[English] 日本語
Yorodumi
- PDB-4cfr: Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with no... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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 / 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 ...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 / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / Helix non-globular / Special / 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: 1.4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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: 1.4→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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more