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- PDB-9jqu: The crystal structure of SFTSV Gn and SD4 antibody complex -

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Basic information

Entry
Database: PDB / ID: 9jqu
TitleThe crystal structure of SFTSV Gn and SD4 antibody complex
Components
  • Envelopment polyprotein
  • SD4 heavy chain
  • SD4 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SFTSV / Gn / SD4 / antibody / severe fever with thrombocytopenia syndrome virus / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to 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 JS4
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsShi, W.F. / Quan, C.S. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32325003 China
CitationJournal: To Be Published
Title: High affinity human-derived antibodies effectively rescue moribund mice with lethal severe fever with thrombocytopenia virus infection
Authors: Quan, C.S. / Qi, J.X. / Shi, W.F.
History
DepositionSep 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 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: Envelopment polyprotein
L: SD4 light chain
H: SD4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3375
Polymers83,3263
Non-polymers1,0112
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-11 kcal/mol
Surface area32720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.856, 46.360, 97.322
Angle α, β, γ (deg.)90.000, 113.302, 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

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Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 35968.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism SFTS virus JS4 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A1S6K8S9.
Source: (gene. exp.) SFTS virus JS4 / Production host: Homo sapiens (human) / References: UniProt: A0A1S6K8S9
#2: Antibody SD4 light chain


Mass: 23476.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody SD4 heavy chain


Mass: 23880.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate pH 4.6, 30% w/v polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 11858 / % possible obs: 97.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 84.38 Å2 / CC1/2: 0.971 / Net I/σ(I): 5.675
Reflection shellResolution: 3.3→3.42 Å / Num. unique obs: 11716 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y10,7L2E

5y10

7l2e


Resolution: 3.3→32.21 Å / SU ML: 0.4631 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9998
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2887 587 5.01 %
Rwork0.25 11129 -
obs0.252 11716 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78 Å2
Refinement stepCycle: LAST / Resolution: 3.3→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 67 0 5781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00395923
X-RAY DIFFRACTIONf_angle_d0.78868028
X-RAY DIFFRACTIONf_chiral_restr0.0504879
X-RAY DIFFRACTIONf_plane_restr0.00621031
X-RAY DIFFRACTIONf_dihedral_angle_d13.28972150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.630.37561400.31062583X-RAY DIFFRACTION89.28
3.63-4.160.33621450.27182799X-RAY DIFFRACTION96.68
4.16-5.230.2821380.22822834X-RAY DIFFRACTION97.28
5.23-32.210.24521640.23562913X-RAY DIFFRACTION97.04
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)
10.6420489201370.0073698867310.287176684570.393705547457-0.08911812170.8428997104940.0729514747505-0.134043173441-0.07306049237210.09564880926-0.0358593670360.02386273562880.0412009441627-0.04760962695630.7317314444920.5289963939340.004451802462620.01973387725610.4961153530770.005745324127860.4589964265826.723-1.007-26.94
20.1088273834140.1352260070450.01052517443910.2545273739450.3577095216310.2474104060520.02498298762130.124416736765-0.180043838673-0.07884523158580.156791154149-0.16749987465-0.1721231029860.0724890429784-4.581378664590.559086951777-0.0136197474647-0.04569762214540.557156523403-0.0431453667160.657470931177-11.339-28.349-70.512
30.4535731151990.5363905124050.1120325208210.738451210082-0.114469063250.3922645058180.0511627421592-0.01268244511590.01064445497390.167687348944-0.05984219449580.06755944508770.110223766146-0.0966168962866-2.209523416810.5375062821450.01507394199230.02980676851530.61530561308-0.0273494692380.579032775056-24.352-36.926-60.124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 21:341 )A21 - 341
2X-RAY DIFFRACTION2( CHAIN H AND RESID 2:223 )H2 - 223
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:211 )L1 - 211

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