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- PDB-4q57: Crystal structure of the plectin 1a actin-binding domain/N-termin... -

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Basic information

Entry
Database: PDB / ID: 4q57
TitleCrystal structure of the plectin 1a actin-binding domain/N-terminal domain of calmodulin complex
Components
  • Calmodulin
  • Plectin
KeywordsCALCIUM BINDING/STRUCTURAL PROTEIN / EF-hand motif / calponin homology domain / CALCIUM BINDING-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


Type I hemidesmosome assembly / protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / Caspase-mediated cleavage of cytoskeletal proteins / tight junction organization / skeletal myofibril assembly / hemidesmosome assembly / hemidesmosome / contractile muscle fiber / leukocyte migration involved in immune response ...Type I hemidesmosome assembly / protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / Caspase-mediated cleavage of cytoskeletal proteins / tight junction organization / skeletal myofibril assembly / hemidesmosome assembly / hemidesmosome / contractile muscle fiber / leukocyte migration involved in immune response / intermediate filament organization / intermediate filament cytoskeleton organization / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / dystroglycan binding / positive regulation of ryanodine-sensitive calcium-release channel activity / : / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / fibroblast migration / cellular response to hydrostatic pressure / adherens junction organization / myelination in peripheral nervous system / regulation of vascular permeability / T cell chemotaxis / establishment of protein localization to mitochondrial membrane / cellular response to fluid shear stress / intermediate filament cytoskeleton / peripheral nervous system myelin maintenance / type 3 metabotropic glutamate receptor binding / myoblast differentiation / CaM pathway / Cam-PDE 1 activation / cardiac muscle cell development / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of peptidyl-threonine phosphorylation / podosome / ankyrin binding / Reduction of cytosolic Ca++ levels / sarcomere organization / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / positive regulation of DNA binding / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / response to food / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / response to corticosterone / skin development / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / nucleus organization / keratinocyte development / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / myofibril / Unblocking of NMDA receptors, glutamate binding and activation / transmission of nerve impulse / RHO GTPases activate PAKs / brush border / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / adenylate cyclase binding / Regulation of MECP2 expression and activity / DARPP-32 events / positive regulation of protein serine/threonine kinase activity / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / establishment of skin barrier / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / activation of adenylate cyclase activity / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / skeletal muscle tissue development
Similarity search - Function
Spectrin repeat / : / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain ...Spectrin repeat / : / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Spectrin-like repeat / Plectin repeat / Plakin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Plectin/S10, N-terminal / Plectin/S10 domain / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Plectin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSong, J.-G. / Kostan, J. / Grishkovskaya, I. / Djinovic-Carugo, K.
CitationJournal: To be Published
Title: Crystal structure of the plectin 1a actin-binding domain/N-terminal domain of calmodulin complex
Authors: Song, J.-G. / Kostan, J. / Grishkovskaya, I. / Djinovic-Carugo, K.
History
DepositionApr 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Plectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,94810
Polymers35,5292
Non-polymers4188
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-44 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.080, 65.379, 87.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Calmodulin / CaM


Mass: 7121.870 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 10-74) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein Plectin / PCN / PLTN / Plectin-1 / Plectin-6


Mass: 28407.518 Da / Num. of mol.: 1
Fragment: actin-binding domain (UNP residues 23-263, SEE REMARK 999)
Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9QXS1

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Non-polymers , 6 types, 435 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN IS ISOFORM PLEC-1A (Q9QXS1-3) OF MUS MUSCULUS PLECTIN.

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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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, pH 6.5, 0.2 M magnesium chloride, 13% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→48.93 Å / Num. all: 32032 / Num. obs: 31749 / Redundancy: 9.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4301

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.929 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 17.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1868 1600 5.04 %
Rwork0.151 --
obs0.1528 31746 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→48.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 22 427 2940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072621
X-RAY DIFFRACTIONf_angle_d0.9633543
X-RAY DIFFRACTIONf_dihedral_angle_d12.8341005
X-RAY DIFFRACTIONf_chiral_restr0.042394
X-RAY DIFFRACTIONf_plane_restr0.005466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.22021310.20082445X-RAY DIFFRACTION90
1.8581-1.92450.22951260.17752737X-RAY DIFFRACTION100
1.9245-2.00160.1941190.16752750X-RAY DIFFRACTION100
2.0016-2.09270.21141430.15212739X-RAY DIFFRACTION100
2.0927-2.2030.19821500.14792723X-RAY DIFFRACTION100
2.203-2.34110.1671440.13792757X-RAY DIFFRACTION100
2.3411-2.52180.18591560.152734X-RAY DIFFRACTION100
2.5218-2.77560.18681680.14822731X-RAY DIFFRACTION100
2.7756-3.17710.17341630.14992766X-RAY DIFFRACTION100
3.1771-4.00260.17641500.13412826X-RAY DIFFRACTION100
4.0026-48.94680.1861500.15662938X-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)
15.023-0.2057-2.07587.43111.0742.00040.0113-0.64080.58590.54140.0408-0.0469-0.8797-0.0497-0.02370.47390.0057-0.01390.238-0.06150.241637.872117.40036.4633
23.33560.3257-2.25572.609-0.24353.16760.0183-0.00190.0229-0.258-0.12840.1497-0.3946-0.0150.11640.25580.0207-0.04760.16260.02190.21338.525912.771-5.1203
31.57941.78851.14583.38242.77022.4442-0.1347-0.0395-0.2962-0.0259-0.2256-0.8010.0230.57470.26330.38770.0180.07750.37560.12450.421850.27969.9945-7.8213
44.50161.2605-3.73174.535-1.68047.77690.0150.02890.1158-0.622-0.0937-0.28290.37640.06980.0670.27520.0185-0.03860.10250.02420.26543.37261.7458-2.9862
52.5325-0.2566-0.4823.8520.33553.03340.0313-0.3522-0.0760.1441-0.09160.29390.0364-0.3810.04690.1461-0.00670.00460.16290.00250.140935.42435.68275.6961
60.43381.05010.21395.83741.45380.61630.07440.0216-0.10160.0205-0.1025-0.17630.11410.00280.03230.13760.0215-0.020.14180.00060.111349.417527.8558.9188
71.1774-0.33990.14991.9208-0.15631.87070.0125-0.0391-0.0238-0.0055-0.040.0061-0.09020.03790.01890.0641-0.0037-0.00540.0671-0.00370.062352.228337.502925.4678
82.382-0.26240.12383.4849-0.30551.4104-0.089-0.41290.01230.31720.20340.3826-0.0618-0.5755-0.0330.10770.01580.02590.29570.02760.175927.975443.59618.6848
91.2428-0.38140.73191.683-0.34621.9029-0.0667-0.04550.11520.04480.0014-0.0736-0.0831-0.02470.04880.0601-0.0121-0.02280.07450.00450.081839.821346.2114-0.4927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 44 )
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 55 )
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 73 )
6X-RAY DIFFRACTION6chain 'B' and (resid -3 through 59 )
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 144 )
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 184 )
9X-RAY DIFFRACTION9chain 'B' and (resid 185 through 263 )

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