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- PDB-3tu5: Actin complex with Gelsolin Segment 1 fused to Cobl segment -

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Basic information

Entry
Database: PDB / ID: 3tu5
TitleActin complex with Gelsolin Segment 1 fused to Cobl segment
Components
  • Actin, alpha skeletal muscle
  • Gelsolin,Protein cordon-bleu,Thymosin beta-4
KeywordsSTRUCTURAL PROTEIN/ACTIN-BINDING PROTEIN / Unusual hairpin conformation in the D-loop / STRUCTURAL PROTEIN-ACTIN-BINDING PROTEIN complex
Function / homology
Function and homology information


positive regulation of proton-transporting ATP synthase activity, rotational mechanism / somite specification / floor plate development / actin filament network formation / terminal web / 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 proton-transporting ATP synthase activity, rotational mechanism / somite specification / floor plate development / actin filament network formation / terminal web / 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 / embryonic axis specification / 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 crosslink formation / sequestering of actin monomers / regulation of podosome assembly / notochord development / 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 / digestive tract development / cell projection assembly / cardiac muscle cell contraction / positive regulation of endothelial cell chemotaxis / collateral sprouting in absence of injury / podosome / sarcoplasm / positive regulation of ruffle assembly / positive regulation of dendrite development / 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 / positive regulation of ATP biosynthetic process / troponin I binding / hepatocyte apoptotic process / actin filament bundle / filamentous actin / dendritic growth cone / 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 / positive regulation of blood vessel endothelial cell migration / skeletal muscle fiber development / phagocytic vesicle / axonal growth cone / stress fiber / negative regulation of canonical NF-kappaB signal transduction / regulation of cell migration / titin binding / ruffle / tumor necrosis factor-mediated signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / protein sequestering activity / platelet alpha granule lumen / filopodium / liver development / central nervous system development / actin filament organization / neural tube closure / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / negative regulation of inflammatory response / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / Platelet degranulation / lamellipodium / cell body / actin binding / cell cortex / actin cytoskeleton organization / blood microparticle / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / cytoskeleton / hydrolase activity / Amyloid fiber formation / axon
Similarity search - Function
Cordon-bleu, ubiquitin-like domain / Protein cordon-bleu-like / Cordon-bleu ubiquitin-like domain / Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / WH2 motif / Wiskott Aldrich syndrome homology region 2 ...Cordon-bleu, ubiquitin-like domain / Protein cordon-bleu-like / Cordon-bleu ubiquitin-like domain / Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / 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 / Thymosin beta-4 / Actin, alpha skeletal muscle / Protein cordon-bleu
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsKudryashov, D.S. / Sawaya, M.R. / Durer, Z.A.O.
CitationJournal: Biophys.J. / Year: 2012
Title: Structural States and dynamics of the d-loop in actin.
Authors: Durer, Z.A. / Kudryashov, D.S. / Sawaya, M.R. / Altenbach, C. / Hubbell, W. / Reisler, E.
History
DepositionSep 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Feb 28, 2024Group: 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_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_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: Actin, alpha skeletal muscle
B: Gelsolin,Protein cordon-bleu,Thymosin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4147
Polymers74,5902
Non-polymers8245
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-67 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.184, 71.184, 222.244
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 42096.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: skeletal / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Gelsolin,Protein cordon-bleu,Thymosin beta-4 / AGEL / Actin-depolymerizing factor / ADF / Brevin / T beta-4 / Fx


Mass: 32493.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Gene: GSN, Cobl, Kiaa0633, TMSB4X, TB4X, THYB4, TMSB4 / Plasmid: pCOLD-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 cells
References: UniProt: P06396, UniProt: Q5NBX1, UniProt: P62328

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Non-polymers , 4 types, 70 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10% (w/v) polyethyleneglycol 20000, 2% (v/v) dioxane, and 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→118 Å / Num. all: 13348 / Num. obs: 13348 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 67.4 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.031 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.117.20.49313321.121198.1
3.11-3.237.20.33913161.155197.9
3.23-3.387.10.22713171.15197.6
3.38-3.567.20.1613331.1197.6
3.56-3.787.10.12313121.001197.2
3.78-4.077.10.09713120.902196.8
4.07-4.487.10.08813460.994196.3
4.48-5.1370.07813320.992195.7
5.13-6.466.80.06113471.004194.7
6.46-1186.70.0414010.887191.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.7 Å33.8 Å
Translation3.7 Å33.8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→25.42 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9378 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 668 5.02 %RANDOM
Rwork0.1652 ---
all0.1672 13348 --
obs0.1672 13297 --
Displacement parametersBiso max: 200.15 Å2 / Biso mean: 74.2852 Å2 / Biso min: 25.74 Å2
Baniso -1Baniso -2Baniso -3
1--4.2979 Å20 Å20 Å2
2---4.2979 Å20 Å2
3---8.5958 Å2
Refine analyzeLuzzati coordinate error obs: 0.392 Å
Refinement stepCycle: LAST / Resolution: 3→25.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3943 0 49 65 4057
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1420SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes103HARMONIC2
X-RAY DIFFRACTIONt_gen_planes585HARMONIC5
X-RAY DIFFRACTIONt_it4077HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion4HARMONIC0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion529SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4673SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4077HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5529HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion22.43
LS refinement shellResolution: 3→3.24 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2872 140 5.12 %
Rwork0.19 2597 -
all0.1948 2737 -
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)
11.15440.1752-0.47182.8935-0.74294.7536-0.14130.0167-0.04580.47570.19150.0249-0.0442-0.611-0.0501-0.1291-0.0834-0.01-0.2648-0.0183-0.27516.3444-8.070922.1341
21.72971.0545-0.50713.3524-0.33523.4015-0.19950.0896-0.1088-0.39470.0887-0.32050.25850.02170.11090.0696-0.18260.1555-0.1761-0.0903-0.089630.7241-17.7104-3.9211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 377
2X-RAY DIFFRACTION2{ B|* }B1 - 132

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