[English] 日本語
Yorodumi
- PDB-4hop: Crystal structure of the computationally designed NNOS-Syntrophin... -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of peptidyl-cysteine S-nitrosylation / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transport / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / anchoring junction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction ...regulation of vasoconstriction by circulating norepinephrine / negative regulation of peptidyl-cysteine S-nitrosylation / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transport / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / anchoring junction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / neuromuscular junction development / retrograde trans-synaptic signaling by nitric oxide / Ion homeostasis / positive regulation of sodium ion transmembrane transport / response to nitric oxide / postsynaptic specialization, intracellular component / negative regulation of cytosolic calcium ion concentration / nitric-oxide synthase binding / peptidyl-cysteine S-nitrosylation / behavioral response to cocaine / postsynaptic density, intracellular component / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / calyx of Held / negative regulation of calcium ion transport / negative regulation of serotonin uptake / sodium channel regulator activity / regulation of neurogenesis / striated muscle contraction / negative regulation of insulin secretion / regulation of postsynaptic membrane potential / response to vitamin E / nitric-oxide synthase (NADPH) / multicellular organismal response to stress / xenobiotic catabolic process / nitric-oxide synthase activity / negative regulation of peptidyl-serine phosphorylation / nitric oxide mediated signal transduction / arginine catabolic process / NADPH binding / regulation of sodium ion transport / response to organonitrogen compound / sarcoplasmic reticulum membrane / T-tubule / cellular response to epinephrine stimulus / photoreceptor inner segment / negative regulation of blood pressure / nitric oxide biosynthetic process / regulation of heart rate / response to hormone / response to nutrient levels / response to activity / response to nicotine / muscle contraction / sarcoplasmic reticulum / secretory granule / female pregnancy / positive regulation of long-term synaptic potentiation / PDZ domain binding / cell periphery / establishment of localization in cell / phosphoprotein binding / response to lead ion / sarcolemma / neuromuscular junction / establishment of protein localization / potassium ion transport / response to organic cyclic compound / response to peptide hormone / cellular response to growth factor stimulus / Z disc / vasodilation / cellular response to mechanical stimulus / response to estrogen / calcium-dependent protein binding / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / actin binding / ATPase binding / response to heat / scaffold protein binding / postsynaptic membrane / response to ethanol / nuclear membrane / negative regulation of neuron apoptotic process / mitochondrial outer membrane / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / response to hypoxia
Similarity search - Function
Syntrophin, split Pleckstrin homology (PH) domain / PH domain / Syntrophin / PDZ domain / Pdz3 Domain / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal ...Syntrophin, split Pleckstrin homology (PH) domain / PH domain / Syntrophin / PDZ domain / Pdz3 Domain / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / PH 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 / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more