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- PDB-1t44: Structural basis of actin sequestration by thymosin-B4: Implicati... -

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Basic information

Entry
Database: PDB / ID: 1t44
TitleStructural basis of actin sequestration by thymosin-B4: Implications for arp2/3 activation
Components
  • Actin, alpha
  • Chimera of Gelsolin domain 1 and C-Terminal domain of thymosin Beta-4
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


Striated Muscle Contraction / dynactin complex / positive regulation of smooth muscle cell differentiation / 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 ...Striated Muscle Contraction / dynactin complex / positive regulation of smooth muscle cell differentiation / 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 / Platelet degranulation / 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 / positive regulation of smooth muscle cell migration / 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 / regulation of cell migration / 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 / cytoskeleton / hydrolase activity / Amyloid fiber formation / protein domain specific binding / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / positive regulation of DNA-templated transcription / magnesium ion binding / enzyme binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain / Severin ...Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / 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 / Thymosin beta-4 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIrobi, E. / Aguda, A.H. / Larsson, M. / Burtnick, L.D. / Robinson, R.C.
CitationJournal: Embo J. / Year: 2004
Title: Structural basis of actin sequestration by thymosin-beta4: implications for WH2 proteins.
Authors: Irobi, E. / Aguda, A.H. / Larsson, M. / Guerin, C. / Yin, H.L. / Burtnick, L.D. / Blanchoin, L. / Robinson, R.C.
History
DepositionApr 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE FUSION OF GELSOLIN DOMAIN 1 FROM HUMAN WITH C-TERMINAL DOMAIN OF THYMOSIN B4 FROM MOUSE ...SEQUENCE FUSION OF GELSOLIN DOMAIN 1 FROM HUMAN WITH C-TERMINAL DOMAIN OF THYMOSIN B4 FROM MOUSE (SEQUENCE:ETQEKNPLPSKETIEQEKQ)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Chimera of Gelsolin domain 1 and C-Terminal domain of thymosin Beta-4
A: Actin, alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5336
Polymers57,9062
Non-polymers6274
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-59 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.850, 69.335, 80.233
Angle α, β, γ (deg.)90.00, 94.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chimera of Gelsolin domain 1 and C-Terminal domain of thymosin Beta-4


Mass: 16632.541 Da / Num. of mol.: 1
Fragment: Chimera of Gelsolin domain 1 (residues 28-152) from human and C-Terminal domain of thymosin Beta-4 from mouse (residues 153-171)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Genus: Homo, Mus / Species: , / Strain: , / Production host: Escherichia coli (E. coli) / References: UniProt: P06396, UniProt: P20065
#2: Protein Actin, alpha / / Alpha-actin 1


Mass: 41273.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P02568, UniProt: P68135*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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.: 427 / 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: 2.55 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: PEG 8000, Sodium acetate, calcium chloride, pH 6.5, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0052 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0052 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 39223 / Num. obs: 39223 / Redundancy: 3.3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.6

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Processing

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

1p8z


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.957 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19531 2079 5 %RANDOM
Rwork0.14445 ---
obs0.14709 39223 98.15 %-
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: 14.977 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20.35 Å2
2---0.42 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 0 34 427 4420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214082
X-RAY DIFFRACTIONr_bond_other_d0.0020.023627
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9635535
X-RAY DIFFRACTIONr_angle_other_deg0.86838473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5745499
X-RAY DIFFRACTIONr_chiral_restr0.0940.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024512
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02809
X-RAY DIFFRACTIONr_nbd_refined0.2030.2784
X-RAY DIFFRACTIONr_nbd_other0.2450.24127
X-RAY DIFFRACTIONr_nbtor_other0.0860.22242
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2304
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0680.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.219
X-RAY DIFFRACTIONr_mcbond_it0.9691.52494
X-RAY DIFFRACTIONr_mcangle_it1.62924025
X-RAY DIFFRACTIONr_scbond_it2.9531588
X-RAY DIFFRACTIONr_scangle_it4.5454.51510
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.196 140
Rwork0.127 2890
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)
10.56050.1648-0.28911.1180.18211.1494-0.019-0.0111-0.0442-0.02770.0356-0.11740.02970.0954-0.01660.0634-0.00430.01150.1292-0.01210.119413.27-8.44223.034
23.43051.4418-0.68668.0116-1.31482.95830.15360.17170.0814-0.1824-0.0247-0.35620.08830.2529-0.12890.0516-0.01360.060.1358-0.02630.074518.5281.1993.708
30.8275-0.09420.06830.7237-0.11211.2282-0.01330.03170.0173-0.02270.02880.03890.0466-0.0964-0.01550.0833-0.01180.00250.14250.00920.1016-10.515-0.45122.771
40.9088-0.1035-0.39061.1919-0.38991.06280.03320.05840.0367-0.1388-0.0017-0.0331-0.01-0.0762-0.03150.1104-0.00160.00490.13410.03510.0662-4.78113.5293.125
50.67970.4544-0.20061.5906-0.06750.91110.0099-0.0591-0.00980.17370.00960.01930.0130.0458-0.01950.13440.00560.00270.10380.00030.0792-2.812-1.78647.438
61.06540.3132-10.9998-4.826532.70260.19430.14730.39590.0083-0.016-0.2443-0.03830.3091-0.17830.0940.02030.09620.07560.0520.15715.59612.6593.664
70.0662-0.0219-0.12750.2688-0.03150.30650.00240.02010.00920.01190.0066-0.010.0121-0.0104-0.0090.1027-0.0148-0.00280.1280.00880.1012-1.0041.34725.051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB6 - 321 - 27
2X-RAY DIFFRACTION1AB71 - 13666 - 131
3X-RAY DIFFRACTION1AB337 - 375332 - 370
4X-RAY DIFFRACTION1AC7001
5X-RAY DIFFRACTION2AB33 - 7028 - 65
6X-RAY DIFFRACTION3AB137 - 180132 - 175
7X-RAY DIFFRACTION3AB274 - 336269 - 331
8X-RAY DIFFRACTION4AB181 - 273176 - 268
9X-RAY DIFFRACTION4AF9001
10X-RAY DIFFRACTION5GA28 - 1524 - 128
11X-RAY DIFFRACTION5GD - E701 - 7021
12X-RAY DIFFRACTION6GA153 - 171129 - 147
13X-RAY DIFFRACTION7AG901 - 11751 - 275

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