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- PDB-1yag: STRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1yag
TitleSTRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX
Components
  • PROTEIN (ACTIN)
  • PROTEIN (GELSOLIN)
KeywordsCONTRACTILE PROTEIN / COMPLEX / ACTIN / GELSOLIN
Function / homology
Function and homology information


RHOA GTPase cycle / cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / ascospore wall assembly / vacuole inheritance / striated muscle atrophy / regulation of establishment of T cell polarity ...RHOA GTPase cycle / cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / ascospore wall assembly / vacuole inheritance / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / actin cortical patch / sequestering of actin monomers / regulation of podosome assembly / Swr1 complex / myosin II binding / Platelet degranulation / : / negative regulation of viral entry into host cell / actin filament severing / Ino80 complex / actin filament capping / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / NuA4 histone acetyltransferase complex / phagocytosis, engulfment / establishment of cell polarity / cortical actin cytoskeleton / hepatocyte apoptotic process / actin filament bundle / protein secretion / cilium assembly / sarcoplasm / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / central nervous system development / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / structural constituent of cytoskeleton / cellular response to type II interferon / endocytosis / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / secretory granule lumen / blood microparticle / ficolin-1-rich granule lumen / amyloid fibril formation / hydrolase activity / chromatin remodeling / Amyloid fiber formation / focal adhesion / DNA repair / DNA-templated transcription / calcium ion binding / chromatin / Neutrophil degranulation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 ...Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Gelsolin / Actin
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVorobiev, S. / Strokopytov, B. / Frieden, C. / Almo, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The structure of nonvertebrate actin: Implications for the ATP hydrolytic mechanism
Authors: Vorobiev, S. / Strokopytov, B. / Drubin, D.G. / Frieden, C. / Ono, S. / Condeelis, J. / Rubenstein, P.A. / Almo, S.C.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: The Structure of an Open State of Beta-Actin at 2.65 A Resolution
Authors: Chik, J.K. / Lindberg, U. / Schutt, C.E.
#2: Journal: Nature / Year: 1993
Title: Structure of Gelsolin Segment 1-Actin Complex and the Mechanism of Filament Severing
Authors: Mclaughlin, P.J. / Gooch, J.T. / Mannherz, H.G. / Weeds, A.G.
#3: Journal: Nature / Year: 1990
Title: Atomic Structure of the Actin:DNase I Complex
Authors: Kabsch, W. / Mannherz, H.G. / Suck, D. / Pai, E.F. / Holmes, K.C.
History
DepositionOct 9, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 9, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ACTIN)
G: PROTEIN (GELSOLIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4756
Polymers55,8072
Non-polymers6684
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-38 kcal/mol
Surface area21100 Å2
MethodPISA, PQS
2
A: PROTEIN (ACTIN)
G: PROTEIN (GELSOLIN)
hetero molecules

A: PROTEIN (ACTIN)
G: PROTEIN (GELSOLIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,95012
Polymers111,6154
Non-polymers1,3358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9290 Å2
ΔGint-130 kcal/mol
Surface area39760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.662, 68.099, 54.598
Angle α, β, γ (deg.)90.00, 102.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-377-

SO4

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein PROTEIN (ACTIN)


Mass: 41735.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: RED STAR / References: UniProt: P60010
#2: Protein PROTEIN (GELSOLIN) / ACTIN-DEPOLYMERIZING FACTOR (ADF)


Mass: 14071.831 Da / Num. of mol.: 1 / Fragment: SUBDOMAIN 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06396

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Non-polymers , 5 types, 431 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAN ORDERED MAGNESIUM ION IS OBSERVED BOUND TO ATP.

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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: 2.87 Å3/Da / Density % sol: 50.5 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.4-1.7 Mammonium sulfate1reservoir
2100 mMHEPES1reservoir
32 mMMg-ATP1reservoir
52 mMTris-HCl1drop
62 mMATP1drop
74 mM1dropMgCl2
80.5 mMEGTA1drop
91 mM1dropNaN3
4gelositin1drop1:1.25 stoichiometry

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 49913 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / % possible all: 99
Reflection
*PLUS
Redundancy: 3.77 %
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RABBIT SKELETAL MUSCLE ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX

Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 -5 %RANDOM
Rwork0.193 ---
obs0.193 49883 100 %-
Displacement parametersBiso mean: 23.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3883 0 38 427 4348
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.89
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH19.SOL
X-RAY DIFFRACTION3PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
X-RAY DIFFRACTION4PARAM.ATPTOPOLOGY.ATP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1915 / Rfactor Rfree: 0.2304 / Rfactor Rwork: 0.1915
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.532
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.89

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