[English] 日本語
Yorodumi
- PDB-1j3y: Direct observation of photolysis-induced tertiary structural chan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j3y
TitleDirect observation of photolysis-induced tertiary structural changes in human hemoglobin; Crystal structure of alpha(Fe)-beta(Ni) hemoglobin (laser photolysed)
Components
  • Hemoglobin alpha Chain
  • Hemoglobin beta Chain
KeywordsOXYGEN STORAGE/TRANSPORT / Tertiary structure changes / Crystal photolysis / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BUT-2-ENEDIAL / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / PROTOPORPHYRIN IX CONTAINING NI(II) / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsAdachi, S. / Park, S.-Y. / Tame, J.R.H. / Shiro, Y. / Shibayama, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Direct observation of photolysis-induced tertiary structural changes in hemoglobin
Authors: Adachi, S. / Park, S.-Y. / Tame, J.R.H. / Shiro, Y. / Shibayama, N.
History
DepositionFeb 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemoglobin alpha Chain
B: Hemoglobin beta Chain
C: Hemoglobin alpha Chain
D: Hemoglobin beta Chain
E: Hemoglobin alpha Chain
F: Hemoglobin beta Chain
G: Hemoglobin alpha Chain
H: Hemoglobin beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,38622
Polymers124,1628
Non-polymers5,22314
Water40,9302272
1
A: Hemoglobin alpha Chain
B: Hemoglobin beta Chain
C: Hemoglobin alpha Chain
D: Hemoglobin beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,69311
Polymers62,0814
Non-polymers2,6127
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hemoglobin alpha Chain
F: Hemoglobin beta Chain
G: Hemoglobin alpha Chain
H: Hemoglobin beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,69311
Polymers62,0814
Non-polymers2,6127
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.494, 94.012, 100.111
Angle α, β, γ (deg.)90.00, 101.65, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Hemoglobin alpha Chain


Mass: 15150.353 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
Hemoglobin beta Chain


Mass: 15890.198 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

-
Non-polymers , 5 types, 2286 molecules

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


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


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Chemical
ChemComp-HNI / PROTOPORPHYRIN IX CONTAINING NI(II)


Mass: 619.336 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32N4NiO4
#6: Chemical ChemComp-2FU / BUT-2-ENEDIAL


Mass: 84.073 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2272 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / pH: 6.6
Details: PEG 4000, 50mM citrate-ammonium buffer, SMALL TUBES, temperature 293K, pH 6.60
Crystal grow
*PLUS
pH: 6.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11-2 %(w/v)CO-saturated11
218 %(w/v)PEG335011
30.15 M11K2SO4
45 mMhomocysteine11
550 mMcitrate-ammonium11pH6.6

-
Data collection

DiffractionMean temperature: 25 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 2002 / Details: MONOCHROMATOR
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. obs: 153793 / % possible obs: 90.7 % / Observed criterion σ(I): 5.8 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.276 / % possible all: 51.8
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 3.9 % / Num. measured all: 600432 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 51.8 %

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→19.61 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.895 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.205 7610 5 %RANDOM
Rwork0.162 ---
obs0.164 153793 90.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.165 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.23 Å2
2---0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8768 0 364 2272 11404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0219426
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4242.02712900
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8751140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027060
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.25304
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.21639
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.2141
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.2202
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6641.55720
X-RAY DIFFRACTIONr_mcangle_it1.2329140
X-RAY DIFFRACTIONr_scbond_it2.14733706
X-RAY DIFFRACTIONr_scangle_it3.334.53760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 334
Rwork0.29 5760
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.48

+
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