[English] 日本語
Yorodumi
- PDB-1coh: STRUCTURE OF HAEMOGLOBIN IN THE DEOXY QUATERNARY STATE WITH LIGAN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1coh
TitleSTRUCTURE OF HAEMOGLOBIN IN THE DEOXY QUATERNARY STATE WITH LIGAND BOUND AT THE ALPHA HAEMS
Components
  • HEMOGLOBIN (COBALTOUS DEOXY) (BETA CHAIN)
  • HEMOGLOBIN (FERROUS CARBONMONOXY) (ALPHA CHAIN)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin binding / cellular oxidant detoxification / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin binding / cellular oxidant detoxification / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / positive regulation of cell death / hydrogen peroxide catabolic process / Late endosomal microautophagy / oxygen carrier activity / response to hydrogen peroxide / carbon dioxide transport / Heme signaling / G protein-coupled receptor binding / platelet aggregation / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / regulation of blood pressure / Cytoprotection by HMOX1 / Chaperone Mediated Autophagy / oxygen binding / positive regulation of nitric oxide biosynthetic process / cytosolic small ribosomal subunit / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / Neutrophil degranulation / heme binding / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hemoglobin subunit beta / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING CO / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsLuisi, B.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Structure of haemoglobin in the deoxy quaternary state with ligand bound at the alpha haems.
Authors: Luisi, B. / Shibayama, N.
#1: Journal: Acc.Chem.Res. / Year: 1987
Title: Stereochemistry of Cooperative Mechanisms in Hemoglobin
Authors: Perutz, M.F. / Fermi, G. / Luisi, B. / Shaanan, B. / Liddington, R.C.
History
DepositionJan 13, 1989-
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 22, 2014Group: Derived calculations
Remark 285THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEMOGLOBIN (FERROUS CARBONMONOXY) (ALPHA CHAIN)
B: HEMOGLOBIN (COBALTOUS DEOXY) (BETA CHAIN)
C: HEMOGLOBIN (FERROUS CARBONMONOXY) (ALPHA CHAIN)
D: HEMOGLOBIN (COBALTOUS DEOXY) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,60910
Polymers62,0814
Non-polymers2,5286
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.090, 83.060, 53.670
Angle α, β, γ (deg.)90.00, 99.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein HEMOGLOBIN (FERROUS CARBONMONOXY) (ALPHA CHAIN)


Mass: 15150.353 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P69905
#2: Protein HEMOGLOBIN (COBALTOUS DEOXY) (BETA CHAIN)


Mass: 15890.198 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P68871

-
Non-polymers , 4 types, 203 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
Conc.: 2.45-2.55 M / Common name: ammonium sulfate

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 11733 / Num. measured all: 55367 / Rmerge(I) obs: 0.108

-
Processing

SoftwareName: EREF / Classification: refinement
RefinementHighest resolution: 2.9 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 176 197 4757

+
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