[English] 日本語
Yorodumi
- PDB-3i9t: Crystal structure of the rat heme oxygenase (HO-1) in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i9t
TitleCrystal structure of the rat heme oxygenase (HO-1) in complex with heme binding dithiothreitol (DTT)
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / heme oxygenase / inhibitor / mammalian / isozyme / Endoplasmic reticulum / Heme / Iron / Metal-binding / Microsome / Phosphoprotein
Function / homology
Function and homology information


arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / heme oxygenase (biliverdin-producing) ...arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / heme oxygenase (biliverdin-producing) / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / negative regulation of muscle cell apoptotic process / wound healing involved in inflammatory response / cellular response to cisplatin / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / cellular response to nutrient / heme catabolic process / negative regulation of mast cell cytokine production / positive regulation of epithelial cell apoptotic process / phospholipase D activity / epithelial cell apoptotic process / negative regulation of ferroptosis / erythrocyte homeostasis / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of macroautophagy / small GTPase-mediated signal transduction / cellular response to cadmium ion / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / phospholipid metabolic process / liver regeneration / response to nicotine / positive regulation of smooth muscle cell proliferation / macroautophagy / negative regulation of smooth muscle cell proliferation / response to hydrogen peroxide / caveola / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / cellular response to heat / angiogenesis / negative regulation of neuron apoptotic process / response to oxidative stress / intracellular iron ion homeostasis / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMatsui, T. / Unno, M. / Ikeda-Saito, M.
CitationJournal: Inorg.Chem. / Year: 2010
Title: Dioxygen activation for the self-degradation of heme: reaction mechanism and regulation of heme oxygenase.
Authors: Matsui, T. / Iwasaki, M. / Sugiyama, R. / Unno, M. / Ikeda-Saito, M.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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 / _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: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0663
Polymers30,2951
Non-polymers7712
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.739, 65.739, 120.663
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Heme oxygenase 1 / HO-1 / HSP32


Mass: 30295.268 Da / Num. of mol.: 1 / Fragment: UNP residues 1-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmox1 / Plasmid: pMW / Production host: Escherichia coli (E. coli)
References: UniProt: P06762, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 4M Sodium Formate, 5mM Sodium azide, 100mM DTT, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 17047

-
Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IVJ

1ivj


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.734 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20855 861 5.1 %RANDOM
Rwork0.16245 ---
obs0.16467 16139 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å21.02 Å20 Å2
2--2.03 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 51 135 1909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221830
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9162.0332491
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8155211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.172490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43415307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9081511
X-RAY DIFFRACTIONr_chiral_restr0.1440.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211410
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1561.51062
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it221709
X-RAY DIFFRACTIONr_scbond_it3.5063768
X-RAY DIFFRACTIONr_scangle_it5.3264.5782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 56 -
Rwork0.186 1169 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.484-0.0774-0.27620.67190.49861.9801-0.013-0.0043-0.00030.01430.0085-0.00880.08520.00670.00450.00390.0010.00080.00660.00370.0024-7.3219-35.8456-164.6782
21.41520.4774-1.34146.15561.83835.6994-0.02170.1796-0.0068-0.1255-0.1234-0.0985-0.2451-0.15950.14510.0164-0.0045-0.00870.03250.00440.0115-2.2948-27.3544-168.6443
312.3828-13.4153-2.923251.0992-8.58864.4718-0.5444-0.05210.19260.1480.67710.00540.2657-0.1904-0.13260.03910.00340.00790.02320.01620.1046-3.426-32.92-169.6492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 222
2X-RAY DIFFRACTION2A300
3X-RAY DIFFRACTION3A2002

+
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