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- PDB-5hy8: Glycation restrains allosteric transition in hemoglobin: The mole... -

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Basic information

Entry
Database: PDB / ID: 5hy8
TitleGlycation restrains allosteric transition in hemoglobin: The molecular basis of oxidative stress under hyperglycemic conditions in diabetes
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Glycation / hemoglobin / diabetes / oxidative stress
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
beta-D-fructofuranose / alpha-D-glucopyranose / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSaraswathi, N.T. / Pannu, N.S. / Syakhovich, V.E. / Saurabh, A. / Bokut, S.B. / Moras, D. / Ruff, M.
CitationJournal: To Be Published
Title: Glycation restrains allosteric transition in hemoglobin: The molecular basis of oxidative stress under hyperglycemic conditions in diabetes
Authors: Saraswathi, N.T. / Pannu, N.S. / Syakhovich, V.E. / Saurabh, A. / Bokut, S.B. / Moras, D. / Ruff, M.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
S: Hemoglobin subunit alpha
T: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,34432
Polymers155,20310
Non-polymers7,14122
Water4,179232
1
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)64,79111
Polymers62,0814
Non-polymers2,7107
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)65,21615
Polymers62,0814
Non-polymers3,13411
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-95 kcal/mol
Surface area24020 Å2
MethodPISA
3
S: Hemoglobin subunit alpha
T: Hemoglobin subunit beta
hetero molecules

S: Hemoglobin subunit alpha
T: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,67512
Polymers62,0814
Non-polymers2,5948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11850 Å2
ΔGint-103 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)237.987, 59.267, 137.024
Angle α, β, γ (deg.)90.000, 125.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Hemoglobin subunit ... , 2 types, 10 molecules ACEGSBDFHT

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


Mass: 15150.353 Da / Num. of mol.: 5 / 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.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Sugars , 2 types, 4 molecules

#5: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose / Fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 250 molecules

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


Mass: 616.487 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 4000 / PH range: 6.7

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.954 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→112.13 Å / Num. obs: 69814 / % possible obs: 87 % / Redundancy: 3.1 % / Net I/av σ(I): 23.7 / Net I/σ(I): 23.7
Reflection shellResolution: 2.3→3.36 Å / Rmerge(I) obs: 0.386 / % possible all: 55.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HHO

1hho


Resolution: 2.3→112.13 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 17.233 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.506 / ESU R Free: 0.269
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 3020 5 %RANDOM
Rwork0.2033 ---
obs0.2053 57698 86.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 410.18 Å2 / Biso mean: 109.574 Å2 / Biso min: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å2-1.21 Å2
2--3.33 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 2.3→112.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10886 0 491 232 11609
Biso mean--58.5 52.23 -
Num. residues----1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01911747
X-RAY DIFFRACTIONr_bond_other_d00.0211094
X-RAY DIFFRACTIONr_angle_refined_deg1.9482.00216085
X-RAY DIFFRACTIONr_angle_other_deg3.85325468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87651418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44323.96447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.779151752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1291528
X-RAY DIFFRACTIONr_chiral_restr0.1420.21776
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02113213
X-RAY DIFFRACTIONr_gen_planes_other0.0390.022761
X-RAY DIFFRACTIONr_mcbond_it1.8062.7985702
X-RAY DIFFRACTIONr_mcbond_other1.7992.7975701
X-RAY DIFFRACTIONr_mcangle_it2.8714.1877110
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 128 -
Rwork0.386 2699 -
all-2827 -
obs--55.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4146-1.1885-0.87342.0713-0.04462.8263-0.0612-0.56030.5502-0.00410.1423-0.4247-0.17830.1768-0.08110.0163-0.00280.00130.1629-0.09620.1355-25.0157.42498.596
23.3046-1.7270.11.6298-0.11181.560.13280.3169-0.9435-0.0004-0.15920.27360.536-0.42730.02650.2099-0.1235-0.03430.2676-0.12570.362-40.731-16.64282.95
33.12640.32720.40851.72330.065310.83630.2194-0.37791.05740.00750.1979-0.1585-1.07871.8733-0.41730.1485-0.28280.17340.6103-0.33560.615912.17339.90311.178
43.4038-1.3669-0.33011.24720.08292.9055-0.218-0.6508-0.08260.28370.18670.1594-0.0004-0.56430.03130.07650.0410.05320.460500.0514-47.1192.268106.119
55.3185-0.17850.15522.20480.6683.03340.12061.00180.3192-0.1299-0.00190.0872-0.262-0.3874-0.11870.02990.07420.01160.45960.05450.0385-46.9864.46773.466
66.2987-3.13381.92363.8212-0.86525.16380.21021.42121.9608-0.2676-1.4175-1.6531-0.0612.54781.20730.03210.00910.12681.66060.85710.983715.54931.07772.663
79.3148-3.41232.80333.1838-1.9114.8014-0.5289-0.99210.66960.29760.0932-0.2613-0.34480.33530.43570.06240.027-0.01520.2538-0.04080.1161-4.78429.49985.36
83.2404-1.1051.04871.7047-0.72257.8619-0.2070.86630.8725-0.0523-0.6309-0.298-0.49691.26010.8380.1571-0.0311-0.03440.44570.32150.4214-10.54940.69555.457
94.5313-1.20372.15313.5051-0.98796.21630.68830.7791-0.629-0.5881-0.56840.24242.1311.4033-0.11990.97140.57650.09010.412-0.07030.2636-8.62716.66755.927
103.89140.4099-0.43520.35470.08311.04950.4356-0.74320.27090.17490.18450.02731.8393-0.3235-0.62010.4186-0.079-0.06190.4228-0.02440.2363-3.35722.21914.957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B12 - 146
2X-RAY DIFFRACTION2C1 - 141
3X-RAY DIFFRACTION3T1 - 146
4X-RAY DIFFRACTION4A1 - 141
5X-RAY DIFFRACTION5D1 - 146
6X-RAY DIFFRACTION6E3 - 139
7X-RAY DIFFRACTION7F1 - 146
8X-RAY DIFFRACTION8G2 - 140
9X-RAY DIFFRACTION9H1 - 146
10X-RAY DIFFRACTION10S1 - 141

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