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- PDB-4z79: Leiomodin-1 Actin-Binding Site 2 (ABS2) -

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Basic information

Entry
Database: PDB / ID: 4z79
TitleLeiomodin-1 Actin-Binding Site 2 (ABS2)
ComponentsLeiomodin-1 Actin-Binding Site 2 (ABS2)
KeywordsPROTEIN BINDING / Leiomodin-1 Actin Binding Site 2 ABS2 Actin nucleator
Function / homology
Function and homology information


pointed-end actin filament capping / myofibril assembly / actin nucleation / tropomyosin binding / myofibril / positive regulation of actin filament polymerization / striated muscle thin filament / Smooth Muscle Contraction / sarcomere / muscle contraction ...pointed-end actin filament capping / myofibril assembly / actin nucleation / tropomyosin binding / myofibril / positive regulation of actin filament polymerization / striated muscle thin filament / Smooth Muscle Contraction / sarcomere / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 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 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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_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.ptnr1_symmetry / _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_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: Leiomodin-1 Actin-Binding Site 2 (ABS2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,92511
Polymers21,2681
Non-polymers65710
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.019, 52.192, 75.890
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 Leiomodin-1 Actin-Binding Site 2 (ABS2) / 64 kDa autoantigen 1D / 64 kDa autoantigen 1D3 / 64 kDa autoantigen D1 / Leiomodin / muscle form / ...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: 21268.312 Da / Num. of mol.: 1 / Fragment: unp residues 299-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29536
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / Details: 0.1M Hepes, 10% Propanol, 20% Peg 3350 / PH range: 7.5

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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: Sep 26, 2014 / Details: QuazarTM Montel multilayer optic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→41.2 Å / Num. all: 29387 / Num. obs: 29387 / % possible obs: 98.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 13.13 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 23.9
Reflection shellResolution: 1.54→1.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.4 / % possible all: 92.2

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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: 4PKI

4pki


Resolution: 1.54→41.176 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1766 1460 5 %
Rwork0.1561 --
obs0.1572 29335 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→41.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 40 191 1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011522
X-RAY DIFFRACTIONf_angle_d1.2932060
X-RAY DIFFRACTIONf_dihedral_angle_d16.691623
X-RAY DIFFRACTIONf_chiral_restr0.053236
X-RAY DIFFRACTIONf_plane_restr0.006270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.5950.31121360.25522529X-RAY DIFFRACTION92
1.595-1.65890.22951430.22142741X-RAY DIFFRACTION99
1.6589-1.73440.18861410.18492763X-RAY DIFFRACTION100
1.7344-1.82590.21921410.16492759X-RAY DIFFRACTION100
1.8259-1.94030.20321490.15772766X-RAY DIFFRACTION100
1.9403-2.09010.15471500.14642782X-RAY DIFFRACTION100
2.0901-2.30040.15271510.13692795X-RAY DIFFRACTION100
2.3004-2.63320.17821450.132808X-RAY DIFFRACTION100
2.6332-3.31730.16791480.14332842X-RAY DIFFRACTION100
3.3173-41.19090.15841560.15772980X-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)
11.0297-0.0611-0.16461.34470.58170.98880.0240.0645-0.0658-0.055-0.06540.198-0.0118-0.11550.03190.0774-0.0003-0.00210.07190.00080.0858-4.9599-18.8655-19.4937
20.94210.09130.03851.25260.38371.0968-0.01450.0987-0.0416-0.03270.1112-0.1715-0.0050.1419-0.01750.0754-0.00720.00980.0891-0.01210.08619.1227-16.7691-18.5367
33.9769-0.7295-1.46413.26161.61555.49210.07010.30230.1014-0.1270.0802-0.2055-0.32140.3103-0.10660.0881-0.040.0230.1988-0.02840.198621.2105-10.9196-18.3695
42.31650.1498-1.15981.9070.55772.7867-0.01420.1907-0.3080.0160.1355-0.28390.09060.12410.06690.07030.0088-0.01880.1601-0.04480.173117.7393-19.9123-15.3816
51.39180.261-2.25740.5398-0.02316.0804-0.03370.1222-0.15160.0878-0.0501-0.05920.165-0.0220.04350.10050.0148-0.04590.1465-0.01110.159717.5293-18.668-0.3076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 314 through 385 )
2X-RAY DIFFRACTION2chain 'A' and (resid 386 through 430 )
3X-RAY DIFFRACTION3chain 'A' and (resid 431 through 443 )
4X-RAY DIFFRACTION4chain 'A' and (resid 444 through 456 )
5X-RAY DIFFRACTION5chain 'A' and (resid 457 through 486 )

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