→29.09 Å / SU ML: 0.16 / σ(F): 1.99 / Phase error: 15.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1752 1756 3.1 %
Rwork0.1605 --
obs0.161 57392 99.54 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.229 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.9436 Å20 Å20 Å2
2--1.9436 Å20 Å2
3----3.8871 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 4 253 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132034
X-RAY DIFFRACTIONf_angle_d1.1522783
X-RAY DIFFRACTIONf_dihedral_angle_d12.503795
X-RAY DIFFRACTIONf_chiral_restr0.07289
X-RAY DIFFRACTIONf_plane_restr0.006352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43790.2731290.25884157X-RAY DIFFRACTION98
1.4379-1.48020.21811220.21584234X-RAY DIFFRACTION100
1.4802-1.52790.18091410.16584219X-RAY DIFFRACTION100
1.5279-1.58250.1771560.14834190X-RAY DIFFRACTION100
1.5825-1.64590.17841260.13354274X-RAY DIFFRACTION100
1.6459-1.72080.14641300.12614230X-RAY DIFFRACTION100
1.7208-1.81150.16021360.11974270X-RAY DIFFRACTION100
1.8115-1.9250.17371310.13154252X-RAY DIFFRACTION100
1.925-2.07360.16271390.1354279X-RAY DIFFRACTION100
2.0736-2.28220.15761290.12974301X-RAY DIFFRACTION100
2.2822-2.61220.15981330.14044339X-RAY DIFFRACTION100
2.6122-3.29040.19771440.1684385X-RAY DIFFRACTION100
3.2904-29.09670.17331400.1914506X-RAY DIFFRACTION97

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