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- PDB-4hop: Crystal structure of the computationally designed NNOS-Syntrophin... -

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Basic information

Entry
Database: PDB / ID: 4hop
TitleCrystal structure of the computationally designed NNOS-Syntrophin complex
Components
  • Alpha-1-syntrophin
  • Nitric oxide synthase, brain
KeywordsMEMBRANE PROTEIN/OXIDOREDUCTASE / PDZ / Protein Binding / Dimerization / Mutation / Membrane / MEMBRANE PROTEIN-OXIDOREDUCTASE complex
Function / homology
Function and homology information


regulation of vasoconstriction by circulating norepinephrine / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of sodium ion transmembrane transport / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / negative regulation of hepatic stellate cell contraction / retrograde trans-synaptic signaling by nitric oxide / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / synaptic signaling by nitric oxide ...regulation of vasoconstriction by circulating norepinephrine / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of sodium ion transmembrane transport / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / negative regulation of hepatic stellate cell contraction / retrograde trans-synaptic signaling by nitric oxide / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / anchoring junction / negative regulation of vasoconstriction / peptidyl-cysteine S-nitrosylation / postsynaptic specialization, intracellular component / negative regulation of cytosolic calcium ion concentration / nitric-oxide synthase binding / Ion homeostasis / response to nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of sodium ion transmembrane transport / neuromuscular junction development / cadmium ion binding / nitric oxide metabolic process / positive regulation of the force of heart contraction / behavioral response to cocaine / negative regulation of potassium ion transport / negative regulation of calcium ion transport / regulation of neurogenesis / regulation of postsynaptic membrane potential / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / sodium channel regulator activity / negative regulation of serotonin uptake / response to vitamin E / postsynaptic density, intracellular component / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / L-arginine catabolic process / negative regulation of insulin secretion / striated muscle contraction / NADPH binding / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / negative regulation of blood pressure / response to hormone / photoreceptor inner segment / sarcoplasmic reticulum membrane / T-tubule / cellular response to epinephrine stimulus / nitric oxide biosynthetic process / calyx of Held / regulation of heart rate / secretory granule / sarcoplasmic reticulum / positive regulation of long-term synaptic potentiation / response to activity / cell periphery / female pregnancy / PDZ domain binding / establishment of localization in cell / phosphoprotein binding / response to nicotine / establishment of protein localization / response to nutrient levels / response to lead ion / potassium ion transport / : / neuromuscular junction / sarcolemma / cellular response to growth factor stimulus / caveola / response to peptide hormone / Z disc / response to estrogen / cellular response to mechanical stimulus / calcium-dependent protein binding / calcium ion transport / vasodilation / FMN binding / flavin adenine dinucleotide binding / NADP binding / actin binding / ATPase binding / response to heat / scaffold protein binding / nuclear membrane / dendritic spine / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to ethanol / mitochondrial outer membrane / postsynaptic membrane / transmembrane transporter binding / cytoskeleton / response to hypoxia / calmodulin binding
Similarity search - Function
Syntrophin, split Pleckstrin homology (PH) domain / PH domain / : / Syntrophin / Syntrophin C-terminal PH domain / PDZ domain / Pdz3 Domain / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily ...Syntrophin, split Pleckstrin homology (PH) domain / PH domain / : / Syntrophin / Syntrophin C-terminal PH domain / PDZ domain / Pdz3 Domain / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / PH domain / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / PH domain profile. / Riboflavin synthase-like beta-barrel / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / Flavoprotein-like superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Nitric oxide synthase 1 / Alpha-1-syntrophin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHarwood, I.M. / Melero, C. / Ollikainen, N. / Kortemme, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.
Authors: Melero, C. / Ollikainen, N. / Harwood, I. / Karpiak, J. / Kortemme, T.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Database references
Revision 1.4Sep 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: Alpha-1-syntrophin
B: Nitric oxide synthase, brain
C: Alpha-1-syntrophin
D: Nitric oxide synthase, brain
E: Alpha-1-syntrophin
F: Nitric oxide synthase, brain


Theoretical massNumber of molelcules
Total (without water)68,0386
Polymers68,0386
Non-polymers00
Water9,026501
1
A: Alpha-1-syntrophin
B: Nitric oxide synthase, brain


Theoretical massNumber of molelcules
Total (without water)22,6792
Polymers22,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-8 kcal/mol
Surface area10910 Å2
MethodPISA
2
C: Alpha-1-syntrophin
D: Nitric oxide synthase, brain


Theoretical massNumber of molelcules
Total (without water)22,6792
Polymers22,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-9 kcal/mol
Surface area11130 Å2
MethodPISA
3
E: Alpha-1-syntrophin
F: Nitric oxide synthase, brain


Theoretical massNumber of molelcules
Total (without water)22,6792
Polymers22,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.196, 102.503, 64.100
Angle α, β, γ (deg.)90.00, 118.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-1-syntrophin / 59 kDa dystrophin-associated protein A1 acidic component 1 / Syntrophin-1


Mass: 9389.835 Da / Num. of mol.: 3 / Fragment: PDZ DOMAIN (RESIDUES 77-162) / Mutation: H142F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snt1, Snta1 / Plasmid: PET47B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61234
#2: Protein Nitric oxide synthase, brain / BNOS / Constitutive NOS / NC-NOS / NOS type I / Neuronal NOS / N-NOS / nNOS / Peptidyl-cysteine S- ...BNOS / Constitutive NOS / NC-NOS / NOS type I / Neuronal NOS / N-NOS / nNOS / Peptidyl-cysteine S-nitrosylase NOS1


Mass: 13289.354 Da / Num. of mol.: 3 / Fragment: PDZ DOMAIN (RESIDUES 4-126) / Mutation: T109M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Bnos, Nos1 / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29476, nitric-oxide synthase (NADPH)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2007
Details: MIRROR1: PLANE PARABOLA PT AND RH-COATED INVAR STEEL, MIRROR2: TOROID (2:1 DEMAGNIFICATION) PT AND RH- COATED SI
RadiationMonochromator: KOHZU DOUBLE FLAT SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.29→48 Å / Num. obs: 31327 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 30.532
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 6 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 12.043 / Rsym value: 0.171 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAV

1qav


Resolution: 2.29→47.57 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.709 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1510 5 %RANDOM
Rwork0.223 ---
obs0.226 28781 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å21.47 Å2
2---0.26 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 0 501 5203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224754
X-RAY DIFFRACTIONr_bond_other_d0.0010.023306
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.9916408
X-RAY DIFFRACTIONr_angle_other_deg0.76538106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07523.743179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16715881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.531539
X-RAY DIFFRACTIONr_chiral_restr0.0540.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02899
X-RAY DIFFRACTIONr_nbd_refined0.1730.2776
X-RAY DIFFRACTIONr_nbd_other0.1850.23307
X-RAY DIFFRACTIONr_nbtor_refined0.160.22263
X-RAY DIFFRACTIONr_nbtor_other0.0770.22631
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2367
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5611.53999
X-RAY DIFFRACTIONr_mcbond_other0.0481.51287
X-RAY DIFFRACTIONr_mcangle_it0.58224954
X-RAY DIFFRACTIONr_scbond_it0.79231860
X-RAY DIFFRACTIONr_scangle_it1.1874.51454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 82 -
Rwork0.23 1715 -
obs--78.68 %

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