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- PDB-4z8g: Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (T... -

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Basic information

Entry
Database: PDB / ID: 4z8g
TitleChimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)
ComponentsTropomodulin-1, Leiomodin-1 chimera (TP1 ABS2)
KeywordsPROTEIN BINDING / Actin Nucleator / Leucine Rich Repeat Domain
Function / homology
Function and homology information


pointed-end actin filament capping / lens fiber cell development / myofibril assembly / actin nucleation / Striated Muscle Contraction / tropomyosin binding / cortical cytoskeleton / myofibril / positive regulation of actin filament polymerization / striated muscle thin filament ...pointed-end actin filament capping / lens fiber cell development / myofibril assembly / actin nucleation / Striated Muscle Contraction / tropomyosin binding / cortical cytoskeleton / myofibril / positive regulation of actin filament polymerization / striated muscle thin filament / Smooth Muscle Contraction / sarcomere / adult locomotory behavior / muscle contraction / actin filament organization / actin filament / actin binding / cytoskeleton / membrane / cytosol
Similarity search - Function
Tropomodulin / Tropomodulin / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Tropomodulin-1 / Leiomodin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBoczkowska, M. / Rebowski, G. / 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 8, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tropomodulin-1, Leiomodin-1 chimera (TP1 ABS2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,32210
Polymers21,7941
Non-polymers5289
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-57 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.468, 53.936, 75.604
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 Tropomodulin-1, Leiomodin-1 chimera (TP1 ABS2) / / TL1 / Erythrocyte tropomodulin / E-Tmod / 64 kDa autoantigen 1D / 64 kDa autoantigen 1D3 / 64 kDa ...TL1 / 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: 21794.061 Da / Num. of mol.: 1
Fragment: Tropomodulin-1 residues 163-228 (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: TMOD1, D9S57E, TMOD, LMOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28289, UniProt: P29536
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35% MPD, 0.1 M MES/NaOH, pH 6.0, 200 mM lithium sulfate

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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: Nov 6, 2014 / Details: QuazarTM Montel multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→43.908 Å / Num. all: 12763 / Num. obs: 12725 / % possible obs: 95.5 % / Redundancy: 7 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.9
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 / % possible all: 73.1

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Processing

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

4pki


Resolution: 2.1→43.908 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 641 5.06 %
Rwork0.1906 --
obs0.1937 12673 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 9 113 1525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151447
X-RAY DIFFRACTIONf_angle_d1.6631956
X-RAY DIFFRACTIONf_dihedral_angle_d18.021576
X-RAY DIFFRACTIONf_chiral_restr0.081228
X-RAY DIFFRACTIONf_plane_restr0.014256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.26220.28771050.23021944X-RAY DIFFRACTION79
2.2622-2.48990.2821330.21212442X-RAY DIFFRACTION99
2.4899-2.85010.29911310.20272494X-RAY DIFFRACTION99
2.8501-3.59060.25291360.19362512X-RAY DIFFRACTION100
3.5906-43.91750.22381360.17112640X-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)
11.5085-0.5013-0.33821.3043-0.15033.3449-0.91830.63910.29040.391-0.30290.7162-0.4441-0.53310.06610.2190.05920.36670.3209-0.1950.4225-15.036835.38190.0231
21.43991.11952.77173.20073.42735.9998-0.06520.23480.2347-0.07650.1591-0.2074-0.52260.36540.00950.17750.00070.03790.2212-0.0160.2451-4.43541.257-6.1406
32.77870.9585-0.27482.37750.01252.3832-0.135-0.1505-0.07430.7141-0.04250.19960.2629-0.22180.0720.3520.01440.10310.2308-0.04320.2001-5.758431.2849-0.3574
41.7499-0.02130.43271.3012-0.20961.6379-0.09410.0621-0.01510.5803-0.0104-0.05110.30710.04870.11150.2651-0.02920.01490.1835-0.03810.1747-0.08727.2725-2.7933
52.43290.9427-0.31363.1526-0.78111.9066-0.0769-0.08170.02440.47980.067-0.25830.13030.14620.00250.24480.03030.00170.2032-0.03520.19144.147424.2242-7.4852
62.70440.5023-0.36372.4881-0.7122.05210.1096-0.0453-0.15430.4027-0.0085-0.36040.39560.44470.00780.20780.0916-0.03850.259-0.05670.24668.008318.2452-12.0926
74.64762.3222-0.51993.8712-0.78252.18090.0672-0.0223-0.13750.30450.03580.190.4342-0.3228-0.09670.2842-0.01740.030.2009-0.03610.1883-3.83416.7792-14.5229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 177 through 201 )
2X-RAY DIFFRACTION2chain 'A' and (resid 202 through 209 )
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 372 )
4X-RAY DIFFRACTION4chain 'A' and (resid 373 through 400 )
5X-RAY DIFFRACTION5chain 'A' and (resid 401 through 430 )
6X-RAY DIFFRACTION6chain 'A' and (resid 431 through 456 )
7X-RAY DIFFRACTION7chain 'A' and (resid 457 through 486 )

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