[English] 日本語
Yorodumi
- PDB-6y3c: Human COX-1 Crystal Structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y3c
TitleHuman COX-1 Crystal Structure
ComponentsProstaglandin G/H synthase 1
KeywordsOXIDOREDUCTASE / COX-1 / CYCLOOXYGENASE / PEROXIDASE / PROSTAGLANDIN / HEME
Function / homology
Function and homology information


prostanoid metabolic process / COX reactions / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / photoreceptor outer segment / regulation of blood pressure ...prostanoid metabolic process / COX reactions / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / photoreceptor outer segment / regulation of blood pressure / peroxidase activity / regulation of cell population proliferation / response to oxidative stress / inflammatory response / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / Golgi apparatus / extracellular exosome / metal ion binding / cytoplasm
Similarity search - Function
Prostaglandin G/H synthase 1 / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain ...Prostaglandin G/H synthase 1 / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.361 Å
AuthorsMiciaccia, M. / Belviso, B.D. / Iaselli, M. / Ferorelli, S. / Perrone, M.G. / Caliandro, R. / Scilimati, A.
CitationJournal: Sci Rep / Year: 2021
Title: Three-dimensional structure of human cyclooxygenase (hCOX)-1.
Authors: Miciaccia, M. / Belviso, B.D. / Iaselli, M. / Cingolani, G. / Ferorelli, S. / Cappellari, M. / Loguercio Polosa, P. / Perrone, M.G. / Caliandro, R. / Scilimati, A.
History
DepositionFeb 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation_author
Revision 1.2Apr 8, 2020Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 3, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prostaglandin G/H synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3987
Polymers66,0711
Non-polymers2,3276
Water30617
1
A: Prostaglandin G/H synthase 1
hetero molecules

A: Prostaglandin G/H synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,79514
Polymers132,1412
Non-polymers4,65412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area12060 Å2
ΔGint29 kcal/mol
Surface area45560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.110, 182.110, 103.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Prostaglandin G/H synthase 1 / Cyclooxygenase-1 / COX-1 / Prostaglandin H2 synthase 1 / PHS 1 / Prostaglandin-endoperoxide synthase 1


Mass: 66070.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTGS1, COX1
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P23219, prostaglandin-endoperoxide synthase
#2: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpN]{[(2+1)][<C1O1>]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: Sodium citrate 0.7M, LiCl 0.72M

-
Data collection

DiffractionMean temperature: 70 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2019
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.36→91.05 Å / Num. obs: 14886 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.467 / Rpim(I) all: 0.103 / Rrim(I) all: 0.473 / Net I/σ(I): 14.3
Reflection shellResolution: 3.36→3.45 Å / Redundancy: 20 % / Rmerge(I) obs: 4.186 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1081 / CC1/2: 0.636 / Rpim(I) all: 0.905 / Rrim(I) all: 4.283 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Sir2014phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WBE

5wbe


Resolution: 3.361→78.856 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 29.28
RfactorNum. reflection% reflection
Rfree0.2629 1215 10.09 %
Rwork0.2085 --
obs0.2141 12047 81.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 200.28 Å2 / Biso mean: 90.9037 Å2 / Biso min: 52.67 Å2
Refinement stepCycle: final / Resolution: 3.361→78.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 0 155 17 4690
Biso mean--112.33 60.91 -
Num. residues----557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3614-3.4960.363390.291740027
3.496-3.65510.2465810.260470349
3.6551-3.84780.31621170.24797167
3.8478-4.08890.34281320.2455122284
4.0889-4.40450.28291650.22144599
4.4045-4.84770.23251450.16631497100
4.8477-5.54910.22111820.16771472100
5.5491-6.99060.30471760.2211511100
6.9906-78.8560.23991780.21391611100
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)
10.51020.0908-0.20290.14260.18490.4614-0.2191-0.2566-0.01790.18980.5373-0.54570.39170.3549-00.9234-0.0370.01810.9602-0.0371.1136-6.4294-59.5674-1.3536
20.09330.16450.06960.29440.11870.0448-0.2297-0.25081.4496-0.17260.098-0.56180.4026-0.1024-0.00111.0506-0.2945-0.09490.8543-0.04111.361-24.4615-32.86242.5498
30.28560.0863-0.31330.0169-0.10140.3208-0.0269-0.3573-0.48290.10050.02270.10660.4082-0.023800.97650.0255-0.07870.92520.02560.9123-31.2426-60.51683.8909
42.312-0.5390.42911.4710.50821.4439-0.06330.0001-0.38450.08960.03540.31590.3431-0.2058-0.00010.7702-0.0554-0.01370.77910.06870.7677-51.1305-51.8111-2.4852
51.43960.0586-0.56690.79750.34910.8561-0.2963-0.5861-0.24930.39310.21950.04830.04130.243900.9342-0.03430.04730.74340.10010.7409-33.9758-49.97537.696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 73 )A28 - 73
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 123 )A74 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 228 )A124 - 228
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 428 )A229 - 428
5X-RAY DIFFRACTION5chain 'A' and (resid 429 through 584 )A429 - 584

+
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