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- PDB-6tb2: Structure of human haptoglobin-hemoglobin bound to S. aureus IsdH -

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Basic information

Entry
Database: PDB / ID: 6tb2
TitleStructure of human haptoglobin-hemoglobin bound to S. aureus IsdH
Components
  • Cell wall surface anchor family protein
  • Haptoglobin
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsMETAL TRANSPORT / Hemoglobin receptor / heme acquisition / inhibitor
Function / homology
Function and homology information


negative regulation of hydrogen peroxide catabolic process / zymogen activation / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / antioxidant activity ...negative regulation of hydrogen peroxide catabolic process / zymogen activation / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / antioxidant activity / oxygen transport / immune system process / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / acute-phase response / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / defense response / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / specific granule lumen / 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 / defense response to bacterium / iron ion binding / inflammatory response / serine-type endopeptidase activity / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / YSIRK type signal peptide ...Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / YSIRK type signal peptide / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / YSIRK Gram-positive signal peptide / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Iron-regulated surface determinant protein H / Haptoglobin / Hemoglobin subunit beta / Hemoglobin subunit alpha / Iron-regulated surface determinant protein H
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMikkelsen, J.H. / Andersen, C.B.F.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR191-2015-733 Denmark
CitationJournal: To Be Published
Title: Haptoglobin is an inhibitor of Staphylococcus aureus IsdH-mediated heme-sequestering
Authors: Mikkelsen, J.H. / Runager, K.S. / Andersen, C.B.F.
History
DepositionOct 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
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: Haptoglobin
D: Cell wall surface anchor family protein
E: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0057
Polymers142,7725
Non-polymers1,2332
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-83 kcal/mol
Surface area55140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.100, 86.770, 217.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: Protein Haptoglobin / Zonulin


Mass: 29787.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HP / Plasmid: pcDNA5 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00738
#4: Protein Cell wall surface anchor family protein / Haptoglobin-binding heme uptake protein HarA / Heme transporter HarA


Mass: 40971.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: isdH, EP54_00915, EQ90_06455, HMPREF3211_02292, NCTC10654_01789
Plasmid: pET22B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E8IWL6, UniProt: Q2FXJ2*PLUS
#5: 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
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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic dihydrate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→78.46 Å / Num. obs: 35967 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 117.56 Å2 / Rrim(I) all: 0.084 / Net I/σ(I): 15.12
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 3445 / Rrim(I) all: 2.96

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WJG,4XS0

4wjg

4xs0


Resolution: 2.9→78.46 Å / SU ML: 0.4993 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.5822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2701 1994 5.54 %
Rwork0.235 33969 -
obs0.237 35963 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 134.36 Å2
Refinement stepCycle: LAST / Resolution: 2.9→78.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9621 0 86 0 9707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006410003
X-RAY DIFFRACTIONf_angle_d1.134513632
X-RAY DIFFRACTIONf_chiral_restr0.06271491
X-RAY DIFFRACTIONf_plane_restr0.00611739
X-RAY DIFFRACTIONf_dihedral_angle_d8.245936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.39251280.41992128X-RAY DIFFRACTION89.03
2.97-3.050.43271430.39422362X-RAY DIFFRACTION100
3.05-3.140.39081430.35922421X-RAY DIFFRACTION100
3.14-3.240.38931350.34812432X-RAY DIFFRACTION100
3.24-3.360.34081490.31972425X-RAY DIFFRACTION100
3.36-3.490.31461350.32022401X-RAY DIFFRACTION100
3.49-3.650.33311490.30282444X-RAY DIFFRACTION99.96
3.65-3.840.34691380.28932407X-RAY DIFFRACTION100
3.84-4.080.3051470.26552428X-RAY DIFFRACTION100
4.08-4.40.30711440.23892451X-RAY DIFFRACTION100
4.4-4.840.2371400.20492474X-RAY DIFFRACTION100
4.84-5.540.27291440.21212465X-RAY DIFFRACTION100
5.54-6.980.25851480.25152494X-RAY DIFFRACTION99.85
6.98-78.460.2111510.17942637X-RAY DIFFRACTION99.71
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)
16.02043496112-4.445729500472.9839631012210.2478965403-1.763502475373.189611547510.249580618532-0.0019983763755-0.873530628373-0.119398524844-0.06605587532161.39259847950.276020603595-0.227668160909-0.1557359142080.5411354950680.02750213345730.1746273287211.051725134560.189301090750.8528221270282.83003253575-5.69143662869-26.7295558862
210.0367638461-3.7818146464.033016252163.156177066640.4983159511274.170509084120.693875066669-0.141535983497-0.655285018770.01621957271690.1957714702040.480361650291.689711626240.929876400892-0.5100888042331.188795864010.04667081368850.2943306749340.9999815132170.1953592764581.0069958727616.3661434304-17.2544971003-17.4689208041
38.569399402430.888320366963-1.126981037546.261602208640.9168279960635.06600683796-0.483476094967-1.25323662893-2.07349569873.18323523316-0.3775082450480.4653674192151.08182991958-0.6258083407310.2367623616730.982837216473-0.1003522885830.3101228555421.321531155040.2259460549641.17945462643.68632458929-12.4747117491-15.4889216875
42.14951090996-0.837689464434-0.1446863844415.792194723660.4853676752745.70487592822-0.889531015266-1.969652599191.746228253921.347647039790.413482012379-0.788217533952-1.11956365009-0.8459506742910.03231691805081.1892367253-0.01734985573450.1695331684361.109341029340.02751326444811.075339624912.53619882550.729752864087-13.2401949364
56.35273113373-0.2134341576030.5031003607215.364006208430.1966704863474.810607215380.4991222820860.7733848765080.2607684214660.210074455764-0.2539135362890.242612170332-0.00444151595251-0.2265395126080.06516784579590.6799836375410.07300266703070.2931341375940.8205220822890.1594264341690.83969693561410.4591498256-4.51492867386-26.8571999225
65.41487547601-5.1215162314-1.430262570879.2804382839-3.598354003095.537933572010.550007709760.0325975084956-1.586074496141.56291067933-0.3699486994650.955087696425-0.9856590102440.2885888923410.1986533233051.21915648701-0.244151138974-0.00852204089231.17548355648-0.003235916098291.1270644208813.7939936643-28.3053714195-37.4365398929
78.48730270473.042501350271.913649752985.612139710331.934656604744.339444411220.02980155140871.623078514820.584101887737-0.8971846284690.256644838744-0.380342553798-0.6389402786570.899055145061-0.2870108896380.8247302792470.1961492052970.2048309175991.194786110770.2960685419020.99783443271814.8971140063-2.69376219742-45.9152250581
82.818100667713.077971600170.07278100465319.10058442904-4.070022997183.90013766663-0.8733000108910.181195593339-0.490686686223-1.290806712190.877727273155-2.97409859593-0.1167472118450.229013691714-0.04451542009491.23223383950.09110605714040.1433614877041.48164372865-0.3712937089021.4200704867923.6405302374-17.0615471885-46.8841443334
93.7144541785-0.921811188062.132323451577.746013082372.077836805627.75958822137-0.113808672304-0.1117518764680.694407963224-0.7809251449860.152497546305-0.732216950960.1543108520530.0314176898719-0.03382103709510.6157910616240.13137003750.1928963158080.8068005494380.1162194392930.76116913246518.6309578204-15.0864455717-37.2926222626
104.252213014573.82295250163-0.3982743880034.96464216682-2.660769517074.76421237117-0.04673374225380.266118035901-0.6833337616660.2276202274490.133026984576-0.738168927616-0.1191141873890.428194906238-0.212365705410.8066430996580.04551865815330.194780136430.8471814483190.01573737449471.0909683526538.90678195051.63556370906-29.4181699881
114.77691618521.810170972561.597460626864.191042587831.518447580856.454526564390.260886791014-1.001466177430.2884459715261.322164637270.175163583577-0.2925861042220.58955647634-0.601714741364-0.5245567149280.9660156746730.00265612571784-0.03877608834490.937381821998-0.01661102399911.0726646210740.65240053644.06084678537-11.5053478095
125.950140742022.66453492251.579051361245.887189139060.2451803030933.67545741666-0.4251427629130.336122308873-0.7830691983370.8954538688180.372362650277-0.8169682981671.990090597611.98420966613-0.03237711025181.00375301560.203406796310.07374650716331.142221563950.03177037784721.5805865620645.1193197733-5.60191542049-21.3373938756
135.89751851792.185021736542.741095929587.26970446786-2.446103423797.625013501240.7651067027640.3532509246790.1173976678450.0756199203061-0.222164298028-0.7076078756290.2651185152280.87781095267-0.5218742024490.888485577596-0.0176240114925-0.009701058284110.850867967381-0.02605551821370.93557511449545.86607599536.75852921161-18.3071885168
144.512780376161.54691920612-3.342590281592.44080003757-1.374321751366.564346876670.1671762745870.05281604377030.6240982268020.1670337115440.03436069363290.00300919041943-0.3914604814850.134316025181-0.211333596190.7289125597870.09941293415370.1942248697920.8268724293790.05887718316370.99826868943331.8147442957.68881668241-30.5277455831
158.2772402826-0.4464879401562.037624775213.718180415342.11003807591.677301433690.422511590776-0.2155092190512.40855418370.033767099980.2771673228470.135508346477-0.555475747919-0.0946559621492-0.6115840405851.132470430830.04824364635970.4307501688711.04423092966-0.04187212490141.458812764521.113085386219.6855167137-18.3010046381
165.8128310621-0.5828034092334.812758315683.515695742232.376062257044.858191300080.01046979266480.7136246416480.719269062617-0.4079370748130.0309852049297-0.756635995013-0.166085142339-0.0237719875044-0.02967870607990.6747071131740.131798082450.3804841572430.9795077700890.2345967137141.348624496432.022805420410.2737165154-32.3882982772
178.59507028721-2.01302534804-0.9373833757784.65102864381-1.07212023411.987427469960.1145071792290.385525250140.9790657720570.45212644460.253342667565-0.553164438169-0.8106979173990.342704154426-0.350789210710.939569671478-0.03227313679390.3408669273330.819717378687-0.07447343677251.0535115442237.093152415713.94545523-21.5800107888
183.008445977620.8430674714191.758083644171.99756401525-0.3141408896056.137646309110.188949327355-0.02876688607290.4825166726590.247593288348-0.3359091268480.263486101364-0.275294012847-0.4677967104070.2005017805990.7545030088960.1199194669430.2953976407160.9183012447530.1763282455371.375535247-8.8095520776615.7493042676-19.9719230305
195.30663379515.50387500718-2.400311897656.59652725823-5.048013232526.00166762045-0.128903910568-0.266575979741-0.960893206706-0.333961629305-0.634919547084-1.127720905690.06140150405841.010302819820.7059171626690.8428374737170.03391950488270.03788299244351.000272207950.2028237876440.947796854471-2.92167067467-15.57973845178.68919101338
207.36737186121-1.33972360794-3.127751407355.207378979492.459201838085.951447779750.006880033534390.386759537544-0.665147924188-0.1092785487830.08435944434710.5877609997280.588848413754-0.00132553538082-0.07636662153750.768282179404-0.1131671456410.04770099558230.88516954599-0.08701546966621.2930001242917.2965924336-41.360919056-51.0018507949
213.260481085-0.706202200361-2.462164378457.58883949535-1.103883220241.662185197190.5546025012590.6950586856471.21345476901-1.673945760320.173336567099-1.27830047885-1.07645240841-0.15132483302-0.8015480859672.08021954692-0.008063328070530.7018343294581.57911912615-0.09699966262481.5186043825830.7230394587-3.61117845613-67.8649783847
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 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 94 )
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 141 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 17 )
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 57 )
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 94 )
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 146 )
10X-RAY DIFFRACTION10chain 'C' and (resid 148 through 190 )
11X-RAY DIFFRACTION11chain 'C' and (resid 191 through 220 )
12X-RAY DIFFRACTION12chain 'C' and (resid 221 through 232 )
13X-RAY DIFFRACTION13chain 'C' and (resid 233 through 267 )
14X-RAY DIFFRACTION14chain 'C' and (resid 268 through 305 )
15X-RAY DIFFRACTION15chain 'C' and (resid 306 through 341 )
16X-RAY DIFFRACTION16chain 'C' and (resid 342 through 367 )
17X-RAY DIFFRACTION17chain 'C' and (resid 368 through 406 )
18X-RAY DIFFRACTION18chain 'D' and (resid 323 through 505 )
19X-RAY DIFFRACTION19chain 'D' and (resid 506 through 655 )
20X-RAY DIFFRACTION20chain 'E' and (resid 323 through 489 )
21X-RAY DIFFRACTION21chain 'E' and (resid 490 through 655 )

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