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Basic information

Entry
Database: PDB / ID: 4pkg
TitleComplex of ATP-actin With the N-terminal Actin-Binding Domain of Tropomodulin
Components
  • Actin, alpha skeletal muscle
  • Gelsolin,Tropomodulin-1 chimera
KeywordsContractile Protein/Actin-Binding Protein / Tmod / Actin Filament / Pointed-End Capping Protein / Tropomyosin / Contractile Protein / Actin-binding Protein / Contractile Protein-Actin-Binding Protein complex
Function / homology
Function and homology information


pointed-end actin filament capping / lens fiber cell development / myofibril assembly / 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 ...pointed-end actin filament capping / lens fiber cell development / myofibril assembly / 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 / Striated Muscle Contraction / Sensory processing of sound by outer hair cells of the cochlea / podosome / relaxation of cardiac muscle / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / myosin heavy chain binding / hepatocyte apoptotic process / tropomyosin binding / cortical cytoskeleton / troponin I binding / filamentous actin / myofibril / mesenchyme migration / actin filament bundle / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / sarcoplasm / skeletal muscle thin filament assembly / actin monomer binding / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / stress fiber / skeletal muscle fiber development / phagocytic vesicle / titin binding / muscle contraction / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / adult locomotory behavior / sarcomere / central nervous system development / actin filament organization / filopodium / actin filament / protein destabilization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / lamellipodium / actin cytoskeleton / actin binding / cell body / secretory granule lumen / blood microparticle / amyloid fibril formation / ficolin-1-rich granule lumen / cytoskeleton / hydrolase activity / protein domain specific binding / Amyloid fiber formation / 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 / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tropomodulin / Tropomodulin / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat ...Tropomodulin / Tropomodulin / 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 / Leucine-rich repeat domain superfamily / 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 / Tropomodulin-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRao, J.N. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM073791 United States
CitationJournal: Science / Year: 2014
Title: Actin cytoskeleton. Mechanism of actin filament pointed-end capping by tropomodulin.
Authors: Rao, J.N. / Madasu, Y. / Dominguez, R.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
G: Gelsolin,Tropomodulin-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5626
Polymers62,9342
Non-polymers6274
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-63 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.471, 75.866, 136.396
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 Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Skeletal Muscle / References: UniProt: P68135
#2: Protein Gelsolin,Tropomodulin-1 chimera / AGEL / Actin-depolymerizing factor / ADF / Brevin / Erythrocyte tropomodulin / E-Tmod


Mass: 20824.406 Da / Num. of mol.: 1
Fragment: Gelsolin (UNP residues 12-136), GGSGGSGGS linker, Tmod1 Actin-binding site 1 (UNP residues 50-101)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN, TMOD1, D9S57E, TMOD / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06396, UniProt: P28289
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.18 M sodium fluoride, 11% w/v PEG3350, 1% v/v PEG1000, 1% v/v PEG400
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 67450 / % possible obs: 99.8 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 43.7
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EQY

1eqy


Resolution: 1.8→40 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 2000 2.97 %
Rwork0.1562 --
obs0.1572 67450 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4253 0 34 511 4798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114511
X-RAY DIFFRACTIONf_angle_d1.2956137
X-RAY DIFFRACTIONf_dihedral_angle_d15.0481723
X-RAY DIFFRACTIONf_chiral_restr0.053666
X-RAY DIFFRACTIONf_plane_restr0.006789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7996-1.84460.29941390.2714528X-RAY DIFFRACTION98
1.8446-1.89440.2821410.23484617X-RAY DIFFRACTION100
1.8944-1.95020.24761410.21014622X-RAY DIFFRACTION100
1.9502-2.01310.22751410.18524629X-RAY DIFFRACTION100
2.0131-2.08510.21371410.17384627X-RAY DIFFRACTION100
2.0851-2.16850.20051440.16924680X-RAY DIFFRACTION100
2.1685-2.26720.19171410.15734623X-RAY DIFFRACTION100
2.2672-2.38670.21420.15054655X-RAY DIFFRACTION100
2.3867-2.53620.18251430.14794663X-RAY DIFFRACTION100
2.5362-2.7320.17111430.15554677X-RAY DIFFRACTION100
2.732-3.00690.21141440.16314716X-RAY DIFFRACTION100
3.0069-3.44170.21151440.16844715X-RAY DIFFRACTION100
3.4417-4.33520.15741450.13374770X-RAY DIFFRACTION100
4.3352-37.94140.14791510.13494925X-RAY DIFFRACTION99
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)
10.77070.24250.42542.7609-1.5111.6133-0.1821-0.00250.30410.03790.05050.2303-0.7469-0.1207-0.01310.42720.0414-0.12050.20970.00480.32065.613115.096-14.0957
20.97940.25880.53962.2596-0.21771.6798-0.1078-0.11640.20070.00070.0155-0.1041-0.29920.08210.09990.1871-0.006-0.04790.18570.00480.204613.54712.95-7.7872
31.381-0.56040.27371.9649-0.78412.12590.07170.1468-0.0267-0.61810.02830.38080.0519-0.2619-0.01880.3787-0.039-0.17120.2290.01940.2715-1.8432-6.4368-26.6969
41.48920.5865-0.23742.3579-0.45791.64260.086-0.4007-0.05310.1219-0.0914-0.19930.09690.05620.03640.17980.0197-0.05020.19550.03910.205813.4158-6.2962-4.2221
52.7172-1.1610.81612.6422-0.72452.67860.1889-0.79160.03920.4444-0.3826-0.6621-0.06760.83910.0950.1882-0.0623-0.10550.71060.28980.311714.8247-19.537611.5093
62.18360.67380.0231.40150.09151.2726-0.0024-0.6382-0.58960.2054-0.030.03440.09970.0632-0.02720.18-0.0031-0.00330.38690.18920.32156.9545-23.6245.0599
72.6238-0.94560.09523.56720.30395.30950.15950.09750.5393-0.1405-0.1930.9484-0.488-1.0750.00150.80820.2334-0.2050.60790.02320.7728-15.185819.5303-28.8396
82.1362-0.4016-0.07822.3622-0.59091.9189-0.0720.040.38480.1348-0.1948-0.1585-0.9144-0.49090.0530.93140.1543-0.02470.549-0.13560.915.096423.6439-7.4851
91.59991.11130.93752.8284-0.59593.4202-0.1704-0.42510.38690.36490.0514-0.7328-0.54790.40570.21130.5744-0.1922-0.09260.7132-0.21690.884730.235712.78140.0111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 320 )
4X-RAY DIFFRACTION4chain 'A' and (resid 321 through 375 )
5X-RAY DIFFRACTION5chain 'G' and (resid 52 through 74 )
6X-RAY DIFFRACTION6chain 'G' and (resid 75 through 177 )
7X-RAY DIFFRACTION7chain 'G' and (resid 1058 through 1076 )
8X-RAY DIFFRACTION8chain 'G' and (resid 1077 through 1091 )
9X-RAY DIFFRACTION9chain 'G' and (resid 1092 through 1099 )

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