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- PDB-2nqc: Crystal structure of ig-like domain 23 from human filamin C -

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Basic information

Entry
Database: PDB / ID: 2nqc
TitleCrystal structure of ig-like domain 23 from human filamin C
ComponentsFilamin-C
KeywordsIMMUNE SYSTEM / FILAMIN / IMMUNOGLOBULIN / METAL BINDING
Function / homology
Function and homology information


Cell-extracellular matrix interactions / costamere / ankyrin binding / sarcomere organization / sarcoplasm / intercellular bridge / cytoskeletal protein binding / sarcolemma / Z disc / actin filament binding ...Cell-extracellular matrix interactions / costamere / ankyrin binding / sarcomere organization / sarcoplasm / intercellular bridge / cytoskeletal protein binding / sarcolemma / Z disc / actin filament binding / cytoskeleton / focal adhesion / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / NICKEL (II) ION / Filamin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsSjekloca, L. / Pudas, R. / Sjoeblom, B. / Konarev, P. / Carugo, O. / Rybin, V. / Kiema, T.R. / Svergun, D. / Ylanne, J. / Djinovic-Carugo, K.
CitationJournal: J Mol Biol / Year: 2007
Title: Crystal structure of human filamin C domain 23 and small angle scattering model for filamin C 23-24 dimer.
Authors: Ljiljana Sjekloća / Regina Pudas / Björn Sjöblom / Peter Konarev / Oliviero Carugo / Vladimir Rybin / Tiila-Riikka Kiema / Dmitri Svergun / Jari Ylänne / Kristina Djinović Carugo /
Abstract: Filamin C is a dimeric, actin-binding protein involved in organization of cortical cytoskeleton and of the sarcomere. We performed crystallographic, small-angle X-ray scattering and analytical ...Filamin C is a dimeric, actin-binding protein involved in organization of cortical cytoskeleton and of the sarcomere. We performed crystallographic, small-angle X-ray scattering and analytical ultracentrifugation experiments on the constructs containing carboxy-terminal domains of the protein (domains 23-24 and 19-21). The crystal structure of domain 23 of filamin C showed that the protein adopts the expected immunoglobulin (Ig)-like fold. Small-angle X-ray scattering experiments performed on filamin C tandem Ig-like domains 23 and 24 reveal a dimer that is formed by domain 24 and that domain 23 has little interactions with itself or with domain 24, while the analytical ultracentrifugation experiments showed that the filamin C domains 19-21 form elongated monomers in diluted solutions.
History
DepositionOct 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
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.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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Filamin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3046
Polymers13,9231
Non-polymers3815
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.141, 52.141, 69.216
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Filamin-C / Gamma-filamin / Filamin-2 / Protein FLNc / Actin-binding- like protein / ABP-L / ABP-280-like protein


Mass: 13922.598 Da / Num. of mol.: 1 / Fragment: Ig-like domain 23
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q14315
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17.5% PEG 10000, 0.2M imidazole malate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 8, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.05→45.17 Å / Num. all: 7116 / Num. obs: 7027 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.061 / Net I/σ(I): 7.1
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.1 / Num. unique all: 950 / Rsym value: 0.298 / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345data collection
DENZOdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→45.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.855 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 329 4.7 %RANDOM
Rwork0.188 ---
all0.19 7116 --
obs0.19 7016 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.963 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.28 Å20 Å2
2--0.55 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms689 0 23 56 768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022712
X-RAY DIFFRACTIONr_bond_other_d0.0040.02651
X-RAY DIFFRACTIONr_angle_refined_deg1.2882.018966
X-RAY DIFFRACTIONr_angle_other_deg0.72831519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.543596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05824.73719
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7851595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.013151
X-RAY DIFFRACTIONr_chiral_restr0.0730.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02131
X-RAY DIFFRACTIONr_nbd_refined0.1810.285
X-RAY DIFFRACTIONr_nbd_other0.2290.2539
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2323
X-RAY DIFFRACTIONr_nbtor_other0.0890.2403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.234
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.28
X-RAY DIFFRACTIONr_mcbond_it1.341.5605
X-RAY DIFFRACTIONr_mcbond_other0.1911.5203
X-RAY DIFFRACTIONr_mcangle_it1.5542766
X-RAY DIFFRACTIONr_scbond_it2.3793267
X-RAY DIFFRACTIONr_scangle_it3.2074.5200
LS refinement shellResolution: 2.05→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 19 -
Rwork0.213 485 -
obs-504 94.38 %

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