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- PDB-4rsv: Human Obscurin Ig58 Domain -

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Basic information

Entry
Database: PDB / ID: 4rsv
TitleHuman Obscurin Ig58 Domain
ComponentsObscurin
KeywordsSTRUCTURAL PROTEIN / Ig-like / cytoskeletal / Titin / Myocytes
Function / homology
Function and homology information


protein localization to M-band / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3-phosphate binding / M band / phosphatidylinositol-4-phosphate binding / regulation of small GTPase mediated signal transduction / structural constituent of muscle / ankyrin binding / sarcomere organization ...protein localization to M-band / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3-phosphate binding / M band / phosphatidylinositol-4-phosphate binding / regulation of small GTPase mediated signal transduction / structural constituent of muscle / ankyrin binding / sarcomere organization / myofibril / NRAGE signals death through JNK / RHOQ GTPase cycle / phosphatidylinositol-3,4,5-trisphosphate binding / RHOA GTPase cycle / titin binding / phosphatidylinositol-4,5-bisphosphate binding / guanyl-nucleotide exchange factor activity / sarcolemma / Z disc / G alpha (12/13) signalling events / calmodulin binding / non-specific serine/threonine protein kinase / nuclear body / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Obscurin, SH3 domain / : / SOS1/NGEF-like PH domain / IQ calmodulin-binding motif / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Obscurin, SH3 domain / : / SOS1/NGEF-like PH domain / IQ calmodulin-binding motif / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain profile. / Pleckstrin homology domain. / Fibronectin type III domain / Pleckstrin homology domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsWright, N.T. / Oehler, M.C. / Berndsen, C.E. / Du Pont, K.E.
CitationJournal: To be Published
Title: Arrhythmia and deregulated Ca2+ cycling underlie the development of hypertrophic cardiomyopathy due to mutant giant obscurin
Authors: Hu, L.Y.R. / Ackermann, M.A. / Hecker, P.A. / Prosser, B.L. / King, B. / O'Connell, K.A. / Asico, L.D. / Jose, P.A. / Wright, N.T. / Oehler, M.C. / Berndsen, C.E. / Du Pont, K.E. / Meyer, L. ...Authors: Hu, L.Y.R. / Ackermann, M.A. / Hecker, P.A. / Prosser, B.L. / King, B. / O'Connell, K.A. / Asico, L.D. / Jose, P.A. / Wright, N.T. / Oehler, M.C. / Berndsen, C.E. / Du Pont, K.E. / Meyer, L.C. / Lederer, W.J. / Kontrogianni-Konstantopoulos, A.
History
DepositionNov 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Obscurin


Theoretical massNumber of molelcules
Total (without water)11,4241
Polymers11,4241
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.482, 44.482, 177.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Obscurin / Obscurin-RhoGEF / Obscurin-myosin light chain kinase / Obscurin-MLCK


Mass: 11423.818 Da / Num. of mol.: 1 / Fragment: UNP residues 4337-4429
Source method: isolated from a genetically manipulated source
Details: This sequence occurs naturally in humans / Source: (gene. exp.) Homo sapiens (human) / Gene: OBSCN, KIAA1556, KIAA1639 / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q5VST9, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 0.3-0.5M NaCl 19-23% PEG 3350 10.52-11.35 mg/ml, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.411→37.64 Å / Num. obs: 4329 / % possible obs: 95.8 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.03344 / Rsym value: 0.04104 / Net I/σ(I): 29.47
Reflection shellResolution: 2.56→2.62 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3173 / Mean I/σ(I) obs: 3.08 / Rsym value: 0.04104 / % possible all: 69.2

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Processing

Software
NameClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CR6, 2YZ8, 2E7B, 2RQ8

2cr6

2yz8

2e7b

2rq8


Resolution: 2.41→37.64 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection
Rfree0.28 433
Rwork0.26 -
obs0.26 4329
all-11201
Refinement stepCycle: LAST / Resolution: 2.41→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms706 0 0 1 707
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.02
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr

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