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- PDB-1p8x: The Calcium-Activated C-terminal half of gelsolin -

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Basic information

Entry
Database: PDB / ID: 1p8x
TitleThe Calcium-Activated C-terminal half of gelsolin
ComponentsGelsolin precursor, plasma
KeywordsSTRUCTURAL PROTEIN / calcium-binding
Function / homology
Function and homology information


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 / actin cap ...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 / actin cap / regulation of podosome assembly / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / Sensory processing of sound by outer hair cells of the cochlea / podosome / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / central nervous system development / actin filament organization / protein destabilization / cellular response to type II interferon / actin filament binding / lamellipodium / actin cytoskeleton / actin binding / secretory granule lumen / blood microparticle / amyloid fibril formation / ficolin-1-rich granule lumen / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNarayan, K. / Burtnick, L.D. / Robinson, R.C.
CitationJournal: FEBS LETT. / Year: 2003
Title: Activation in isolation: Exposure of the actin-binding site in the C-terminal half of gelsolin does not require actin
Authors: Narayan, K. / Chumnarnsilpa, S. / Choe, H. / Irobi, E. / Urosev, D. / Lindberg, U. / Schutt, C.E. / Burtnick, L.D. / Robinson, R.C.
History
DepositionMay 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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: Gelsolin precursor, plasma
B: Gelsolin precursor, plasma
C: Gelsolin precursor, plasma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,64712
Polymers113,2863
Non-polymers3619
Water18,7361040
1
A: Gelsolin precursor, plasma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8824
Polymers37,7621
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gelsolin precursor, plasma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8824
Polymers37,7621
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gelsolin precursor, plasma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8824
Polymers37,7621
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.750, 90.110, 156.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gelsolin precursor, plasma / Actin-depolymerizing factor / ADF / Brevin / AGEL


Mass: 37762.098 Da / Num. of mol.: 3 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue cell / References: UniProt: P06396
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% (w/v) PEG 8000, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
215 %(w/v)PEG80001reservoir
3100 mMTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.068 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.068 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 6 / Num. unique all: 11619 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 81129 / Num. measured all: 512059
Reflection shell
*PLUS
% possible obs: 98.7 % / Num. unique obs: 11619 / Num. measured obs: 70689 / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The gelsolin (G4-G6) portion of PDB Entry 1H1V

1h1v


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.245 4056 RANDOM
Rwork0.205 --
all0.205 --
obs0.205 81073 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.622 Å20 Å20 Å2
2---3.951 Å20 Å2
3---0.329 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7495 0 9 1040 8544
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_mcbond_it1.5981.5
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_mcangle_it2.5092
X-RAY DIFFRACTIONc_scangle_it3.4392.5
LS refinement shellResolution: 2→2.1 Å
RfactorNum. reflection% reflection
Rfree0.276 3534 -
Rwork0.216 --
obs-70689 98.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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