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- PDB-4z94: Actin Complex With a Chimera of Tropomodulin-1 and Leiomodin-1 Ac... -

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Basic information

Entry
Database: PDB / ID: 4z94
TitleActin Complex With a Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2
Components
  • Actin, alpha skeletal muscle
  • Gelsolin, Tropomodulin-1, Leiomodin-1 chimera
KeywordsPROTEIN BINDING/STRUCTURAL PROTEIN / Actin Nucleator / ATP-actin / PROTEIN BINDING-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


pointed-end actin filament capping / lens fiber cell development / myofibril assembly / actin nucleation / 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 ...pointed-end actin filament capping / lens fiber cell development / myofibril assembly / actin nucleation / 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 capping / actin filament depolymerization / cell projection assembly / actin polymerization or depolymerization / Striated Muscle Contraction / cardiac muscle cell contraction / relaxation of cardiac muscle / Sensory processing of sound by outer hair cells of the cochlea / podosome / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / myosin heavy chain binding / hepatocyte apoptotic process / tropomyosin binding / actin filament bundle / cortical cytoskeleton / positive regulation of actin filament polymerization / troponin I binding / filamentous actin / myofibril / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / sarcoplasm / cilium assembly / Smooth Muscle Contraction / Caspase-mediated cleavage of cytoskeletal proteins / skeletal muscle fiber development / stress fiber / phagocytic vesicle / titin binding / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / muscle contraction / actin filament organization / sarcomere / central nervous system development / adult locomotory behavior / actin filament / filopodium / protein destabilization / cellular response to type II interferon / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / lamellipodium / actin cytoskeleton / cell body / actin binding / secretory granule lumen / blood microparticle / amyloid fibril formation / ficolin-1-rich granule lumen / cytoskeleton / hydrolase activity / Amyloid fiber formation / protein domain specific binding / 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 / cytoplasm / cytosol
Similarity search - Function
Tropomodulin / Tropomodulin / Wiskott Aldrich syndrome homology region 2 / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / WH2 motif / WH2 domain profile. / WH2 domain / Villin/Gelsolin / Gelsolin homology domain ...Tropomodulin / Tropomodulin / Wiskott Aldrich syndrome homology region 2 / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / WH2 motif / WH2 domain profile. / WH2 domain / 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 / Leiomodin-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRebowski, G. / Boczkowska, M. / 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: Nat Commun / Year: 2015
Title: How Leiomodin and Tropomodulin use a common fold for different actin assembly functions.
Authors: Boczkowska, M. / Rebowski, G. / Kremneva, E. / Lappalainen, P. / Dominguez, R.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
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 / 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, Leiomodin-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2716
Polymers78,6432
Non-polymers6274
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-55 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.234, 70.799, 81.324
Angle α, β, γ (deg.)90.00, 101.74, 90.00
Int Tables number4
Space group name H-MP1211

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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) / References: UniProt: P68135
#2: Protein Gelsolin, Tropomodulin-1, Leiomodin-1 chimera / AGEL / Actin-depolymerizing factor / ADF / Brevin / Erythrocyte tropomodulin / E-Tmod / 64 kDa ...AGEL / Actin-depolymerizing factor / ADF / Brevin / Erythrocyte tropomodulin / E-Tmod / 64 kDa autoantigen 1D / 64 kDa autoantigen 1D3 / 64 kDa autoantigen D1 / Leiomodin / muscle form / Smooth muscle leiomodin / SM-Lmod / Thyroid-associated ophthalmopathy autoantigen


Mass: 36533.457 Da / Num. of mol.: 1
Fragment: Gelsolin residues 12-136 (UNP), linker,Tropomodulin-1 residues 160-228 (UNP), Leiomodin-1 Actin-Binding Site 2 (UNP residues 364-486)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN, TMOD1, D9S57E, TMOD, LMOD1 / Production host: Escherichia coli (E. coli)
References: UniProt: P06396, UniProt: P28289, UniProt: P29536
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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.: 182 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 20% PEG3350, 200 mM lithium sulfate, 100 mM Tris, pH 8.8, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Feb 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→39.9 Å / Num. all: 27926 / Num. obs: 27914 / % possible obs: 89.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.92 / % possible all: 50.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SAINTdata reduction
SAINTdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PKI

4pki


Resolution: 2.4→39.812 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 1393 5 %
Rwork0.1853 --
obs0.1883 27843 89.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→39.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5350 0 34 182 5566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155511
X-RAY DIFFRACTIONf_angle_d1.6977470
X-RAY DIFFRACTIONf_dihedral_angle_d19.4662069
X-RAY DIFFRACTIONf_chiral_restr0.073830
X-RAY DIFFRACTIONf_plane_restr0.01964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.2991780.24571478X-RAY DIFFRACTION50
2.4858-2.58530.31191050.22911998X-RAY DIFFRACTION68
2.5853-2.70290.29871290.23282432X-RAY DIFFRACTION82
2.7029-2.84540.26781450.22552760X-RAY DIFFRACTION94
2.8454-3.02360.28841550.21122937X-RAY DIFFRACTION100
3.0236-3.2570.31031540.20812947X-RAY DIFFRACTION100
3.257-3.58450.22381550.19512934X-RAY DIFFRACTION99
3.5845-4.10280.2391540.16582944X-RAY DIFFRACTION99
4.1028-5.16730.17341570.14292981X-RAY DIFFRACTION100
5.1673-39.81740.22511610.16473039X-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)
10.0085-0.0291-0.00220.0026-0.00770.0225-0.0232-0.1274-0.06790.0040.02310.0296-0.01330.045900.0436-0.0013-0.01130.0265-0.00250.030316.26893.332721.1377
20.00670.01140.00570.01170.01090.00510.04560.11680.0732-0.0375-0.0866-0.08140.0216-0.113-0-0.0229-0.1213-0.09030.0193-0.07740.07296.8355-6.2211-0.0187
30.0019-0.00040.00360.00070.0016-0.0020.041-0.02840.00760.00030.0017-0.0061-0.02170.03100.051-0.0865-0.03370.0795-0.08640.099630.672611.661716.5542
40.0052-0.00890.0050.0083-0.00030.00540.1032-0.0930.0316-0.06570.0368-0.10960.037-0.00610-0.04830.15510.0979-0.1453-0.06950.181541.49410.32320.5137
50.01-0.0157-0.0140.0120.00860.016-0.0386-0.15190.0138-0.00540.1199-0.0136-0.1141-0.0400.29440.14630.01660.37180.0307-0.08494.954318.336338.0388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 165 )
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 337 )
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 375 )
4X-RAY DIFFRACTION4chain 'G' and (resid 1 through 1176 )
5X-RAY DIFFRACTION5chain 'G' and (resid 1177 through 1486 )

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