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- PDB-7ud7: Crystal structure of deoxygenated hemoglobin in complex with 5HMF... -

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Basic information

Entry
Database: PDB / ID: 7ud7
TitleCrystal structure of deoxygenated hemoglobin in complex with 5HMF-NO at 1.8 Angstrom
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / hemoglobin / sickle cell disease / antisickling / NO release / oxygen equilibrium
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / organic acid binding / 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 / membrane / metal ion binding / 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 / dihydroxy[(5-methylfuran-2-yl)methoxy]amine / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDonkor, A.K. / Musayev, F.N. / Safo, M.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)R01MD009124 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R61HL156158 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10OD021756 United States
CitationJournal: Biomolecules / Year: 2022
Title: Design, Synthesis, and Antisickling Investigation of a Nitric Oxide-Releasing Prodrug of 5HMF for the Treatment of Sickle Cell Disease.
Authors: Alhashimi, R.T. / Ghatge, M.S. / Donkor, A.K. / Deshpande, T.M. / Anabaraonye, N. / Alramadhani, D. / Danso-Danquah, R. / Huang, B. / Zhang, Y. / Musayev, F.N. / Abdulmalik, O. / Safo, M.K.
History
DepositionMar 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 29, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)65,39010
Polymers62,6064
Non-polymers2,7846
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-108 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.344, 82.031, 53.454
Angle α, β, γ (deg.)90.000, 99.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15281.550 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 16021.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Homo sapiens (human) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MWC / dihydroxy[(5-methylfuran-2-yl)methoxy]amine


Mass: 159.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO4
Details: The ligand MWC is an aromatic aldehyde. The aldehyde moiety reacts with the N-terminal amine of Val1 of Hb forming a Schiff-base. That is C1 makes a double bond interaction with the amine ...Details: The ligand MWC is an aromatic aldehyde. The aldehyde moiety reacts with the N-terminal amine of Val1 of Hb forming a Schiff-base. That is C1 makes a double bond interaction with the amine nitrogen of hemoglobin. The leaving group is water.
Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3.2-3.6M Sulfate/phosphate precipitant, pH 6.5, ferrous citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 15, 2019 / Details: VariMax TM-VHF Arc)Sec Confocal Optical System
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.8→29.92 Å / Num. obs: 46300 / % possible obs: 94.1 % / Redundancy: 4.06 % / Biso Wilson estimate: 13.89 Å2 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.039 / Χ2: 0.97 / Net I/σ(I): 25.9 / Num. measured all: 189338 / Scaling rejects: 1421
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsΧ2Rejects% possible all
1.8-1.863.810.08210.81671143670.698889.4
1.86-1.944.090.098111875945860.731793.8
1.94-2.034.170.06614.51933646330.612794.5
2.03-2.134.010.068161879546640.97494.6
2.13-2.273.890.05919.41754644860.9611091.6
2.27-2.444.190.04122.41990247380.665496.4
2.44-2.694.220.03926.92020347700.825697.1
2.69-3.084.240.03432.82049048180.925597.9
3.08-3.883.810.03341.91769444861.4461490.7
3.88-29.924.120.02660.9199024752232694.9

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Processing

Software
NameVersionClassification
d*TREK9.2SSIdata scaling
PHENIX1.13.2998refinement
PDB_EXTRACT3.27data extraction
CrysalisPro41.64.69adata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IC0

3ic0


Resolution: 1.8→26.361 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.63 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 2339 5.05 %
Rwork0.1511 43952 -
obs0.1531 46291 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.22 Å2 / Biso mean: 15.6372 Å2 / Biso min: 2.98 Å2
Refinement stepCycle: final / Resolution: 1.8→26.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 194 781 5359
Biso mean--13.74 26.18 -
Num. residues----574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.83680.26571390.1977236186
1.8368-1.87670.21891560.1783253694
1.8767-1.92030.2241210.1704260094
1.9203-1.96830.24061260.1591256694
1.9683-2.02150.19461290.1445259495
2.0215-2.0810.21951230.1599259794
2.081-2.14810.19671390.15260895
2.1481-2.22490.19631460.1461263696
2.2249-2.31390.20791280.1585240989
2.3139-2.41920.1941230.1468266497
2.4192-2.54660.1731450.1496266197
2.5466-2.7060.21651330.1564268297
2.706-2.91470.17321580.1522266298
2.9147-3.20760.20151650.1547268298
3.2076-3.67060.19041210.1381252491
3.6706-4.62050.16151290.1256239186
4.6205-26.3610.15731580.1597277999

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