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- PDB-5ni1: CryoEM structure of haemoglobin at 3.2 A determined with the Volt... -

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Basic information

Entry
Database: PDB / ID: 5ni1
TitleCryoEM structure of haemoglobin at 3.2 A determined with the Volta phase plate
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Volta phase plate / Single particle analysis / Hemoglobin / oxygen transport
Function/homologynitric oxide transport / haptoglobin-hemoglobin complex / hemoglobin binding / cellular oxidant detoxification / regulation of blood vessel size / renal absorption / oxygen transport / Haemoglobin, pi / Haemoglobin, beta-type / Haemoglobin, alpha-type ...nitric oxide transport / haptoglobin-hemoglobin complex / hemoglobin binding / cellular oxidant detoxification / regulation of blood vessel size / renal absorption / oxygen transport / Haemoglobin, pi / Haemoglobin, beta-type / Haemoglobin, alpha-type / hemoglobin complex / Scavenging of heme from plasma / endocytic vesicle lumen / positive regulation of cell death / platelet aggregation / cytosolic small ribosomal subunit / hydrogen peroxide catabolic process / protein heterooligomerization / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Globin family profile. / Globin / receptor-mediated endocytosis / response to hydrogen peroxide / regulation of blood pressure / oxygen binding / bicarbonate transport / oxygen carrier activity / Globin-like superfamily / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / positive regulation of nitric oxide biosynthetic process / ficolin-1-rich granule lumen / blood coagulation / blood microparticle / |Globin / iron ion binding / Neutrophil degranulation / neutrophil degranulation / heme binding / extracellular space / membrane / extracellular exosome / extracellular region / cytosol / Hemoglobin subunit beta / Hemoglobin subunit alpha
Function and homology information
Specimen sourceHomo sapiens / human /
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsKhoshouei, M. / Radjainia, M. / Bunker, R. / Baumeister, W. / Danev, R.
CitationJournal: Elife / Year: 2016
Title: Cryo-EM single particle analysis with the Volta phase plate.
Authors: Radostin Danev / Wolfgang Baumeister
Abstract: We present a method for in-focus data acquisition with a phase plate that enables near-atomic resolution single particle reconstructions. Accurate focusing is the determining factor for obtaining ...We present a method for in-focus data acquisition with a phase plate that enables near-atomic resolution single particle reconstructions. Accurate focusing is the determining factor for obtaining high quality data. A double-area focusing strategy was implemented in order to achieve the required precision. With this approach we obtained a 3.2 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome. The phase plate matches or slightly exceeds the performance of the conventional defocus approach. Spherical aberration becomes a limiting factor for achieving resolutions below 3 Å with in-focus phase plate images. The phase plate could enable single particle analysis of challenging samples in terms of small size, heterogeneity and flexibility that are difficult to solve by the conventional defocus approach.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 22, 2017 / Release: Apr 12, 2017

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Structure visualization

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Assembly

Deposited unit
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)64,5478
Polyers62,0814
Non-polymers2,4664
Water43224
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 15150.353 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / human / / Gene: HBA1, HBA2 / Production host: Homo sapiens / References: UniProt:P69905
#2: Protein/peptide Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / human / / Gene: HBB / Production host: Homo sapiens / References: UniProt:P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4 / : Heme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Formula: H2O / : Water

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Hemoglobin / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 175300 / Symmetry type: POINT
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLOverall ESU RStereochemistry target valuesSolvent model details
160.032-1.39-1.67-0.010.67-0.010.720.574HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.370770.370773.20105.0074004100.0018.1680.2780.340MAXIMUM LIKELIHOOD WITH PHASESPARAMETERS FOR MASK CACLULATION
ELECTRON MICROSCOPY
Number of atoms included #1Total: 4580
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0100.0194703
ELECTRON MICROSCOPYr_bond_other_d0.0020.0204331
ELECTRON MICROSCOPYr_angle_refined_deg1.5322.0006449
ELECTRON MICROSCOPYr_angle_other_deg1.2963.00010003
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.7125.000570
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.07723.889180
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.44615.000705
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.35715.00012
ELECTRON MICROSCOPYr_chiral_restr0.1040.200708
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0215272
ELECTRON MICROSCOPYr_gen_planes_other0.0030.020984
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.5645.6852292
ELECTRON MICROSCOPYr_mcbond_other5.5205.6732291
ELECTRON MICROSCOPYr_mcangle_it9.8188.4842858
ELECTRON MICROSCOPYr_mcangle_other9.8338.4962859
ELECTRON MICROSCOPYr_scbond_it7.1026.4952411
ELECTRON MICROSCOPYr_scbond_other7.0916.4922409
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.7439.2523591
ELECTRON MICROSCOPYr_long_range_B_refined18.71764.9355272
ELECTRON MICROSCOPYr_long_range_B_other18.72164.9435273
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints ncs

Refine ID: ELECTRON MICROSCOPY / Type: tight thermal / Weight position: 0.5

Dom IDAuth asym IDEns IDNumberRms dev position
1A110680.34
2B211230.12
Refine LS shellHighest resolution: 3.2 Å / R factor R work: 0.965 / Lowest resolution: 3.283 Å / Number reflection R free: 0 / Number reflection R work: 5475 / Total number of bins used: 20 / Percent reflection obs: 1

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