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- PDB-1yvn: THE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SE... -

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Basic information

Entry
Database: PDB / ID: 1yvn
TitleTHE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SEGMENT 1.
Components
  • PROTEIN (ACTIN)
  • PROTEIN (GELSOLIN)
KeywordsSTRUCTURAL PROTEIN / YEAST / ACTIN / MUTANT V159N / GELSOLIN / ACTIN-BINDING / MG-ATP
Function / homology
Function and homology information


mitotic actomyosin contractile ring contraction / RHOA GTPase cycle / cellular bud neck contractile ring / 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 ...mitotic actomyosin contractile ring contraction / RHOA GTPase cycle / cellular bud neck contractile ring / 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 / Swr1 complex / sequestering of actin monomers / regulation of podosome assembly / 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 filament depolymerization / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / NuA4 histone acetyltransferase complex / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / establishment of cell polarity / hepatocyte apoptotic process / actin filament bundle / cilium assembly / protein secretion / 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 / blood microparticle / secretory granule lumen / 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: 2.1 Å
AuthorsVorobiev, S.M. / Belmont, L.D. / Drubin, D.G. / Almo, S.C.
Citation
Journal: To be Published
Title: Crystal structure of yeast actin V159N mutant
Authors: Vorobiev, S.M. / Belmont, L.D. / Drubin, D.D. / Almos, C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: A change in actin conformation associated with filament instability after Pi release.
Authors: Belmont, L.D. / Orlova, A. / Drubin, D.G. / Egelman, E.H.
#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
DepositionMar 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 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_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 (ACTIN)
G: PROTEIN (GELSOLIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4906
Polymers55,8222
Non-polymers6684
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-49 kcal/mol
Surface area20920 Å2
MethodPISA
2
A: PROTEIN (ACTIN)
G: PROTEIN (GELSOLIN)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)112,98012
Polymers111,6454
Non-polymers1,3358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9230 Å2
ΔGint-133 kcal/mol
Surface area39410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.098, 68.077, 54.691
Angle α, β, γ (deg.)90.00, 102.24, 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: 41750.520 Da / Num. of mol.: 1 / Mutation: V159N / Source method: isolated from a natural source / Details: THE GENE NAME IS ACT. / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ACT1-159 / References: UniProt: P60010
#2: Protein PROTEIN (GELSOLIN)


Mass: 14071.831 Da / Num. of mol.: 1 / Fragment: FRAGMENT 1
Source method: isolated from a genetically manipulated source
Details: CA(2+)-BOUND PROTEIN / Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC GENE / Plasmid: PMW172 / 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, 287 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.: 283 / 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: 2.51 Å3/Da / Density % sol: 50.55 %
Crystal growpH: 8
Details: 0.1 M HEPES, 1.60 M (NH4)2SO4, 2 MM MG-ATP, PH=8.0.

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.0702
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0702 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 33130 / % possible obs: 86.8 % / Redundancy: 2.95 % / Rmerge(I) obs: 0.057

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YAG

1yag


Resolution: 2.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 -4 %RANDOM
Rwork0.187 ---
obs-32577 84.4 %-
Displacement parametersBiso mean: 22.69 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 38 283 4190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.404
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.35
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.736
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
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
Rfactor% reflection
Rfree0.275 3.5 %
Rwork0.229 -
obs-62.82 %
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

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