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- PDB-5ksi: Crystal structure of deoxygenated hemoglobin in complex with sphi... -

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Basic information

Entry
Database: PDB / ID: 5ksi
TitleCrystal structure of deoxygenated hemoglobin in complex with sphingosine phosphate and 2,3-Bisphosphoglycerate
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Hemoglobin / Sphingosine-1-phosphate / Complex / ALLOSTERIC EFFECTOR
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 / response to hydrogen peroxide / carbon dioxide transport / 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
(2R)-2,3-diphosphoglyceric acid / PROTOPORPHYRIN IX CONTAINING FE / Chem-S1P / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAhmed, M.H. / Safo, M.K. / Xia, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)MD009124 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA16059 United States
CitationJournal: Sci Rep / Year: 2017
Title: Structural and Functional Insight of Sphingosine 1-Phosphate-Mediated Pathogenic Metabolic Reprogramming in Sickle Cell Disease.
Authors: Sun, K. / D'Alessandro, A. / Ahmed, M.H. / Zhang, Y. / Song, A. / Ko, T.P. / Nemkov, T. / Reisz, J.A. / Wu, H. / Adebiyi, M. / Peng, Z. / Gong, J. / Liu, H. / Huang, A. / Wen, Y.E. / Wen, A. ...Authors: Sun, K. / D'Alessandro, A. / Ahmed, M.H. / Zhang, Y. / Song, A. / Ko, T.P. / Nemkov, T. / Reisz, J.A. / Wu, H. / Adebiyi, M. / Peng, Z. / Gong, J. / Liu, H. / Huang, A. / Wen, Y.E. / Wen, A.Q. / Berka, V. / Bogdanov, M.V. / Abdulmalik, O. / Han, L. / Tsai, A.L. / Idowu, M. / Juneja, H.S. / Kellems, R.E. / Dowhan, W. / Hansen, K.C. / Safo, M.K. / Xia, Y.
History
DepositionJul 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: 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
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)66,97615
Polymers62,0814
Non-polymers4,89511
Water14,124784
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-101 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.940, 98.080, 65.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Hemoglobin subunit ... , 2 types, 4 molecules ACBD

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


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


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 795 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-S1P / (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate / sphingosine 1-phosphate / Sphingosine-1-phosphate


Mass: 379.472 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H38NO5P
#5: Chemical ChemComp-DG2 / (2R)-2,3-diphosphoglyceric acid / 2,3-Bisphosphoglyceric acid / 2,3-bisphosphoglycerate / 2,3-BPG / 2,3-diphosphoglyceric acid / 2,3-diphosphoglycerate / 2,3-DPG / (2~{R})-2,3-diphosphonooxypropanoic acid / 2,3-Bisphosphoglyceric acid


Mass: 266.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O10P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 784 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5 and 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 54124 / % possible obs: 93.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.4 / % possible all: 96.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIX1.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DN2

2dn2


Resolution: 1.8→30 Å / σ(F): 0
Details: Author provided the following evidence of direct S1P binding to hemoglobin: S1P beads successfully pulled down HbA from normal human erythrocyte lysates, while sphingosine or ...Details: Author provided the following evidence of direct S1P binding to hemoglobin: S1P beads successfully pulled down HbA from normal human erythrocyte lysates, while sphingosine or lysophosphatidic acid beads failed to pull down Hb. In addition, co-binding of 2,3-DPG and S1P to hemoglobin (Hb) is required for S1P-induced decrease in Hb-O2 affinity. We measured Oxygen Equilibration Curves (OEC) of purified HbA in the presence of 2,3-DPG along with S1P. We found that S1P decreased HbA-O2 binding affinity with increased P50 in a dose-dependent manner. Thus, we provide biochemical and functional evidence that S1P binds directly to Hb but requires cobinding of 2,3-DPG to decrease the protein affinity for O2
RfactorNum. reflection% reflection
Rfree0.22 2764 4.8 %
Rwork0.1801 51359 -
obs-54123 93.8 %
Solvent computationBsol: 89.8946 Å2
Displacement parametersBiso max: 74.53 Å2 / Biso mean: 22.7998 Å2 / Biso min: 7.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.667 Å20 Å20 Å2
2---4.465 Å20 Å2
3---2.798 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 286 784 5454
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1991.5
X-RAY DIFFRACTIONc_scbond_it1.9872
X-RAY DIFFRACTIONc_mcangle_it1.6022
X-RAY DIFFRACTIONc_scangle_it2.762.5

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