[English] 日本語
Yorodumi
- PDB-2yrs: Human hemoglobin D Los Angeles: crystal structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yrs
TitleHuman hemoglobin D Los Angeles: crystal structure
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsTRANSPORT PROTEIN / OXYGEN BINDING / Hemoglobin / human / D Los Angeles / Substitution / Mutation / Oxygen Storage/transport
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / 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 / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPoy, C.D. / Moreno, F. / Bonini-Domingos, C.R. / Filgueira de Azevedo Jr., W. / Bonilla-Rodriguez, G.O.
CitationJournal: to be published
Title: Human Hemoglobin D Los Angeles: crystal structure
Authors: Poy, C.D. / Moreno, F. / Bonini-Domingos, C.R. / Filgueira de Azevedo Jr., W. / Bonilla-Rodriguez, G.O.
History
DepositionApr 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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.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_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_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: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
I: Hemoglobin subunit alpha
K: Hemoglobin subunit beta
M: Hemoglobin subunit alpha
O: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,09016
Polymers124,1588
Non-polymers4,9328
Water2,432135
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5458
Polymers62,0794
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-108.7 kcal/mol
Surface area22910 Å2
MethodPISA
2
I: Hemoglobin subunit alpha
K: Hemoglobin subunit beta
M: Hemoglobin subunit alpha
O: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5458
Polymers62,0794
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-106.3 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.702, 62.759, 110.216
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Hemoglobin subunit alpha / / Hemoglobin alpha chain / Alpha-globin


Mass: 15150.353 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Blood / Source: (natural) Homo sapiens (human) / Tissue: Blood / Tissue fraction: Hemoglobin / References: UniProt: P69905
#2: Protein
Hemoglobin subunit beta / / Hemoglobin beta chain / Beta-globin


Mass: 15889.214 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Blood / Source: (natural) Homo sapiens (human) / Tissue: Blood / Tissue fraction: Hemoglobin / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 122TH RESIDUE IN THE BETA SUBUNIT IS GLN AND IT OCCURS NATURALLY IN D-LOS ANGELES/D-PUNJAB/D- ...THE 122TH RESIDUE IN THE BETA SUBUNIT IS GLN AND IT OCCURS NATURALLY IN D-LOS ANGELES/D-PUNJAB/D-PORTUGAL/D-CHICAGO/D-OAK RIDGE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
ReflectionResolution: 2.3→41.42 Å / Num. all: 50559 / Num. obs: 45030 / Redundancy: 2.8 % / Rmerge(I) obs: 0.094 / Rsym value: 0.114
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.256 / Num. unique all: 45030 / Rsym value: 0.317

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DXT

1dxt


Resolution: 2.3→41.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.891 / SU B: 6.865 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.495 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25248 2300 5.1 %RANDOM
Rwork0.16029 ---
obs0.16493 42729 89.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.02 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8768 0 344 135 9247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0229400
X-RAY DIFFRACTIONr_angle_refined_deg2.1522.0612900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48351140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24723.889360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.435151412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1811524
X-RAY DIFFRACTIONr_chiral_restr0.1430.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027132
X-RAY DIFFRACTIONr_nbd_refined0.2350.24982
X-RAY DIFFRACTIONr_nbtor_refined0.3190.26402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2411
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.23
X-RAY DIFFRACTIONr_mcbond_it1.1871.55801
X-RAY DIFFRACTIONr_mcangle_it2.0229148
X-RAY DIFFRACTIONr_scbond_it3.19534052
X-RAY DIFFRACTIONr_scangle_it4.6764.53738
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 168 -
Rwork0.175 3267 -
obs--93.01 %

+
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