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- PDB-3ia3: A cis-proline in alpha-hemoglobin stabilizing Protein directs the... -

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Basic information

Entry
Database: PDB / ID: 3ia3
TitleA cis-proline in alpha-hemoglobin stabilizing Protein directs the structural reorganization of alpha-hemoglobin
Components
  • Alpha-hemoglobin-stabilizing protein
  • Hemoglobin subunit alpha
KeywordsOXYGEN TRANSPORT / Hemoglobin / cis-proline / ahsp / stabilization / Chaperone / Cytoplasm / Polymorphism / Acetylation / Disease mutation / Glycation / Glycoprotein / Heme / Iron / Metal-binding / Phosphoprotein / Transport
Function / homology
Function and homology information


hemoglobin metabolic process / nitric oxide transport / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / hemoglobin complex / hemopoiesis / oxygen transport / Scavenging of heme from plasma ...hemoglobin metabolic process / nitric oxide transport / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / hemoglobin complex / hemopoiesis / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / erythrocyte differentiation / hydrogen peroxide catabolic process / oxygen carrier activity / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / unfolded protein binding / protein folding / blood microparticle / protein stabilization / iron ion binding / heme binding / extracellular space / extracellular exosome / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Alpha-haemoglobin stabilising protein / AHSP superfamily / Alpha-haemoglobin stabilising protein / AHSP / Hemoglobin, pi / Hemoglobin, alpha-type / Globin/Protoglobin / Globins / Globin family profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Alpha-haemoglobin stabilising protein / AHSP superfamily / Alpha-haemoglobin stabilising protein / AHSP / Hemoglobin, pi / Hemoglobin, alpha-type / Globin/Protoglobin / Globins / Globin family profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Globin-like / Globin / Globin / Globin-like superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Alpha-hemoglobin-stabilizing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFeng, L. / Jeffrey, P.D. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: A cis-proline in alpha-hemoglobin stabilizing protein directs the structural reorganization of alpha-hemoglobin.
Authors: Gell, D.A. / Feng, L. / Zhou, S. / Jeffrey, P.D. / Bendak, K. / Gow, A. / Weiss, M.J. / Shi, Y. / Mackay, J.P.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-hemoglobin-stabilizing protein
B: Hemoglobin subunit alpha
C: Alpha-hemoglobin-stabilizing protein
D: Hemoglobin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7296
Polymers52,4964
Non-polymers1,2332
Water0
1
A: Alpha-hemoglobin-stabilizing protein
D: Hemoglobin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8643
Polymers26,2482
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-31 kcal/mol
Surface area11900 Å2
MethodPISA
2
B: Hemoglobin subunit alpha
C: Alpha-hemoglobin-stabilizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8643
Polymers26,2482
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-30 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.230, 65.230, 439.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsHeterodimer of alpha-hemoglobin stabilizing protein and alpha-hemoglobin with heme, two copies in the asymmetric unit.

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Components

#1: Protein Alpha-hemoglobin-stabilizing protein / Erythroid-associated factor / Erythroid differentiation-related factor


Mass: 10684.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AHSP, EDRF, ERAF / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD4
#2: Protein Hemoglobin subunit alpha / / Hemoglobin alpha chain / Alpha-globin


Mass: 15563.827 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 4% acetonitrile and 14.5% (w/v) PEG3000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 8764 / Num. obs: 8764 / % possible obs: 85 % / Observed criterion σ(I): -3 / Rsym value: 0.058
Reflection shellResolution: 3→3.11 Å / Rsym value: 0.453 / % possible all: 51.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→21.25 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 2259220.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.293 439 5.1 %RANDOM
Rwork0.23 ---
all0.242 8538 --
obs0.23 8538 84.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.8254 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 82.2 Å2
Baniso -1Baniso -2Baniso -3
1--15.96 Å20 Å20 Å2
2---15.96 Å20 Å2
3---31.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.2→21.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 86 0 3606
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 37 4.2 %
Rwork0.287 852 -
obs--54.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5hem.paramhem.top

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