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- PDB-5ucu: STRUCTURAL AND MECHANISTIC INSIGHTS INTO HEMOGLOBIN-CATALYZED HYD... -

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Basic information

Entry
Database: PDB / ID: 5ucu
TitleSTRUCTURAL AND MECHANISTIC INSIGHTS INTO HEMOGLOBIN-CATALYZED HYDROGEN SULFIDE OXIDATION AND THE FATE OF POLYSULFIDE PRODUCTS
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Mechanism of hemoglobin catalyzed H2S oxidation
Function / homology
Function and homology information


nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid 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 / regulation of blood pressure / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / Factors involved in megakaryocyte development and platelet production / tertiary granule lumen / ficolin-1-rich granule lumen / blood microparticle / 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 domain profile. / Globin-like / Globin / Globin ...: / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HYDROSULFURIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsVitvitsky, V. / Yadav, P.K. / An, S. / Seravalli, J. / Cho, U.-S. / Banerjee, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112455 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK111465 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and Mechanistic Insights into Hemoglobin-catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products.
Authors: Vitvitsky, V. / Yadav, P.K. / An, S. / Seravalli, J. / Cho, U.S. / Banerjee, R.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.3Nov 27, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3767
Polymers31,0412
Non-polymers1,3355
Water3,045169
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,75214
Polymers62,0814
Non-polymers2,67010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area11940 Å2
ΔGint-150 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.766, 53.766, 193.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-392-

HOH

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Components

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


Mass: 15150.353 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHydrogen Sulfide H2S A203 forms hydrogen bond with carboxyl groups of the polypeptide

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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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 10% Toluene, 2.3 M K2HPO4/NH2PO4 pH, 7.2.

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: under liquid N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.797→50 Å / Num. obs: 27405 / % possible obs: 99.9 % / Redundancy: 11.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.025 / Net I/σ(I): 28.97
Reflection shellResolution: 1.797→1.86 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.463 / Mean I/σ(I) obs: 2.8 / CC1/2: 0.558 / Rrim(I) all: 0.654

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D7O

3d7o


Resolution: 1.797→37.303 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 2000 7.3 %10%
Rwork0.1857 ---
obs0.1883 27405 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.797→37.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 89 169 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042390
X-RAY DIFFRACTIONf_angle_d0.6883292
X-RAY DIFFRACTIONf_dihedral_angle_d6.3911832
X-RAY DIFFRACTIONf_chiral_restr0.041358
X-RAY DIFFRACTIONf_plane_restr0.005414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7972-1.84220.32831370.27131731X-RAY DIFFRACTION98
1.8422-1.8920.30551390.2441779X-RAY DIFFRACTION100
1.892-1.94770.26171410.20791778X-RAY DIFFRACTION100
1.9477-2.01050.21221390.19631778X-RAY DIFFRACTION100
2.0105-2.08240.2081410.18731781X-RAY DIFFRACTION100
2.0824-2.16570.18691410.18921795X-RAY DIFFRACTION100
2.1657-2.26430.23171400.18221789X-RAY DIFFRACTION100
2.2643-2.38370.22791420.18431806X-RAY DIFFRACTION100
2.3837-2.5330.2481420.18761801X-RAY DIFFRACTION100
2.533-2.72850.21591440.19671821X-RAY DIFFRACTION100
2.7285-3.0030.25121440.19551830X-RAY DIFFRACTION100
3.003-3.43720.22871450.18921841X-RAY DIFFRACTION100
3.4372-4.32950.21051480.15931879X-RAY DIFFRACTION100
4.3295-37.31130.20351570.18571996X-RAY DIFFRACTION99
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)
12.9053-0.2139-0.20832.0461-0.19460.89120.09550.54990.063-0.2569-0.0644-0.3268-0.06350.20080.01390.22530.03740.03210.445-0.03930.2323-13.920231.2329-18.9182
22.41850.64530.8162.0988-0.76742.13180.05410.57990.4991-0.24850.03160.3186-0.086-0.044-0.1110.23430.05140.02580.37620.03730.2851-26.477436.8917-20.7698
36.3834-2.2435-2.46352.84440.16984.98280.3797-0.8230.68380.6301-0.0482-0.6143-0.22160.3377-0.17710.3122-0.0807-0.03910.4017-0.0790.3988-9.569844.8447-9.9396
46.22244.5778-1.87338.2332-1.86933.94190.3801-0.03751.03470.9810.06320.3916-1.4572-0.6382-0.44780.44470.08290.08490.2760.02130.4001-25.971545.5975-9.195
52.6510.94480.25312.2184-1.17551.33960.13680.1978-0.03040.1088-0.1561-0.12150.01380.1468-0.0150.1845-0.0065-0.00290.3003-0.03250.1845-16.474530.5603-11.8355
64.4452-2.1231.60854.0372-0.95453.44860.42480.4018-0.7117-0.6388-0.02180.23330.67040.0071-0.2770.4958-0.0628-0.06720.3956-0.17780.4435-27.37549.4703-19.0134
71.4105-0.4311-0.6382.29060.01852.8887-0.1005-0.0299-0.47460.33040.018-0.31190.73820.43280.03890.40940.1371-0.03290.2943-0.05210.3572-12.631711.6173-4.3584
83.33181.61830.19114.02610.91393.41560.1059-0.2654-0.47351.0306-0.18340.88060.9591-0.521-0.10590.6962-0.02590.04560.2913-0.02460.5522-28.05848.88822.4945
91.86450.20630.56662.9027-0.27981.69310.05820.2319-0.30510.097-0.03540.13130.1755-0.1261-0.03680.23980.0019-0.02590.2545-0.0940.3122-24.588216.8482-10.6832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 94 )
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 140 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 22 )
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 77 )
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 99 )
9X-RAY DIFFRACTION9chain 'B' and (resid 100 through 146 )

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