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- PDB-4f14: Structure of the SH3 domain of human nebulette in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 4f14
TitleStructure of the SH3 domain of human nebulette in complex with a peptide of XIRP2
Components
  • Nebulette
  • Xin actin-binding repeat-containing protein 2
KeywordsACTIN-BINDING PROTEIN/PEPTIDE / SH3 domain / heart muscle / ACTIN-BINDING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


cardiac muscle thin filament assembly / filamin binding / regulation of actin filament organization / cell-cell junction organization / cardiac muscle tissue morphogenesis / Sensory processing of sound by outer hair cells of the cochlea / I band / Sensory processing of sound by inner hair cells of the cochlea / structural constituent of muscle / ventricular septum development ...cardiac muscle thin filament assembly / filamin binding / regulation of actin filament organization / cell-cell junction organization / cardiac muscle tissue morphogenesis / Sensory processing of sound by outer hair cells of the cochlea / I band / Sensory processing of sound by inner hair cells of the cochlea / structural constituent of muscle / ventricular septum development / tropomyosin binding / alpha-actinin binding / stress fiber / cytoskeletal protein binding / positive regulation of protein localization / actin filament organization / Z disc / actin filament binding / cell-cell junction / extracellular exosome
Similarity search - Function
Actin-binding, Xin repeat / Xin actin-binding repeat-containing protein 1/2 / Nebulette, SH3 domain / Xin repeat / Xin repeat profile. / : / Nebulin repeat / Nebulin repeat / Nebulin repeat profile. / NEBU ...Actin-binding, Xin repeat / Xin actin-binding repeat-containing protein 1/2 / Nebulette, SH3 domain / Xin repeat / Xin repeat profile. / : / Nebulin repeat / Nebulin repeat / Nebulin repeat profile. / NEBU / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Xin actin-binding repeat-containing protein 2 / Nebulette
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSauer, F. / Vahokoski, J. / Wilmanns, M.
CitationJournal: Mol Biol Cell / Year: 2013
Title: Identification of Xin-repeat proteins as novel ligands of the SH3 domains of nebulin and nebulette and analysis of their interaction during myofibril formation and remodeling.
Authors: Eulitz, S. / Sauer, F. / Pelissier, M.C. / Boisguerin, P. / Molt, S. / Schuld, J. / Orfanos, Z. / Kley, R.A. / Volkmer, R. / Wilmanns, M. / Kirfel, G. / van der Ven, P.F. / Furst, D.O.
History
DepositionMay 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

Downloads & links

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Assembly

Deposited unit
A: Nebulette
B: Xin actin-binding repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8733
Polymers8,8082
Non-polymers651
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-25 kcal/mol
Surface area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.640, 38.420, 43.260
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 Nebulette / Actin-binding Z-disk protein


Mass: 7354.065 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEBL / Production host: Escherichia coli (E. coli) / References: UniProt: O76041
#2: Protein/peptide Xin actin-binding repeat-containing protein 2 / Beta-xin / Cardiomyopathy-associated protein 3 / Xeplin


Mass: 1453.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: A4UGR9
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.68 Å3/Da / Density % sol: 26.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10 mM ZnCl2, 20% PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 19181 / Num. obs: 18936 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.34 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 18.99
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.2-1.23198
1.23-1.26198.2
1.26-1.3198.4
1.3-1.34198.7
1.34-1.39199
1.39-1.4199

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→18.491 Å / SU ML: 0.15 / σ(F): 1.11 / Phase error: 12.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1705 979 5.18 %random
Rwork0.144 ---
obs0.1454 18915 98.64 %-
all-19181 --
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.358 Å2 / ksol: 0.473 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.2→18.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 0 1 104 639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011591
X-RAY DIFFRACTIONf_angle_d1.471811
X-RAY DIFFRACTIONf_dihedral_angle_d13.185229
X-RAY DIFFRACTIONf_chiral_restr0.08584
X-RAY DIFFRACTIONf_plane_restr0.012108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.26320.20171420.19062491X-RAY DIFFRACTION98
1.2632-1.34230.19721400.16472512X-RAY DIFFRACTION99
1.3423-1.44590.17871230.13752570X-RAY DIFFRACTION99
1.4459-1.59140.15451500.1222539X-RAY DIFFRACTION100
1.5914-1.82150.14841350.11572572X-RAY DIFFRACTION99
1.8215-2.29420.15211420.11992592X-RAY DIFFRACTION99
2.2942-18.49320.18171470.16212660X-RAY DIFFRACTION97

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