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- PDB-1h1v: gelsolin G4-G6/actin complex -

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Basic information

Entry
Database: PDB / ID: 1h1v
Titlegelsolin G4-G6/actin complex
Components
  • ACTIN
  • GELSOLIN
KeywordsACTIN-BINDING / SEVERING / CAPPING / CALCIUM / AMYLOID / MUSCLE CONTRACTION
Function / homology
Function and homology information


Striated Muscle Contraction / dynactin complex / 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 ...Striated Muscle Contraction / dynactin complex / 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 / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / sarcoplasm / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / hepatocyte apoptotic process / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / cilium assembly / actin monomer binding / Caspase-mediated cleavage of cytoskeletal proteins / skeletal muscle fiber development / phagocytic vesicle / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / filopodium / 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 / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / cell body / actin binding / blood microparticle / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / hydrolase activity / Amyloid fiber formation / protein domain specific binding / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / 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 / Actin, alpha skeletal muscle / Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
ORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.99 Å
AuthorsChoe, H. / Burtnick, L.D. / Mejillano, M. / Yin, H.L. / Robinson, R.C. / Choe, S.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: The Calcium Activation of Gelsolin:Insights from the 3A Structure of the G4-G6/Actin Complex
Authors: Choe, H. / Burtnick, L.D. / Mejillano, M. / Yin, H.L. / Robinson, R.C. / Choe, S.
#1: Journal: Science / Year: 1999
Title: Domain Movement in Gelsolin: A Calcium-Activated Switch
Authors: Choe, H. / Burtnick, L.D. / Mejillano, M. / Yin, H.L. / Robinson, R.C. / Choe, S.
History
SupersessionJul 23, 2002ID: 1DB0
DepositionJul 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2003Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIN
G: GELSOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9788
Polymers78,2702
Non-polymers7086
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.350, 113.450, 159.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE COMPLEX IS A HETERODIMER WITH ONE MOLECULE OF ACTINAND ONE MOLECULE OF GELSOLIN.

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Components

#1: Protein ACTIN /


Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLESkeletal muscle / References: UniProt: P02568, UniProt: P68135*PLUS
#2: Protein GELSOLIN / / ACTIN-DEPOLYMERIZING FACTOR / BREVIN / AGEL


Mass: 36407.551 Da / Num. of mol.: 1 / Fragment: G4-G6, RESIDUES 412-742 OF CYTOPLASMIC ISOFORM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P06396
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGELSOLIN: CALCIUM-REGULATED, ACTIN-MODULATING PROTEIN THAT BINDS TO ACTIN MONOMERS OR FILAMENTS AT ...GELSOLIN: CALCIUM-REGULATED, ACTIN-MODULATING PROTEIN THAT BINDS TO ACTIN MONOMERS OR FILAMENTS AT THE BARBED END. ACTIN: HIGHLY CONSERVED PROTEINS INVOLVED IN CELL MOTILITY AND EXPRESSED IN ALL EUKARYOTIC CELLS.
Sequence detailsSWISSPROT HAS MERGED THE SEQUENCE OF RABBIT, HUMAN PIG, RAT AND MOUSE ACTIN AND GIVEN THE SWISSPROT ID P02568.

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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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 100MM HEPES BUFFER, PH 7.5, 20% GLYCEROL, 10 % PEG 8000
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion / Details: Robinson, R.C., (1999) Science, 286, 1939.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMTris-HCl1droppH8.0
20.2 mMATP1drop
30.1 mM1dropCaCl2
40.5 mMdithiothreitol1drop
510 mg/mlprotein1drop
610 %PEG80001reservoir
720 %glycerol1reservoir
8100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.07
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 20076 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.2
Reflection shellRmerge(I) obs: 0.3
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 98 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1DB0

1db0
PDB Unreleased entry


Resolution: 2.99→19.73 Å / SU B: 24.358 / SU ML: 0.464 / Cross valid method: THROUGHOUT / ESU R Free: 0.45
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1010 5 %RANDOM
Rwork0.219 ---
obs-19066 100 %-
Displacement parametersBiso mean: 26.173 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.99→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 36 346 5796
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.58
LS refinement shell
*PLUS
Highest resolution: 2.994 Å / Lowest resolution: 3.07 Å / Rfactor Rfree: 0.414 / % reflection Rfree: 65 % / Rfactor Rwork: 0.295 / Num. reflection Rwork: 1141 / Total num. of bins used: 20

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