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- PDB-6nbc: human methemoglobin state 1 determined using single-particle cryo... -

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Basic information

Entry
Database: PDB / ID: 6nbc
Titlehuman methemoglobin state 1 determined using single-particle cryo-EM at 200 keV
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / heme-binding / hetero-4-mer / globin
Function / homologyScavenging of heme from plasma / Globin/Protoglobin / Neutrophil degranulation / Haemoglobin, alpha-type / Haemoglobin, pi / Globin / Globin-like superfamily / Globin / Factors involved in megakaryocyte development and platelet production / Erythrocytes take up oxygen and release carbon dioxide ...Scavenging of heme from plasma / Globin/Protoglobin / Neutrophil degranulation / Haemoglobin, alpha-type / Haemoglobin, pi / Globin / Globin-like superfamily / Globin / Factors involved in megakaryocyte development and platelet production / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Haemoglobin, beta-type / Globin family profile. / nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / regulation of blood vessel size / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / cellular oxidant detoxification / oxygen transport / hemoglobin complex / endocytic vesicle lumen / positive regulation of cell death / platelet aggregation / hydrogen peroxide catabolic process / protein heterooligomerization / cytosolic small ribosomal subunit / response to hydrogen peroxide / regulation of blood pressure / oxygen carrier activity / bicarbonate transport / receptor-mediated endocytosis / oxygen binding / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / ficolin-1-rich granule lumen / blood microparticle / blood coagulation / iron ion binding / neutrophil degranulation / heme binding / extracellular space / extracellular exosome / membrane / extracellular region / metal ion binding / cytosol / Hemoglobin subunit beta / Hemoglobin subunit alpha
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.8 Å resolution
AuthorsHerzik Jr., M.A. / Wu, M. / Lander, G.C.
CitationJournal: Nat Commun / Year: 2019
Title: High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM.
Authors: Mark A Herzik / Mengyu Wu / Gabriel C Lander
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 6, 2018 / Release: Mar 13, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 13, 2019Structure modelrepositoryInitial release
1.1Mar 20, 2019Structure modelData collection / Database referencescitation / citation_author_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 / _citation_author.identifier_ORCID

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Structure visualization

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  • Deposited structure unit
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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)63,3728
Polyers60,9064
Non-polymers2,4664
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models4

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Components

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


Mass: 14993.159 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
Plasmid details: Obtained in lyophilized form from Sigma Aldrich
References: UniProt: P69905
#2: Protein/peptide Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain


Mass: 15459.697 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
Plasmid details: Obtained in lyophilized form from Sigma Aldrich
References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4 / Heme

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: methemoglobin from human / Type: COMPLEX
Details: Lyophilized human methemoglobin purchased from Sigma Aldrich
Entity ID: 1, 2 / Source: NATURAL
Molecular weightValue: 0.064 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
110 mMPhosphateNa2HPO41
2137 mMSodium chlorideNaCl1
32.7 mMPotassium ChlorideKCL1
42 mMPotassium PhosphateKH2PO41
SpecimenConc.: 12 mg/ml
Details: Lyophilized human methemoglobin (Sigma Aldrich) was solubilized.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grids were plasma cleaned using a Solarus plasma cleaner (Gatan, Inc.).
Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 kelvins
Details: Sample was manually blotted for 4-5 seconds using Whatman No. 1 filter paper immediately prior to plunge-freezing.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 73000 / Nominal defocus max: 16000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 11 sec. / Electron dose: 69 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 2 / Number of real images: 1673
Image scansSampling size: 5 microns / Width: 3710 / Height: 3838 / Movie frames/image: 44 / Used frames/image: 1-44

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2580: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2Leginon3.2image acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.11.2model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.11.1_2580model refinement
Image processingDetails: Counting mode, 250 ms frames, exposure rate of ~1.95 e- pixel-1 s-1, total exposure of ~69 e- angstrom-2 (1.57 e- angstrom-2 frame-1).
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Difference-of-Gaussian-picked. / Number of particles selected: 1232543
SymmetryPoint symmetry: C2
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 24308 / Symmetry type: POINT
Atomic model buildingOverall b value: 67 / Ref protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model buildingPDB-ID: 4N7P
Pdb chain ID: A
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0094616
ELECTRON MICROSCOPYf_angle_d1.0036334
ELECTRON MICROSCOPYf_dihedral_angle_d7.0952616
ELECTRON MICROSCOPYf_chiral_restr0.055692
ELECTRON MICROSCOPYf_plane_restr0.011792

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