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- PDB-9bcj: Crystal structure of human hemoglobin in complex with the HbpA re... -

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Basic information

Entry
Database: PDB / ID: 9bcj
TitleCrystal structure of human hemoglobin in complex with the HbpA receptor from Corynebacterium diphtheriae
Components
  • (Hemoglobin subunit ...) x 2
  • Membrane protein
KeywordsPROTEIN BINDING / Complex / Hemoglobin / heme / beta-sandwich
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 / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha / Membrane protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae NCTC 13129 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.691 Å
AuthorsMahoney, B.J. / Cascio, D. / Clubb, R.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI161828 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Molecular basis of hemoglobin binding and heme removal in Corynebacterium diphtheriae.
Authors: Mahoney, B.J. / Lyman, L.R. / Ford, J. / Soule, J. / Cheung, N.A. / Goring, A.K. / Ellis-Guardiola, K. / Collazo, M.J. / Cascio, D. / Ton-That, H. / Schmitt, M.P. / Clubb, R.T.
History
DepositionApr 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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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: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5639
Polymers52,9593
Non-polymers1,6046
Water4,846269
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Membrane protein
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,12718
Polymers105,9186
Non-polymers3,20812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area17660 Å2
ΔGint-153 kcal/mol
Surface area36630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.925, 58.925, 286.146
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

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Hemoglobin subunit ... , 2 types, 2 molecules AB

#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

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Protein , 1 types, 1 molecules C

#3: Protein Membrane protein


Mass: 21918.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A31S, TEV cleavage scar
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Gene: DIP2330 / Plasmid: pMAPLe4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6NEE5

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Non-polymers , 4 types, 275 molecules

#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG-2000 MME, 100 mM Tris, 240 mM TMAO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97903 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.691→19.596 Å / Num. obs: 43427 / % possible obs: 94.5 % / Redundancy: 11.33 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.198 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.0284 / Rrim(I) all: 0.0955 / AbsDiff over sigma anomalous: 0.749 / Net I/σ(I): 12.86 / Num. measured all: 492180 / % possible anomalous: 94.6 / % possible ellipsoidal: 94.5 / % possible ellipsoidal anomalous: 94.6 / % possible spherical: 75.1 / % possible spherical anomalous: 73.8 / Redundancy anomalous: 6.18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
5.227-19.5969.870.060531.812142521425217021700.999-0.0910.020.06390.69799.199.699.199.699.16.0399.6
4.116-5.22710.830.062233.122353323533217221720.998-0.2990.01950.06530.65910099.810099.81006.2199.8
3.579-4.11611.440.067431.932484724847217221720.998-0.3050.02070.07060.6761001001001001006.41100
3.24-3.57911.260.074926.912443924439217021700.992-0.2140.02340.07870.6871001001001001006.23100
2.998-3.2410.460.088321.142271822718217121710.997-0.1680.02850.0930.71399.599.599.599.599.55.7499.5
2.816-2.99811.50.105117.862497524975217221720.998-0.0870.03280.11020.7231001001001001006.27100
2.671-2.81611.750.126815.582551625516217221720.997-0.10.03860.13270.7311001001001001006.41100
2.552-2.67111.960.158712.432594625946217021700.996-0.1480.04790.1660.7321001001001001006.49100
2.45-2.55212.180.186511.162646626466217321730.994-0.0690.05550.19480.7591001001001001006.57100
2.363-2.4512.320.22189.612675526755217121710.993-0.1220.06570.23160.7251001001001001006.64100
2.288-2.36312.30.26758.32672726727217321730.992-0.040.07880.27910.7741001001001001006.63100
2.221-2.28810.520.29376.822282222822217021700.986-0.0270.09390.30890.77299.910099.910099.95.62100
2.16-2.22111.280.3516.162449224492217121710.988-0.0480.10860.36780.7661001001001001006.04100
2.106-2.1611.730.45555.142545925459217021700.979-0.0520.13770.47630.7710099.910099.91006.2399.9
2.057-2.10611.870.54954.472577525775217221720.974-0.0330.16460.5740.7911001001001001006.35100
2.012-2.05712.010.66163.852607526075217221720.96-0.0060.19660.69070.78598.598.498.598.498.56.3998.4
1.967-2.01212.050.86333.152617026170217121710.9390.0160.25530.90090.80792.992.492.992.492.96.492.4
1.91-1.96711.840.86363.152571925719217221720.932-0.0080.25740.90190.80172.672.872.665.965.26.3372.8
1.835-1.9111.130.90092.862416624166217221720.918-0.0710.27650.94350.77779.279.279.243426.0179.2
1.691-1.8358.361.18941.811815518155217121710.695-0.0580.4221.26630.79973.270.473.217.6174.5470.4

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Processing

Software
NameVersionClassification
XDSBUILT=20220820data reduction
XSCALEdata scaling
STARANISOdata scaling
PHASER2.8.3phasing
BUCCANEER1.6.5model building
Coot0.9.3model building
BUSTER2.10.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.691→19.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.133 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 2174 -RANDOM
Rwork0.1885 ---
obs0.1898 43427 75.1 %-
Displacement parametersBiso mean: 32.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.3796 Å20 Å20 Å2
2--0.3796 Å20 Å2
3----0.7592 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.691→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 109 269 3960
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093805HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.915182HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1258SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes696HARMONIC5
X-RAY DIFFRACTIONt_it3805HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion475SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3383SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion15.3
LS refinement shellResolution: 1.691→1.78 Å
RfactorNum. reflection% reflection
Rfree0.2632 42 -
Rwork0.274 --
obs--11.35 %
Refinement TLS params.

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)
11.0356-0.2933-0.33130.71930.33981.85370.01250.05840.23750.05840.04910.09380.23750.0938-0.06160.00710.0295-0.0045-0.01960.0074-0.0289-32.8658-45.868512.3822
20.70760.3296-0.34562.1749-0.78252.98810.06760.1641-0.60760.1641-0.0167-0.1467-0.6076-0.1467-0.05090.09420.05010.0178-0.1114-0.0233-0.0401-39.3228-15.78143.2935
31.35710.0205-0.52721.2499-1.14183.6231-0.02740.0749-0.02980.07490.1992-0.4559-0.0298-0.4559-0.1719-0.10390.00940.00820.08940.0576-0.0727-59.1084-47.290131.3708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 141
2X-RAY DIFFRACTION1{ A|* }A201
3X-RAY DIFFRACTION2{ B|* }B1 - 142
4X-RAY DIFFRACTION2{ B|* }B201
5X-RAY DIFFRACTION3{ C|* }C36 - 228

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