[English] 日本語
Yorodumi
- PDB-3czy: Crystal Structure of Human Heme Oxygenase-1 in Complex with 1-(Ad... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3czy
TitleCrystal Structure of Human Heme Oxygenase-1 in Complex with 1-(Adamantan-1-yl)-2-(1H-imidazol-1-yl)ethanone
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / heme oxygenase-1 inhibitor complex / Endoplasmic reticulum / Heme / Iron / Metal-binding / Microsome / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxygenase (biliverdin-producing) / smooth muscle hyperplasia / heme oxidation / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Regulation of HMOX1 expression and activity / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxygenase (biliverdin-producing) / smooth muscle hyperplasia / heme oxidation / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / heme catabolic process / cellular response to arsenic-containing substance / positive regulation of epithelial cell apoptotic process / endothelial cell proliferation / erythrocyte homeostasis / negative regulation of ferroptosis / epithelial cell apoptotic process / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / positive regulation of cell migration involved in sprouting angiogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of macroautophagy / positive regulation of macroautophagy / The NLRP3 inflammasome / regulation of angiogenesis / Purinergic signaling in leishmaniasis infection / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of chemokine production / cellular response to cadmium ion / macroautophagy / response to nicotine / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / Iron uptake and transport / Heme signaling / Cytoprotection by HMOX1 / response to hydrogen peroxide / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / Interleukin-4 and Interleukin-13 signaling / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / response to oxidative stress / mitochondrial outer membrane / intracellular signal transduction / 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 / extracellular space / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / 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
1-(adamantan-1-yl)-2-(1H-imidazol-1-yl)ethanone / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsJia, Z. / Rahman, M.N.
CitationJournal: J.Med.Chem. / Year: 2008
Title: X-ray crystal structure of human heme oxygenase-1 in complex with 1-(adamantan-1-yl)-2-(1H-imidazol-1-yl)ethanone: a common binding mode for imidazole-based heme oxygenase-1 inhibitors.
Authors: Rahman, M.N. / Vlahakis, J.Z. / Szarek, W.A. / Nakatsu, K. / Jia, Z.
History
DepositionApr 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5196
Polymers53,7972
Non-polymers1,7224
Water9,062503
1
A: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7593
Polymers26,8991
Non-polymers8612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7593
Polymers26,8991
Non-polymers8612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.000, 52.446, 74.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Heme oxygenase 1 / HO-1


Mass: 26898.615 Da / Num. of mol.: 2 / Fragment: Residues 1-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1, HO, HO1 / Plasmid: DELTA233-HHO-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha
References: UniProt: P09601, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-AD8 / 1-(adamantan-1-yl)-2-(1H-imidazol-1-yl)ethanone / 2-(1H-imidazol-1-yl)-1-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]ethanone


Mass: 244.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 1.89 Å3/Da / Density % sol: 34.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.16M ammonium sulfate, 0.9% 1,6-hexanediol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2007
Details: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block. Rh-coated Si mirror for vertical focusing.
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. all: 57555 / Num. obs: 55840 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 36.5
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.4 / Num. unique all: 4836 / Rsym value: 0.356 / % possible all: 82.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1N3U

1n3u


Resolution: 1.54→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.44 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22633 2899 5 %RANDOM
Rwork0.19377 ---
obs0.19544 54625 96.85 %-
all-54625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20.07 Å2
2---0.46 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 122 503 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223714
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2172.0485056
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5165426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73523.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09415634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0061526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022830
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.22042
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22586
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3480.2452
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8651.52218
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34123470
X-RAY DIFFRACTIONr_scbond_it2.32631696
X-RAY DIFFRACTIONr_scangle_it3.5964.51582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.581 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 172 -
Rwork0.238 3234 -
obs-3406 79.01 %

+
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