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- PDB-8ybf: Crystal structure of canine distemper virus hemagglutinin -

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Basic information

Entry
Database: PDB / ID: 8ybf
TitleCrystal structure of canine distemper virus hemagglutinin
ComponentsHemagglutinin glycoprotein
KeywordsVIRAL PROTEIN / hemagglutinin / viral entry
Function / homology
Function and homology information


host cell membrane / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin glycoprotein
Similarity search - Component
Biological speciesMorbillivirus canis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFukuhara, H. / Yumoto, K. / Sako, M. / Kajikawa, M. / Ose, T. / Hashiguchi, T. / Kamishikiryo, J. / Maita, N. / Kuroki, K. / Maenaka, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H02384 Japan
Japan Society for the Promotion of Science (JSPS)22121007 Japan
CitationJournal: Elife / Year: 2024
Title: Glycan-shielded homodimer structure and dynamical features of the canine distemper virus hemagglutinin relevant for viral entry and efficient vaccination
Authors: Fukuhara, H. / Yumoto, K. / Sako, M. / Kajikawa, M. / Ose, T. / Kawamura, M. / Yoda, M. / Chen, S. / Ito, Y. / Takeda, S. / Mwaba, M.H. / Wang, J. / Hashiguchi, T. / Kamishikiryo, J. / ...Authors: Fukuhara, H. / Yumoto, K. / Sako, M. / Kajikawa, M. / Ose, T. / Kawamura, M. / Yoda, M. / Chen, S. / Ito, Y. / Takeda, S. / Mwaba, M.H. / Wang, J. / Hashiguchi, T. / Kamishikiryo, J. / Maita, N. / Kitatsuji, C. / Takeda, M. / Kuroki, K. / Maenaka, K.
History
DepositionFeb 13, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 31, 2024ID: 8IAY
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin glycoprotein
B: Hemagglutinin glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1084
Polymers99,6662
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-16 kcal/mol
Surface area35400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.156, 86.156, 302.936
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 161 through 169 or resid 171...
d_2ens_1(chain "B" and ((resid 161 through 162 and (name N...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSPROPROAA161 - 1695 - 13
d_12ARGARGALAALAAA171 - 17415 - 18
d_13PROPROPROPROAA18428
d_14GLYGLYPROPROAA190 - 23634 - 80
d_15GLUGLUPROPROAA247 - 27591 - 119
d_16ASNASNGLUGLUAA277 - 298121 - 142
d_17SERSERLEULEUAA300 - 304144 - 148
d_18ASPASPILEILEAA313 - 331157 - 175
d_19LYSLYSASPASPAA333 - 369177 - 213
d_110GLNGLNGLNGLNAA371 - 374215 - 218
d_111GLYGLYARGARGAA376 - 401220 - 245
d_112LEULEUGLYGLYAA403 - 457247 - 301
d_113ILEILEILEILEAA459303
d_114GLYGLYASPASPAA461 - 470305 - 314
d_115PHEPHEVALVALAA472 - 478316 - 322
d_116CYSCYSCYSCYSAA490334
d_117ASPASPILEILEAA503 - 506347 - 350
d_118SERSERTHRTHRAA508 - 515352 - 359
d_119SERSERARGARGAA517 - 529361 - 373
d_120ASPASPILEILEAA531 - 542375 - 386
d_121THRTHRPHEPHEAA544 - 551388 - 395
d_122LEULEUCYSCYSAA553 - 602397 - 446
d_123NAGNAGNAGNAGAC901
d_21LYSLYSPROPROBB161 - 1695 - 13
d_22ARGARGALAALABB171 - 17415 - 18
d_23PROPROPROPROBB18428
d_24GLYGLYPROPROBB190 - 23634 - 80
d_25GLUGLUPROPROBB247 - 27591 - 119
d_26ASNASNGLUGLUBB277 - 298121 - 142
d_27SERSERLEULEUBB300 - 304144 - 148
d_28ASPASPILEILEBB313 - 331157 - 175
d_29LYSLYSASPASPBB333 - 369177 - 213
d_210GLNGLNGLNGLNBB371 - 374215 - 218
d_211GLYGLYARGARGBB376 - 401220 - 245
d_212LEULEUGLYGLYBB403 - 457247 - 301
d_213ILEILEILEILEBB459303
d_214GLYGLYASPASPBB461 - 470305 - 314
d_215PHEPHEVALVALBB472 - 478316 - 322
d_216CYSCYSCYSCYSBB490334
d_217ASPASPILEILEBB503 - 506347 - 350
d_218SERSERTHRTHRBB508 - 515352 - 359
d_219SERSERILEILEBB517 - 542361 - 386
d_220THRTHRPHEPHEBB544 - 551388 - 395
d_221LEULEUCYSCYSBB553 - 602397 - 446
d_222NAGNAGNAGNAGBD901

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Components

#1: Protein Hemagglutinin glycoprotein


Mass: 49832.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Morbillivirus canis / Production host: Homo sapiens neanderthalensis (Neandertal) / References: UniProt: C0LEZ2
#2: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 20mM Tris-HCl pH 8.0, 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 23165 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 68.47 Å2 / Rpim(I) all: 0.069 / Rrim(I) all: 0.173 / Net I/σ(I): 13.4
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 1.248 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2276 / CC1/2: 0.761 / Rpim(I) all: 0.492

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→34.67 Å / SU ML: 0.4001 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.4845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3075 1088 5.06 %
Rwork0.2644 20430 -
obs0.2664 21518 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.56 Å2
Refinement stepCycle: LAST / Resolution: 3.1→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 28 0 6564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286713
X-RAY DIFFRACTIONf_angle_d0.69799136
X-RAY DIFFRACTIONf_chiral_restr0.04811067
X-RAY DIFFRACTIONf_plane_restr0.0061153
X-RAY DIFFRACTIONf_dihedral_angle_d27.1015914
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.05485524701 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.240.39081290.34322504X-RAY DIFFRACTION99.92
3.24-3.410.32711470.30242484X-RAY DIFFRACTION99.77
3.41-3.630.34391440.30262523X-RAY DIFFRACTION99.81
3.63-3.90.34621380.3032508X-RAY DIFFRACTION99.36
3.9-4.30.35551360.28672489X-RAY DIFFRACTION97.95
4.3-4.920.28361270.22212542X-RAY DIFFRACTION98.89
4.92-6.190.28081360.23412621X-RAY DIFFRACTION99.82
6.19-34.670.25171310.24072759X-RAY DIFFRACTION98.9
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)
11.58950788826-1.18769428488-2.111301783351.51945728387-0.8204362112551.087602614840.19574484612-0.4159137065770.5675089774211.05330834102-0.109098425372-0.0861950443963-0.4103258783970.440354540055-0.03595662496340.906946318728-0.138477097659-0.02186860437180.6667528546840.08990065035140.77877957236119.497628627552.01685588727.9866676344
23.2222324567-2.25833484572-1.734604744893.15501934341-0.3941727223271.82685034957-0.01007424253970.750243553009-0.05352572618960.0680495032728-0.05398717553040.7624088493070.2417806710770.2294981053638.33470187494E-50.51554543988-0.03179885992030.01514329939360.6727186963290.0423001011780.55923569322917.701971862838.23284589814.2094452693
32.22547006947-1.195822051661.574055718353.33630465457-2.724365785144.140345623380.01703872904990.156815851253-0.000210220308007-0.349071647326-0.0992714525827-0.2361083860030.3228514427840.546281098425-6.85142873549E-60.415665393652-0.01459330548660.1087828794410.5993071326260.05070418135530.50689657936530.476858315235.714232924518.490668613
4-0.0485168905761-0.0639396797056-0.0106106495115-0.0377795647695-0.01874584659110.1669659299580.268917036154-0.934569831876-0.8741352361990.4570600200080.3491842759520.6203015158411.18952488844-0.9255454055740.002646661551590.6659523665010.003552417276540.04163366054961.165806460290.2104490939421.0380896569629.165405694413.203557261844.9350900464
52.67550001838-1.78301820065-0.9010275985292.224198209890.8059092300814.693852075680.09573322182910.2988036657220.185537238629-0.287389159716-0.0902098449081-0.0442551247722-0.1045248565410.3234950205430.0003250492815760.4572086845750.0696704795412-0.007157096584930.644922938490.116003910550.64778673997434.090346904327.778117403129.7464333923
63.76552725748-2.735887216630.7369550316072.95636956331-0.2320688470292.45180632836-0.0645173559519-0.541292798621-0.1902619631330.2868260114240.25880417959-0.0735838277139-0.1415546664930.08955251847215.19859099585E-50.541989851138-0.04097585246170.05721855207460.5904510179060.0732315523610.59386783901121.286617521934.112092966740.0540414558
73.87734864488-1.39943649776-0.4448432826232.36918336814-2.161563065213.25047975062-0.127536061353-0.101616273829-0.43099242907-0.2682749324010.210984184610.0452349895437-0.0815000683707-0.1544374957750.0003744942567990.5227601466680.07024299681920.07305316293330.7029617733070.1033446728410.54349841557811.089662616441.934212760428.0598429651
83.845768718341.376582427811.644694790763.443257242661.535460056554.14771802881-0.1587699333010.0443681305567-0.254585880243-0.246854089855-0.08858444415560.04802796496360.363650257233-0.0586351559761-0.0001432364960590.5547290953380.0817993610210.08518466567010.522258330770.0996873316660.49862042244515.390333976557.54393323353.11277967209
91.725729538620.15399711053-0.5165684583323.97405482198-1.641734206734.06850085328-0.0350762433506-0.07760613398550.1829018453810.1720359737130.03266878992150.0618817991683-0.826283172606-0.1268459384076.14117397696E-50.6948261672510.0817946916151-0.006438624751440.5369657072160.0215495598070.52233379276719.67433646872.83064388152.63491994175
102.095285456450.5032994917830.4673918424074.090231680791.23997929765.038534411930.2177981423480.1319468437720.0709543699354-0.377329996244-0.3721629439250.194476696826-0.543994711688-0.5713051316580.0001414809768780.8197995291460.110018007855-0.009834890593790.5663429459210.02915214221870.55949016896212.236097939777.1202418045-12.6742180709
111.751321860160.4070454754752.24038958222.97843490015-1.541503024283.702030344210.00137193247511-0.0657971928837-0.121729017954-0.1195812556710.01213527056930.4066059671190.417527984541-0.978987578711-0.0001181351890310.580952178966-0.0208489552516-0.01171019341690.6956664025060.02811743247160.6827035269153.208294346657.1630221479-6.00058392152
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 161 through 211 )AA161 - 2111 - 43
22chain 'A' and (resid 212 through 246 )AA212 - 24644 - 74
33chain 'A' and (resid 247 through 370 )AA247 - 37075 - 193
44chain 'A' and (resid 371 through 391 )AA371 - 391194 - 214
55chain 'A' and (resid 392 through 446 )AA392 - 446215 - 269
66chain 'A' and (resid 447 through 552 )AA447 - 552270 - 371
77chain 'A' and (resid 553 through 602 )AA553 - 602372 - 421
88chain 'B' and (resid 158 through 247 )BB158 - 2471 - 81
99chain 'B' and (resid 248 through 379 )BB248 - 37982 - 209
1010chain 'B' and (resid 380 through 518 )BB380 - 518210 - 337
1111chain 'B' and (resid 519 through 602 )BB519 - 602338 - 420

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