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- PDB-9av9: R2-state HbG-Makassar hemoglobin -

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Basic information

Entry
Database: PDB / ID: 9av9
TitleR2-state HbG-Makassar hemoglobin
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / hemoglobin / Makassar / sickle / E6A
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 / Globin domain profile. / Globin / Globin / Globin-like superfamily
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: 1.94 Å
AuthorsFeliciano, P.R. / Lee, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0012704 United States
Department of Energy (DOE, United States)KP1605010 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
CitationJournal: Nat Commun / Year: 2025
Title: Base editing HbS to HbG-Makassar improves hemoglobin function supporting its use in sickle cell disease.
Authors: Kostamo, Z. / Ortega, M.A. / Xu, C. / Feliciano, P.R. / Budak, E. / Lam, D. / Winton, V. / Jenkins, R. / Venugopal, A. / Zhang, M. / Jamieson, J. / Coisman, B. / Goldsborough, K. / ...Authors: Kostamo, Z. / Ortega, M.A. / Xu, C. / Feliciano, P.R. / Budak, E. / Lam, D. / Winton, V. / Jenkins, R. / Venugopal, A. / Zhang, M. / Jamieson, J. / Coisman, B. / Goldsborough, K. / Hernandez, B. / Kanne, C.K. / Evans, E.N. / Zgodny, J. / Zhang, Y. / Darazim, J. / Patel, A. / Pendergast, M.A. / Manis, J. / Hartigan, A.J. / Ciaramella, G. / Lee, S.J. / Chu, S.H. / Sheehan, V.A.
History
DepositionMar 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)64,89113
Polymers61,9654
Non-polymers2,9269
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-108 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.566, 58.962, 171.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15150.353 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Mus musculus (house mouse) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15832.163 Da / Num. of mol.: 2 / Mutation: E6A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Mus musculus (house mouse) / References: UniProt: P68871
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 0.1 M TRIS pH 8.0; 26-36% (v/v) PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97932 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 14, 2022
Details: white beam slits, a double crystal Si(111) monochromator with horizontal axis, tandem flat beam deflecting mirrors (Pd coating), and Kirkpatrick-Baez focusing mirrors, which are Pd coated ...Details: white beam slits, a double crystal Si(111) monochromator with horizontal axis, tandem flat beam deflecting mirrors (Pd coating), and Kirkpatrick-Baez focusing mirrors, which are Pd coated and able to bend adaptively using 16 piezo actuators. Each optical element is preceded by slits and its transmitted beam is monitored by beam position monitors or retractable screens
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.94→58.59 Å / Num. obs: 45038 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rpim(I) all: 0.053 / Net I/σ(I): 9
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3278 / CC1/2: 0.912 / Rpim(I) all: 0.77 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487-000refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→34.69 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 2310 5.16 %
Rwork0.1954 --
obs0.1968 44764 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 202 220 4611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064607
X-RAY DIFFRACTIONf_angle_d0.796356
X-RAY DIFFRACTIONf_dihedral_angle_d12.69647
X-RAY DIFFRACTIONf_chiral_restr0.045703
X-RAY DIFFRACTIONf_plane_restr0.007803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.39911470.3512579X-RAY DIFFRACTION98
1.98-2.030.36041650.29852598X-RAY DIFFRACTION99
2.03-2.080.32261130.27322604X-RAY DIFFRACTION99
2.08-2.130.28271330.23522603X-RAY DIFFRACTION99
2.13-2.20.2811370.21652627X-RAY DIFFRACTION99
2.2-2.270.26391490.22712616X-RAY DIFFRACTION99
2.27-2.350.24331260.21262636X-RAY DIFFRACTION100
2.35-2.440.27311360.20922657X-RAY DIFFRACTION100
2.44-2.550.24941570.19632615X-RAY DIFFRACTION100
2.55-2.690.2421430.2032648X-RAY DIFFRACTION100
2.69-2.860.24321340.18762649X-RAY DIFFRACTION100
2.86-3.080.24161620.19582664X-RAY DIFFRACTION100
3.08-3.390.20181200.18692677X-RAY DIFFRACTION100
3.39-3.880.18291780.16882682X-RAY DIFFRACTION100
3.88-4.880.18441800.162723X-RAY DIFFRACTION100
4.88-34.690.21771300.20652876X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.7876 Å / Origin y: -27.0644 Å / Origin z: 21.8895 Å
111213212223313233
T0.2516 Å20.0112 Å2-0.037 Å2-0.2347 Å20.0347 Å2--0.2847 Å2
L1.2625 °2-0.2554 °2-0.2777 °2-2.0188 °21.9618 °2--5.1083 °2
S0.0211 Å °0.1164 Å °-0.1151 Å °-0.2619 Å °-0.017 Å °0.171 Å °-0.47 Å °-0.0359 Å °-0.0452 Å °
Refinement TLS groupSelection details: all

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