[English] 日本語
Yorodumi
- PDB-3hr4: Human iNOS Reductase and Calmodulin Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hr4
TitleHuman iNOS Reductase and Calmodulin Complex
Components
  • Calmodulin
  • Nitric oxide synthase, inducible
KeywordsOxidoreductase/METAL BINDING PROTEIN / inducible nitric oxide synthase / NOS / iNOS / calmodulin / Calmodulin-binding / FAD / FMN / Heme / Iron / Metal-binding / NADP / Oxidoreductase / Phosphoprotein / Isopeptide bond / Methylation / Oxidoreductase-METAL BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / : / establishment of protein localization to mitochondrial membrane / Nitric oxide stimulates guanylate cyclase / type 3 metabotropic glutamate receptor binding / prostaglandin secretion / positive regulation of killing of cells of another organism / ROS and RNS production in phagocytes / regulation of cellular respiration ...positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / : / establishment of protein localization to mitochondrial membrane / Nitric oxide stimulates guanylate cyclase / type 3 metabotropic glutamate receptor binding / prostaglandin secretion / positive regulation of killing of cells of another organism / ROS and RNS production in phagocytes / regulation of cellular respiration / tetrahydrobiopterin binding / arginine binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / regulation of synaptic vesicle endocytosis / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / response to corticosterone / cortical cytoskeleton / superoxide metabolic process / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / protein phosphatase activator activity / RHO GTPases activate PAKs / regulation of insulin secretion / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / peroxisomal matrix / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / nitric-oxide synthase (NADPH) / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / nitric oxide mediated signal transduction / Protein methylation / nitric-oxide synthase activity / phosphatidylinositol 3-kinase binding / eNOS activation / arginine catabolic process / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / Ion homeostasis / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / nitric oxide biosynthetic process / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / negative regulation of blood pressure / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #410 / Flavodoxin domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #410 / Flavodoxin domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / 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. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / EF-hand domain pair / Helix non-globular / EF-hand, calcium binding motif / Special / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Calmodulin-1 / Nitric oxide synthase, inducible / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXia, C. / Misra, I. / Iyanaki, T. / Kim, J.J.K.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Regulation of Interdomain Interactions by CaM in Inducible Nitric Oxide Synthase
Authors: Xia, C. / Misra, I. / Iyanaki, T. / Kim, J.J.K.
History
DepositionJun 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitric oxide synthase, inducible
B: Calmodulin
C: Nitric oxide synthase, inducible
D: Calmodulin
E: Nitric oxide synthase, inducible
F: Calmodulin
G: Nitric oxide synthase, inducible
H: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,05728
Polymers167,5908
Non-polymers2,46720
Water1,27971
1
A: Nitric oxide synthase, inducible
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5147
Polymers41,8982
Non-polymers6175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-36 kcal/mol
Surface area16400 Å2
2
C: Nitric oxide synthase, inducible
D: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5147
Polymers41,8982
Non-polymers6175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Nitric oxide synthase, inducible
F: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5147
Polymers41,8982
Non-polymers6175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Nitric oxide synthase, inducible
H: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5147
Polymers41,8982
Non-polymers6175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.600, 160.840, 127.770
Angle α, β, γ (deg.)90.00, 90.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Nitric oxide synthase, inducible / Inducible NO synthase / Inducible NOS / iNOS / NOS type II / Hepatocyte NOS / HEP-NOS


Mass: 25045.004 Da / Num. of mol.: 4 / Fragment: Residues 503-715
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: Calmodulin, Inducible Nitric Oxide Synthase, NOS2, NOS2A
Plasmid: PCWORI+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P35228, nitric-oxide synthase (NADPH)
#2: Protein
Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pKK-CaM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8K, SODIUM ACETATE, SODIUM CHLORATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→29.69 Å / Num. obs: 48283 / % possible obs: 94.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 60.9 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TLL, 1NIW, 1FOT

1tll

1niw

1fot


Resolution: 2.5→29.69 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 428243.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.309 2414 5 %RANDOM
Rwork0.237 ---
obs0.237 48283 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.8557 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 64.4 Å2
Baniso -1Baniso -2Baniso -3
1-11.64 Å20 Å23.21 Å2
2--12.86 Å20 Å2
3----24.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.39 Å
Luzzati d res low-30 Å
Luzzati sigma a0.55 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10383 0 140 71 10594
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 309 5 %
Rwork0.382 5888 -
obs--73.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cofac_fmcofac_fm
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top

+
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://pdbjlvh1.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