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- PDB-3aa6: Crystal structure of Actin capping protein in complex with the Cp... -

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Basic information

Entry
Database: PDB / ID: 3aa6
TitleCrystal structure of Actin capping protein in complex with the Cp-binding motif derived from CD2AP
Components
  • 23mer peptide from CD2-associated protein
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta isoforms 1 and 2
KeywordsPROTEIN BINDING / ACTIN CAPPING PROTEIN / BARBED END REGULATION / CARMIL FAMILY PROTEIN / CONFORMATIONAL CHANGE / CELL MOTILITY / CD2AP / Actin capping / Actin-binding / Cytoskeleton / Cell cycle / Cell division / Cell projection / Mitosis / SH3 domain / SH3-binding
Function / homology
Function and homology information


Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / negative regulation of small GTPase mediated signal transduction / Factors involved in megakaryocyte development and platelet production / transforming growth factor beta1 production / WASH complex ...Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / negative regulation of small GTPase mediated signal transduction / Factors involved in megakaryocyte development and platelet production / transforming growth factor beta1 production / WASH complex / sperm connecting piece / F-actin capping protein complex / negative regulation of transforming growth factor beta1 production / negative regulation of filopodium assembly / response to transforming growth factor beta / immunological synapse formation / substrate-dependent cell migration, cell extension / protein heterooligomerization / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / podosome / regulation of cell morphogenesis / regulation of lamellipodium assembly / Nephrin family interactions / lamellipodium assembly / cortical cytoskeleton / cell leading edge / filamentous actin / brush border / centriolar satellite / stress-activated MAPK cascade / cytoskeleton organization / ruffle / hippocampal mossy fiber to CA3 synapse / phosphatidylinositol 3-kinase/protein kinase B signal transduction / kidney development / actin filament organization / positive regulation of protein secretion / regulation of actin cytoskeleton organization / synapse organization / protein catabolic process / neuromuscular junction / Schaffer collateral - CA1 synapse / cell morphogenesis / structural constituent of cytoskeleton / fibrillar center / Z disc / SH3 domain binding / positive regulation of protein localization to nucleus / male gonad development / actin filament binding / cell-cell junction / cell migration / actin cytoskeleton / late endosome / lamellipodium / T cell receptor signaling pathway / actin cytoskeleton organization / protein-containing complex assembly / vesicle / postsynaptic density / cadherin binding / cell cycle / inflammatory response / cell division / axon / dendrite / apoptotic process / signal transduction / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit ...F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Ribosomal protein S3 C-terminal domain / Variant SH3 domain / Aspartate Aminotransferase, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2 / CD2-associated protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTakeda, S. / Minakata, S. / Narita, A. / Kitazawa, M. / Yamakuni, T. / Maeda, Y. / Nitanai, Y.
CitationJournal: Plos Biol. / Year: 2010
Title: Two distinct mechanisms for actin capping protein regulation--steric and allosteric inhibition
Authors: Takeda, S. / Minakata, S. / Koike, R. / Kawahata, I. / Narita, A. / Kitazawa, M. / Ota, M. / Yamakuni, T. / Maeda, Y. / Nitanai, Y.
History
DepositionNov 11, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_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: F-actin-capping protein subunit alpha-1
B: F-actin-capping protein subunit beta isoforms 1 and 2
C: 23mer peptide from CD2-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2344
Polymers63,0973
Non-polymers1371
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-55 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.119, 63.871, 141.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ORIGOMETRIC STATE OF THE ACTIN CAPPING PROTEIN IS A HETERO DIMER COMPOSE OF SUBUNIT A (CHAIN A) AND SUBUNIT B (CHAIN B) IN VIVO AND IN VITRO.

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Components

#1: Protein F-actin-capping protein subunit alpha-1 / CapZ 36/32 / Beta-actinin subunit I


Mass: 33001.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZA1 / Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 (DE3) / References: UniProt: P13127
#2: Protein F-actin-capping protein subunit beta isoforms 1 and 2 / CapZ B1 and B2 / CapZ 36/32 / Beta-actinin subunit II


Mass: 27473.070 Da / Num. of mol.: 1 / Mutation: residues 244-277 deletion mutation
Source method: isolated from a genetically manipulated source
Details: BETA TENTACLE DELETION / Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZB / Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 (DE3) / References: UniProt: P14315
#3: Protein/peptide 23mer peptide from CD2-associated protein / CD2AP / Cas ligand with multiple SH3 domains / Adapter protein CMS


Mass: 2622.107 Da / Num. of mol.: 1 / Fragment: recidues 485-507 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) homo sapiens (human) / References: UniProt: Q9Y5K6
#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG 400, 20MM BACL2, 100MM MES-NAOH, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 10, 2009 / Details: mirrors
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 41167 / % possible obs: 96 % / Redundancy: 6.6 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.43
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 4.71 / Num. unique all: 3026 / % possible all: 71.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IZN

1izn


Resolution: 1.9→45.311 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.502 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2079 5.1 %RANDOM
Rwork0.18373 ---
obs0.18652 39034 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.624 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.77 Å20 Å2
3---1.19 Å2
Refine analyzeLuzzati coordinate error obs: 0.195 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 1 411 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9536150
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30624.526232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53815820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4171534
X-RAY DIFFRACTIONr_chiral_restr0.1120.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213495
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0511.52737
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92324454
X-RAY DIFFRACTIONr_scbond_it2.83531783
X-RAY DIFFRACTIONr_scangle_it4.6954.51672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 127 -
Rwork0.226 2038 -
obs--69.88 %

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