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- PDB-9ayz: T-state HbG Makassar hemoglobin -

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Basic information

Entry
Database: PDB / ID: 9ayz
TitleT-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: 2.24 Å
AuthorsFeliciano, P.R. / Lee, S.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 9, 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
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,86216
Polymers123,9308
Non-polymers4,9328
Water2,396133
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)64,4318
Polymers61,9654
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-102 kcal/mol
Surface area23230 Å2
MethodPISA
2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4318
Polymers61,9654
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-102 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.625, 109.187, 82.096
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15150.353 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein
Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15832.163 Da / Num. of mol.: 4 / Mutation: E6A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.055 M Citric acid, 0.045 M Bis-Tris propane, pH 4.5, 22% PEG 3,350 under low oxygen conditions on an MBraun anaerobic glove box

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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: 0.9201 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: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.24→41.07 Å / Num. obs: 52302 / % possible obs: 98.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 53.02 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.14 / Net I/σ(I): 3.9
Reflection shellResolution: 2.24→2.3 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3801 / CC1/2: 0.142 / Rpim(I) all: 1.152 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→41.05 Å / Cross valid method: FREE R-VALUE / σ(F): 79.1 / Phase error: 35.47 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2589 2611 5 %
Rwork0.2297 --
obs0.2317 52234 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→41.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8426 0 258 133 8817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029052
X-RAY DIFFRACTIONf_angle_d0.49512498
X-RAY DIFFRACTIONf_dihedral_angle_d11.3021268
X-RAY DIFFRACTIONf_chiral_restr0.0351381
X-RAY DIFFRACTIONf_plane_restr0.0051580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.280.33231330.34762666X-RAY DIFFRACTION91
2.28-2.330.34491370.31082726X-RAY DIFFRACTION93
2.33-2.380.31471420.30062740X-RAY DIFFRACTION93
2.38-2.430.34281440.31292715X-RAY DIFFRACTION93
2.43-2.50.33181280.30642778X-RAY DIFFRACTION94
2.5-2.560.33081430.312713X-RAY DIFFRACTION93
2.56-2.640.31871440.29952745X-RAY DIFFRACTION93
2.64-2.720.32521360.29512798X-RAY DIFFRACTION93
2.72-2.820.30781450.29592695X-RAY DIFFRACTION93
2.82-2.930.28641700.28642749X-RAY DIFFRACTION93
2.93-3.070.29421680.26972728X-RAY DIFFRACTION93
3.07-3.230.26731130.25892799X-RAY DIFFRACTION95
3.23-3.430.24881560.24462761X-RAY DIFFRACTION93
3.43-3.70.23951550.2122789X-RAY DIFFRACTION94
3.7-4.070.21131410.19232774X-RAY DIFFRACTION94
4.07-4.660.21571480.17352788X-RAY DIFFRACTION94
4.66-5.860.22411250.19552833X-RAY DIFFRACTION95
5.86-41.050.24691350.18122874X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -14.3173 Å / Origin y: 1.5645 Å / Origin z: -20.6235 Å
111213212223313233
T0.3111 Å20.0376 Å2-0.0099 Å2-0.2952 Å2-0.0538 Å2--0.2325 Å2
L0.4223 °2-0.1204 °20.1713 °2-0.3114 °2-0.4833 °2--0.7793 °2
S-0.0335 Å °-0.1112 Å °-0.0013 Å °0.0268 Å °0.028 Å °0.0003 Å °-0.0219 Å °-0.0746 Å °0.0106 Å °
Refinement TLS groupSelection details: all

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