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- PDB-9h0b: Crystal structure of the Porcine Hemagglutinating Encephalomyelit... -

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Basic information

Entry
Database: PDB / ID: 9h0b
TitleCrystal structure of the Porcine Hemagglutinating Encephalomyelitis Virus (PHEV) receptor binding domain in complex with porcine DPEP1.
Components
  • Dipeptidase 1
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / RBD Receptor Spike Entry
Function / homology
Function and homology information


Aflatoxin activation and detoxification / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene D4 catabolic process / membrane dipeptidase / antibiotic metabolic process / GPI anchor binding / glutathione catabolic process / modified amino acid binding / homocysteine metabolic process / leukotriene metabolic process ...Aflatoxin activation and detoxification / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene D4 catabolic process / membrane dipeptidase / antibiotic metabolic process / GPI anchor binding / glutathione catabolic process / modified amino acid binding / homocysteine metabolic process / leukotriene metabolic process / dipeptidase activity / metallodipeptidase activity / microvillus membrane / side of membrane / cellular response to nitric oxide / cellular response to calcium ion / negative regulation of cell migration / beta-lactamase activity / beta-lactamase / cellular response to insulin stimulus / apical part of cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / endoplasmic reticulum membrane / host cell plasma membrane / virion membrane / proteolysis / extracellular space / zinc ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Membrane dipeptidase, active site / Renal dipeptidase active site. / Spike (S) protein S1 subunit, receptor-binding domain, HEV / Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Metal-dependent hydrolase ...Membrane dipeptidase, active site / Renal dipeptidase active site. / Spike (S) protein S1 subunit, receptor-binding domain, HEV / Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Metal-dependent hydrolase / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Dipeptidase 1 / Spike glycoprotein
Similarity search - Component
Biological speciesSus scrofa (pig)
Porcine hemagglutinating encephalomyelitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFernandez, I. / Rey, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: DPEP1 is the cell receptor of thePorcine Hemagglutinanting Encephalomyelitis Virus
Authors: Dufloo, J. / Fernandez, I. / Rey, F.A. / Sanjuan, R.
History
DepositionOct 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Dipeptidase 1
A: Spike glycoprotein
C: Dipeptidase 1
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,53128
Polymers144,3174
Non-polymers4,21424
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.720, 73.010, 136.620
Angle α, β, γ (deg.)90.000, 91.940, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "D"
d_1ens_2chain "B"
d_2ens_2chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASPASPTHRTHRAB327 - 6031 - 277
d_12ens_1NAGNAGNAGNAGAR701
d_13ens_1NAGNAGNAGNAGAS702
d_21ens_1ASPASPTHRTHRDD327 - 6031 - 277
d_22ens_1NAGNAGNAGNAGDY701
d_23ens_1NAGNAGNAGNAGDZ702
d_11ens_2ASPASPSERSERBA17 - 3841 - 368
d_12ens_2NAGNAGNAGNAGEE1
d_13ens_2NAGNAGNAGNAGEE2
d_14ens_2NAGNAGNAGNAGFF1
d_15ens_2NAGNAGNAGNAGFF2
d_16ens_2FUCFUCFUCFUCFF3
d_17ens_2FUCFUCFUCFUCEE3
d_21ens_2ASPASPSERSERCC17 - 3841 - 368
d_22ens_2NAGNAGNAGNAGGG1
d_23ens_2NAGNAGNAGNAGGG2
d_24ens_2NAGNAGNAGNAGHH1
d_25ens_2NAGNAGNAGNAGHH2
d_26ens_2FUCFUCFUCFUCHH3
d_27ens_2FUCFUCFUCFUCGG3

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.998946639943, -0.0357651485265, -0.0287482990415), (-0.035650348554, -0.999354210245, 0.00449612197657), (-0.0288905381548, -0.00346649906011, -0.999576570448)2.29541059993, -12.3766298978, 70.6491974077
2given(0.996014019931, -0.0533196874241, 0.0715058251797), (-0.0534228931332, -0.998571867134, -0.000469741871219), (0.0714287518504, -0.00335217856749, -0.997440071537)-2.7790889908, -11.8297968602, 68.5052033787

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Components

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Protein , 2 types, 4 molecules BCAD

#1: Protein Dipeptidase 1 / Beta-lactamase / Microsomal dipeptidase / Renal dipeptidase


Mass: 41029.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DPEP1, RDP / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: P22412, membrane dipeptidase, beta-lactamase
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 31128.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine hemagglutinating encephalomyelitis virus
Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q2QKN3

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Sugars , 2 types, 8 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 522 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES (pH 6.0), 0.2 M zinc acetate, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.25→48.33 Å / Num. obs: 90076 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.238 / Net I/σ(I): 8.4
Reflection shellResolution: 2.25→2.28 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 6350 / CC1/2: 0.454 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.33 Å / SU ML: 0.3518 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 4502 5 %
Rwork0.198 85564 -
obs0.1999 90066 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.82 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9896 0 224 506 10626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005110328
X-RAY DIFFRACTIONf_angle_d0.7514044
X-RAY DIFFRACTIONf_chiral_restr0.04831594
X-RAY DIFFRACTIONf_plane_restr0.00631828
X-RAY DIFFRACTIONf_dihedral_angle_d11.9543946
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BAX-RAY DIFFRACTIONTorsion NCS0.407565767191
ens_2d_2ABX-RAY DIFFRACTIONTorsion NCS0.258582352429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.47431350.39142580X-RAY DIFFRACTION90.2
2.28-2.30.39861490.35232827X-RAY DIFFRACTION99.93
2.3-2.330.34771480.33162819X-RAY DIFFRACTION99.93
2.33-2.360.32891510.31012866X-RAY DIFFRACTION99.9
2.36-2.390.32631490.29522814X-RAY DIFFRACTION99.93
2.39-2.430.28811490.26932862X-RAY DIFFRACTION99.83
2.43-2.460.30271500.26052850X-RAY DIFFRACTION99.97
2.46-2.50.31151510.26092853X-RAY DIFFRACTION99.93
2.5-2.540.28631510.23982874X-RAY DIFFRACTION99.97
2.54-2.580.2871490.23662836X-RAY DIFFRACTION100
2.58-2.620.25121490.22822818X-RAY DIFFRACTION99.97
2.62-2.670.28261480.2272821X-RAY DIFFRACTION99.93
2.67-2.720.26811510.232858X-RAY DIFFRACTION99.97
2.72-2.780.27031500.23352863X-RAY DIFFRACTION100
2.78-2.840.27621490.23662825X-RAY DIFFRACTION99.93
2.84-2.90.28191520.24822877X-RAY DIFFRACTION99.97
2.9-2.980.27141490.21492841X-RAY DIFFRACTION100
2.98-3.060.28371500.2142852X-RAY DIFFRACTION100
3.06-3.150.25131520.2042876X-RAY DIFFRACTION100
3.15-3.250.23921500.20122847X-RAY DIFFRACTION100
3.25-3.360.22041500.19412868X-RAY DIFFRACTION99.97
3.36-3.50.25981520.19342876X-RAY DIFFRACTION100
3.5-3.660.22021510.18582864X-RAY DIFFRACTION99.97
3.66-3.850.21571510.1682870X-RAY DIFFRACTION99.97
3.85-4.090.18891510.15372871X-RAY DIFFRACTION100
4.09-4.410.15921510.14182880X-RAY DIFFRACTION99.93
4.41-4.850.17221530.14162903X-RAY DIFFRACTION99.93
4.85-5.550.18841510.15982872X-RAY DIFFRACTION99.97
5.55-6.990.19881540.17682914X-RAY DIFFRACTION100
6.99-48.330.19911560.18052987X-RAY DIFFRACTION99.53
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)
15.8957043442.22217369505-3.266204439183.32104392089-2.183590009984.40812627405-0.04854157874480.480642908499-0.147810159947-0.3455256615170.00443787594371-0.1412843304690.410267247248-0.2107030504580.1167090179580.4191625663770.0429583239531-0.06195221992790.264561721201-0.03347592684830.2458682366557.17593945766-15.461660447711.0022556066
20.75665249108-0.573836493321-0.8066309232041.587693205920.2716860555482.289083502860.08344860747220.1313167750560.0791583949742-0.161546175984-0.0122282488008-0.08379610578310.165505171442-0.0747440515895-0.0666450317360.3354046306650.0102017700406-0.04190925331310.2892101298390.02413856969920.2812551595054.74388664556-9.7241624108221.5481295162
31.76536161251-0.1805834121281.271558012150.4067177740590.3381969003634.19921831210.1172542686920.07272373820350.133986736113-0.269171767590.0008697319842710.0856744198294-0.353521596762-0.250337426362-0.09673242019670.4451180500930.048260879238-0.01324836981580.237246643490.08625262846240.305515944011-4.146902018437.7877275347115.8147340513
41.453633893980.2162611688830.2497585264150.9941933245740.3842236247882.805042103750.1139707124150.2148635689610.117475663413-0.4423239848530.00536354329671-0.05353969015530.02426526990820.019753947614-0.1103083614250.5330540809730.04159750554470.01158274389850.2948787303540.05743615925230.2976930431316.6072973329-1.436978182363.10996252053
56.728860435763.33976607639-1.566362057914.0963529664-1.20489368621.90840018137-0.1730476393370.06390738007410.351346967421-0.1149981269330.2514709512730.521264642021-0.349143176735-0.269662404666-0.08594242370870.3157369020130.0719680117398-0.03833457790610.2822140827180.0002527781410440.250364942091-6.620961884977.920843783735.9408310913
63.815828831070.821712841563-1.348587560682.156690666591.353689379824.05298078330.0558135641742-0.0519480758751-0.18520344549-0.295422322435-0.00955366818575-0.5434056478440.5196899928780.621810226358-0.06216052892150.5120772957790.156431461678-0.01112847044250.5721718254470.05711752189060.42669136828167.7173141659-37.035878369324.8369696247
74.43415676427-3.349668272191.802609067293.40105456573-1.854640699820.8957937893440.02833829308180.1436108360530.3254503474220.0353123448109-0.0871407841702-0.242109619741-0.0980617943803-0.01464546001180.06758052351860.3678207690960.0410122616850.0180673007970.4478838652950.02973894492780.3742544496747.7895411693-18.598074220922.7890126288
81.99998613987-5.090896988547.668581951351.999996206781.873208186572.000012315891.59674364175-7.089658597343.60811608574-3.066580851721.972087054934.32181696404-1.22082090083.7025599926-3.59623852381.00372865940.32915159485-0.1396111155621.18641793801-0.3509499731810.80473956266476.6585812078-46.281038902123.0878713341
92.61044742702-1.505374427162.520590466393.76281286605-2.048552002525.034085062950.060700824792-0.1140368940260.1319169570320.126587493825-0.0283127916236-0.0754983054389-0.249615801469-0.100836763714-0.0166623333990.190399959432-0.02229167827840.03243704255370.225186402721-0.02926101569930.2941555643416.031415331263.2524806838858.0783769533
10-0.03894520350740.1220515646910.2018540586481.58082285940.1473128103181.833152688920.055607069190.006485224034420.041468100364-0.0385986144935-0.0152079798032-0.0316663992303-0.0199800555515-0.0042577504503-0.03975000423240.248091153421-0.00212442617036-0.01545321409140.2645880784470.01636610749030.3102501343684.04703739022-2.3356254724647.3688547967
111.57500096626-0.253600635638-1.582845595010.9320828763450.3718649501894.645339705710.06104256216680.112813861021-0.1127042692770.0204389616599-0.0169955833530.1393075539080.296762798124-0.311236720103-0.03677011951630.305557637646-0.0442323240811-0.07509023273790.2294156724480.03816564290640.321452622902-6.18655748897-19.345257471952.4533235875
120.769218044034-0.518368713012-0.05455957193432.086931609580.3305641628851.572633329730.0165134764544-0.096550927668-0.0345638789330.3089974009190.0423188860961-0.09733768541650.03688723767270.0236992654298-0.06286264253390.283294618167-0.0217540103781-0.06288654829650.2388492486210.02092983961770.2900890449014.11545010142-10.660424221865.8981676144
136.33023092092-1.401848489371.765935865772.29808623445-0.8483128874972.59959413870.03883217846630.213193403494-0.382136649375-0.2178691327490.142107418970.3105271229650.287234808985-0.277277695713-0.2036576362880.346147991198-0.0393939585692-0.06360683442150.330364348628-0.02465277182890.303301568392-7.25078955531-19.387526203832.176270293
143.42907382599-0.3035530472541.74837254252.79283433755-0.1934935661654.10169391660.1118712071220.3255133605220.1049148712870.125989537236-0.121476088759-0.312006364951-0.286880528950.685479497331-0.01196818560680.298152017638-0.0557270748102-0.03501704368320.510975805583-0.0180225636990.41663030926565.015723420721.315173854742.888744267
153.34294881732.65600611975-0.7668178172921.77221027608-0.8795332937170.5321549497970.00588701594649-0.0574150900301-0.321176557798-0.0195552577201-0.0954642858908-0.2415668579470.02559556221240.06350825178770.09711586221170.3150134566350.0281558613623-0.1013170456490.349927483465-0.04528369584790.53838709818246.30308579753.6735882671747.1263816002
161.999990921871.999970499996.128549663981.999982494172.000012933472.00000629438-5.43455687979-1.364615904916.348436843085.299748491414.48863101655-7.34947009298-0.0304048145198-1.938693895110.9859935888560.851603053128-0.0734582513864-0.1972942473561.53745530108-0.2346809533251.0072215821675.96724187331.835874537844.8758532602
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 17 through 57 )CC17 - 571 - 41
22chain 'C' and (resid 58 through 165 )CC58 - 16542 - 149
33chain 'C' and (resid 166 through 249 )CC166 - 249150 - 233
44chain 'C' and (resid 250 through 356 )CC250 - 356234 - 340
55chain 'C' and (resid 357 through 384 )CC357 - 384341 - 368
66chain 'D' and (resid 327 through 388 )DD327 - 3881 - 62
77chain 'D' and (resid 389 through 602 )DD389 - 60263 - 276
88chain 'D' and (resid 603 through 603 )DD603277
99chain 'B' and (resid 17 through 57 )BA17 - 571 - 41
1010chain 'B' and (resid 58 through 165 )BA58 - 16542 - 149
1111chain 'B' and (resid 166 through 249 )BA166 - 249150 - 233
1212chain 'B' and (resid 250 through 356 )BA250 - 356234 - 340
1313chain 'B' and (resid 357 through 384 )BA357 - 384341 - 368
1414chain 'A' and (resid 327 through 405 )AH327 - 4051 - 79
1515chain 'A' and (resid 406 through 602 )AH406 - 60280 - 276
1616chain 'A' and (resid 603 through 603 )AH603277

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