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- PDB-1rgi: Crystal structure of gelsolin domains G1-G3 bound to actin -

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Basic information

Entry
Database: PDB / ID: 1rgi
TitleCrystal structure of gelsolin domains G1-G3 bound to actin
Components
  • Actin, alpha skeletal muscle
  • Gelsolin
KeywordsCONTRACTILE PROTEIN / Domain movement
Function / homology
Function and homology information


actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle ...actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / 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 / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / filopodium / central nervous system development / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular space / ATP binding / identical protein binding / metal ion binding / 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
Similarity search - Component
Biological speciesEquus caballus (horse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBurtnick, L.D. / Urosev, D. / Irobi, E. / Narayan, K. / Robinson, R.C.
CitationJournal: Embo J. / Year: 2004
Title: Structure of the N-terminal half of gelsolin bound to actin: roles in severing, apoptosis and FAF
Authors: Burtnick, L.D. / Urosev, D. / Irobi, E. / Narayan, K. / Robinson, R.C.
History
DepositionNov 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE DURING THE COURSE OF THE CRYSTALLIZATION THE GELSOLIN BECAME CLEAVED. THE AUTHORS STATE ...SEQUENCE DURING THE COURSE OF THE CRYSTALLIZATION THE GELSOLIN BECAME CLEAVED. THE AUTHORS STATE THEY DO NOT KNOW EXACTLY THE SEQUENCE OF WHAT IS IN THE CRYSTALS, ONLY WHAT THEY SEE IN THE DENSITY, WHICH IS WHAT IS REPORTED HERE IN THE SEQRES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Gelsolin
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6037
Polymers80,9362
Non-polymers6675
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-61 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.245, 145.245, 129.948
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Gelsolin / / Actin-depolymerizing factor / ADF / Brevin


Mass: 38838.965 Da / Num. of mol.: 1 / Fragment: domains G1-G3 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: Q28372
#2: Protein Actin, alpha skeletal muscle / / Alpha-actin 1


Mass: 42096.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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.: 26 / 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: 4.89 Å3/Da / Density % sol: 74.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2% PEG 8000, 100 mM Sodium acetate, 1 mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0052 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0052 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 31104 / Num. obs: 31104 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.059 / Net I/σ(I): 21.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.87 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.383 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P8Z

1p8z


Resolution: 3→19.96 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.213 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.599 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25755 1570 5 %RANDOM
Rwork0.22408 ---
obs0.22579 29527 97.53 %-
all-31101 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.414 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 3→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 0 35 26 5541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215632
X-RAY DIFFRACTIONr_bond_other_d0.0020.025048
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.967623
X-RAY DIFFRACTIONr_angle_other_deg0.812311777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026245
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021134
X-RAY DIFFRACTIONr_nbd_refined0.2080.21284
X-RAY DIFFRACTIONr_nbd_other0.2260.26214
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.23745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5091.53452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00525559
X-RAY DIFFRACTIONr_scbond_it1.43632180
X-RAY DIFFRACTIONr_scangle_it2.524.52064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.003→3.079 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.421 105
Rwork0.301 2126
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9501-1.08420.08632.28470.08823.1768-0.1046-0.0747-0.21530.06730.04180.60260.2211-0.54690.06280.41680.1-0.13590.2823-0.03060.401140.30928.4678.97
210.9391.7610.47266.74025.308517.6022-0.1196-1.3494-0.32571.57860.40110.39061.0415-0.238-0.28140.80110.351-0.04850.35780.10650.307849.29323.70628.312
32.8248-1.83970.79713.0966-1.173.03320.38650.5424-0.6804-0.4325-0.09150.53190.6618-0.0667-0.2950.68040.17-0.24650.2363-0.19770.387253.65412.703-5.08
43.7446-0.41541.16871.7972-0.25582.45860.1076-0.1525-0.38430.07940.05920.16950.47430.1229-0.16680.69830.2327-0.12290.0806-0.06820.266668.99211.21613.796
51.9344-0.48850.37521.8603-0.63873.77890.19240.7011-0.0217-0.4379-0.00630.3210.5187-0.1329-0.18610.40120.15-0.16750.4809-0.04980.309646.99732.712-17.205
64.4535-0.3850.30227.7134.35416.9209-0.6925-0.94240.62770.92141.1172-1.5146-0.10091.2589-0.42470.65140.4334-0.48250.8273-0.35710.586461.58846.87333.214
731.1003-2.6032-6.96275.45587.203513.7865-0.0556-3.37372.14160.29660.4467-0.9324-1.4811.5664-0.39111.0170.1419-0.30.5283-0.07690.56158.79459.17439.268
87.7965-2.75083.63497.04551.02597.7905-0.22710.13890.29260.07910.131-0.2093-0.23520.31540.09610.3870.2816-0.13580.2499-0.09540.24239.27352.85223.313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB5 - 327 - 34
2X-RAY DIFFRACTION1AB71 - 13673 - 138
3X-RAY DIFFRACTION1AB337 - 365339 - 367
4X-RAY DIFFRACTION1AH403 - 4082 - 7
5X-RAY DIFFRACTION2AB33 - 7035 - 72
6X-RAY DIFFRACTION3AB137 - 180139 - 182
7X-RAY DIFFRACTION3AB274 - 336276 - 338
8X-RAY DIFFRACTION3AB375377
9X-RAY DIFFRACTION3AH4098
10X-RAY DIFFRACTION3AH417 - 42016 - 19
11X-RAY DIFFRACTION4AB181 - 273183 - 275
12X-RAY DIFFRACTION4AH410 - 4169 - 15
13X-RAY DIFFRACTION4AF4011
14X-RAY DIFFRACTION4AG3801
15X-RAY DIFFRACTION5GA26 - 1621 - 137
16X-RAY DIFFRACTION5GI4082
17X-RAY DIFFRACTION5GC - D403 - 4041
18X-RAY DIFFRACTION5AH4021
19X-RAY DIFFRACTION6GI410 - 4114 - 5
20X-RAY DIFFRACTION6GA163 - 248138 - 223
21X-RAY DIFFRACTION7GA249 - 271224 - 246
22X-RAY DIFFRACTION8GA272 - 371247 - 346
23X-RAY DIFFRACTION8GE4061
24X-RAY DIFFRACTION8GI412 - 4136 - 7

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