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- PDB-9ub6: Crystal structure of SFTSV Gn head with nanobody VHH261 -

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Basic information

Entry
Database: PDB / ID: 9ub6
TitleCrystal structure of SFTSV Gn head with nanobody VHH261
Components
  • Glycoprotein N
  • Nanobody VHH261
KeywordsVIRAL PROTEIN / SFTSV
Function / homology
Function and homology information


host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion membrane / membrane
Similarity search - Function
Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesSFTS virus HB29
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsWu, Y. / Chang, Z. / Wu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32090014 China
CitationJournal: To Be Published
Title: Crystal structure of SFTSV Gn head with nanobody VHH261
Authors: Wu, Y. / Chang, Z.
History
DepositionApr 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 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: Glycoprotein N
B: Nanobody VHH261
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8064
Polymers47,6742
Non-polymers1,1322
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint14 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.710, 172.710, 136.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein Glycoprotein N / Gn / Glycoprotein G1


Mass: 35050.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism SFTS virus HB29 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id R4V2Q5.
Source: (gene. exp.) SFTS virus HB29 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: R4V2Q5
#2: Antibody Nanobody VHH261


Mass: 12623.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector pCAGGS (others)
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 1 / 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
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: 6.24 Å3/Da / Density % sol: 80.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Ammonium sulfate, 0.3M Sodium formate, 0.1M Sodium acetate, pH5.0, 3% w/v gama-PGA (Na+ form, LM), 3% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.89→52.2 Å / Num. obs: 27305 / % possible obs: 99.92 % / Redundancy: 36.7 % / Biso Wilson estimate: 66.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 16
Reflection shellResolution: 2.89→2.97 Å / Num. unique obs: 10 / CC1/2: 0.709

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→52.2 Å / SU ML: 0.3266 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 2000 7.33 %
Rwork0.1912 25302 -
obs0.1933 27302 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.68 Å2
Refinement stepCycle: LAST / Resolution: 2.89→52.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 75 0 3350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01063426
X-RAY DIFFRACTIONf_angle_d1.1224625
X-RAY DIFFRACTIONf_chiral_restr0.0602504
X-RAY DIFFRACTIONf_plane_restr0.0077589
X-RAY DIFFRACTIONf_dihedral_angle_d7.274509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.960.31751390.30081757X-RAY DIFFRACTION99.95
2.96-3.040.3441400.28361773X-RAY DIFFRACTION100
3.04-3.130.32731400.27831772X-RAY DIFFRACTION100
3.13-3.230.28821400.25751778X-RAY DIFFRACTION100
3.23-3.350.28071410.2291769X-RAY DIFFRACTION100
3.35-3.480.28271400.2141790X-RAY DIFFRACTION100
3.48-3.640.22631420.19511785X-RAY DIFFRACTION100
3.64-3.830.20981420.18021791X-RAY DIFFRACTION100
3.83-4.070.19731410.17361796X-RAY DIFFRACTION100
4.07-4.390.15241440.14531810X-RAY DIFFRACTION100
4.39-4.830.18551440.14531818X-RAY DIFFRACTION100
4.83-5.530.18991440.15511826X-RAY DIFFRACTION100
5.53-6.960.21871470.19821863X-RAY DIFFRACTION100
6.96-52.20.21691560.19621974X-RAY DIFFRACTION99.44
Refinement TLS params.Method: refined / Origin x: 71.732 Å / Origin y: -24.187 Å / Origin z: -31.146 Å
111213212223313233
T0.54328862392 Å2-0.0414931326365 Å2-0.0462686137945 Å2-0.465505939789 Å20.0189662456207 Å2--0.504717737508 Å2
L0.594785838381 °20.553558523141 °20.0710643454422 °2-2.09868607804 °20.774823842255 °2--0.892472978361 °2
S0.00179378908469 Å °0.0200548690877 Å °0.263856245665 Å °-0.084267455609 Å °-0.16475779813 Å °0.247621108807 Å °-0.187579245837 Å °-0.0566978338409 Å °0.174704132977 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:339 OR RESID 400:400 ) ) OR ( CHAIN B AND RESID 1:115 )A22 - 339
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:339 OR RESID 400:400 ) ) OR ( CHAIN B AND RESID 1:115 )A400
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:339 OR RESID 400:400 ) ) OR ( CHAIN B AND RESID 1:115 )B1 - 115

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