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- PDB-4pki: Complex of ATP-actin With the C-terminal Actin-Binding Domain of ... -

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Basic information

Entry
Database: PDB / ID: 4pki
TitleComplex of ATP-actin With the C-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


lens fiber cell development / pointed-end actin filament capping / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / positive regulation of keratinocyte apoptotic process / renal protein absorption / positive regulation of protein processing in phagocytic vesicle / myofibril assembly ...lens fiber cell development / pointed-end actin filament capping / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / positive regulation of keratinocyte apoptotic process / renal protein absorption / positive regulation of protein processing in phagocytic vesicle / myofibril assembly / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of actin nucleation / actin cap / myosin II binding / host-mediated suppression of symbiont invasion / cell projection assembly / actin filament severing / hepatocyte apoptotic process / actin polymerization or depolymerization / barbed-end actin filament capping / actin filament depolymerization / Striated Muscle Contraction / actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / phagocytosis, engulfment / relaxation of cardiac muscle / cardiac muscle cell contraction / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / cortical cytoskeleton / response to muscle stretch / myofibril / sarcoplasm / skeletal muscle myofibril / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / actin monomer binding / Caspase-mediated cleavage of cytoskeletal proteins / skeletal muscle fiber development / cilium assembly / actin filament polymerization / stress fiber / titin binding / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / muscle contraction / actin filament organization / central nervous system development / sarcomere / filopodium / actin filament / protein destabilization / 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 / actin binding / cell body / secretory granule lumen / blood microparticle / amyloid fibril formation / ficolin-1-rich granule lumen / cytoskeleton / Amyloid fiber formation / protein domain specific binding / focal adhesion / hydrolase activity / positive regulation of gene expression / calcium ion binding / Neutrophil degranulation / magnesium ion binding / : / extracellular exosome / extracellular region / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tropomodulin / Tropomodulin / TMOD/LMOD Leucine-rich domain / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain ...Tropomodulin / Tropomodulin / TMOD/LMOD Leucine-rich domain / 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 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / ATPase, substrate binding domain, subdomain 4 / Alpha-Beta Horseshoe / 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: 2.3 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)78,7806
Polymers78,1532
Non-polymers6274
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-60 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.393, 81.211, 170.708
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: 36042.801 Da / Num. of mol.: 1
Fragment: Gelsolin (UNP residues 12-136), GGSGGSGGS linker, Tmod1 Actin-binding site 2 (UNP residues 160-349)
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.: 208 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.25 M sodium chloride, 12% w/v PEG3350 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 22, 2013
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 43679 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.8
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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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 1IO0

1io0


Resolution: 2.3→45 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 1998 4.58 %
Rwork0.1682 --
obs0.1697 43647 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 34 208 5567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145527
X-RAY DIFFRACTIONf_angle_d1.4317504
X-RAY DIFFRACTIONf_dihedral_angle_d17.1782091
X-RAY DIFFRACTIONf_chiral_restr0.055831
X-RAY DIFFRACTIONf_plane_restr0.008971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2982-2.35570.27671360.252836X-RAY DIFFRACTION97
2.3557-2.41940.28961410.23052936X-RAY DIFFRACTION100
2.4194-2.49060.23691410.21232944X-RAY DIFFRACTION100
2.4906-2.5710.23431410.19472921X-RAY DIFFRACTION100
2.571-2.66280.23311400.19122962X-RAY DIFFRACTION100
2.6628-2.76940.25541410.19812934X-RAY DIFFRACTION100
2.7694-2.89550.23331430.19032978X-RAY DIFFRACTION100
2.8955-3.04810.23331430.20462961X-RAY DIFFRACTION100
3.0481-3.2390.24371420.19732961X-RAY DIFFRACTION100
3.239-3.4890.19711420.18572968X-RAY DIFFRACTION100
3.489-3.83990.19641450.16863010X-RAY DIFFRACTION100
3.8399-4.39520.17791430.13262999X-RAY DIFFRACTION100
4.3952-5.53580.17351470.12893041X-RAY DIFFRACTION100
5.5358-44.88480.14961530.14493198X-RAY DIFFRACTION100
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)
10.77310.38620.46771.73030.18950.98320.09260.0976-0.3263-0.2351-0.0926-0.05350.30380.0331-0.00430.37510.06610.04310.3413-0.0650.4501-1.4431-9.9781-18.0412
21.4090.0934-0.44761.6616-0.04060.7330.11490.0467-0.1103-0.4211-0.19130.21650.094-0.01980.10410.3140.03840.00970.2928-0.03360.274-6.19536.3213-16.7662
32.2276-0.3972-0.51591.8933-0.20262.45630.23910.11390.0878-1.0162-0.1619-0.38920.07750.3403-0.13630.64550.05630.2420.38650.02810.32318.941614.0027-28.9172
40.5547-0.03540.23271.89640.39981.15360.1393-0.09610.02890.0634-0.15810.1256-0.0674-0.0194-0.00670.2450.00290.07180.3333-0.03650.3508-8.12488.4194-6.291
52.6217-1.09680.68132.75230.41890.80040.3557-1.114-0.41070.4807-0.45040.27530.4039-0.72580.44060.4228-0.13220.13980.9225-0.23520.2956-10.006619.753311.0369
61.17791.27441.98111.66182.46524.25790.5871-0.6641-0.09790.5221-0.455-0.54490.2574-0.6150.1170.4476-0.14710.02410.616-0.06190.3170.518917.240713.6815
71.7306-0.29560.20461.35490.16261.7598-0.0734-0.35480.59060.3749-0.2067-0.05990.1187-0.4670.03060.1948-0.06380.05150.5475-0.20010.4296-3.123826.9086.7245
83.6426-1.3591-0.06062.2138-0.04531.10590.0934-0.47250.05070.0302-0.03990.08180.1285-0.26170.08610.2297-0.05270.060.4049-0.06870.3061-5.320616.44331.6451
91.13160.33720.82881.55420.09840.58540.0057-0.2290.86930.0036-0.16090.166-0.0699-0.06430.09230.22420.01080.0210.3948-0.12870.451-2.541229.38121.2579
101.82660.76591.02351.6126-0.59861.34560.1237-0.39490.12650.5112-0.2606-0.04760.10630.00710.07450.3034-0.0433-0.00250.5067-0.08360.39198.424623.00699.1759
110.1043-0.0226-0.01670.01890.0241-0.0297-0.3565-0.31070.0639-0.62330.1568-1.40970.08670.71-0.14670.78760.22840.04960.8741-0.01561.13954.7006-26.5804-21.4312
121.62970.3717-0.28492.7559-0.45182.7442-0.1565-0.0487-0.3326-0.25970.04240.04230.82650.120.09080.8410.04670.01830.3255-0.03710.4512-14.0159-35.2293-23.8015
131.2793-0.347-0.79231.19280.42.21760.13010.20250.1866-0.58180.01530.37820.0948-0.2532-0.17080.67020.0207-0.08030.4068-0.00250.5478-21.2443-19.5565-28.4206
143.09-0.86291.13083.98710.90471.74170.4412-0.15250.1734-0.1369-0.19760.46780.064-0.0841-0.07180.51990.01360.06190.4169-0.07120.7639-25.8803-9.067-13.9243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 97 )
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 196 )
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 320 )
4X-RAY DIFFRACTION4chain 'A' and (resid 321 through 375 )
5X-RAY DIFFRACTION5chain 'G' and (resid 52 through 73 )
6X-RAY DIFFRACTION6chain 'G' and (resid 74 through 85 )
7X-RAY DIFFRACTION7chain 'G' and (resid 86 through 121 )
8X-RAY DIFFRACTION8chain 'G' and (resid 122 through 138 )
9X-RAY DIFFRACTION9chain 'G' and (resid 139 through 160 )
10X-RAY DIFFRACTION10chain 'G' and (resid 161 through 177 )
11X-RAY DIFFRACTION11chain 'G' and (resid 1170 through 1182 )
12X-RAY DIFFRACTION12chain 'G' and (resid 1183 through 1237 )
13X-RAY DIFFRACTION13chain 'G' and (resid 1238 through 1321 )
14X-RAY DIFFRACTION14chain 'G' and (resid 1322 through 1349 )

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