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- PDB-9jqv: The crystal structure of SFTSV Gn and SD12 antibody complex -

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Basic information

Entry
Database: PDB / ID: 9jqv
TitleThe crystal structure of SFTSV Gn and SD12 antibody complex
Components
  • Envelopment polyprotein
  • SD12 heavy chain
  • SD12 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SFTSV / Gn / SD12 / 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 HB29
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
H: SD12 heavy chain
L: SD12 light chain
B: Envelopment polyprotein
C: SD12 heavy chain
D: SD12 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,97710
Polymers166,1586
Non-polymers1,8194
Water6,071337
1
A: Envelopment polyprotein
H: SD12 heavy chain
L: SD12 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0905
Polymers83,0793
Non-polymers1,0112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Envelopment polyprotein
C: SD12 heavy chain
D: SD12 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8875
Polymers83,0793
Non-polymers8082
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.064, 82.342, 125.293
Angle α, β, γ (deg.)90.000, 104.310, 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

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Antibody , 2 types, 4 molecules HCLD

#2: Antibody SD12 heavy chain


Mass: 23511.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody SD12 light chain


Mass: 23599.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 339 molecules AB

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 35968.695 Da / Num. of mol.: 2
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 HB29 / Production host: Homo sapiens (human) / References: UniProt: A0A1S6K8S9
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 4 molecules

#4: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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 / 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

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Details

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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M magnesium chloride hexahydrate, 0.1 M sodium HEPES, 7.0, 15 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 74450 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 37.92 Å2 / CC1/2: 0.979 / Net I/σ(I): 11.105
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 66789 / CC1/2: 0.614

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.92 Å / SU ML: 0.3303 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 3373 5.05 %
Rwork0.2254 63416 -
obs0.227 66789 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11345 0 120 337 11802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004111740
X-RAY DIFFRACTIONf_angle_d0.711615901
X-RAY DIFFRACTIONf_chiral_restr0.04491752
X-RAY DIFFRACTIONf_plane_restr0.00582038
X-RAY DIFFRACTIONf_dihedral_angle_d16.26984268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.4059900.32941502X-RAY DIFFRACTION51.21
2.43-2.470.34821050.32321647X-RAY DIFFRACTION56.64
2.47-2.510.4005870.31561859X-RAY DIFFRACTION63.2
2.51-2.550.4162940.291993X-RAY DIFFRACTION67.78
2.55-2.590.37881040.28282190X-RAY DIFFRACTION73.86
2.59-2.640.29881230.27862260X-RAY DIFFRACTION78.39
2.64-2.690.27261180.28182476X-RAY DIFFRACTION83.33
2.69-2.750.33851510.27242563X-RAY DIFFRACTION87.75
2.75-2.80.34041520.27222705X-RAY DIFFRACTION93.18
2.8-2.870.2951600.27372893X-RAY DIFFRACTION98.01
2.87-2.940.34041320.27072941X-RAY DIFFRACTION98.97
2.94-3.020.29721730.282873X-RAY DIFFRACTION99.87
3.02-3.110.29131530.27012949X-RAY DIFFRACTION99.94
3.11-3.210.30621600.25882941X-RAY DIFFRACTION100
3.21-3.330.28881630.24082931X-RAY DIFFRACTION99.87
3.33-3.460.29351390.23542949X-RAY DIFFRACTION100
3.46-3.620.26431410.23072972X-RAY DIFFRACTION99.9
3.62-3.810.23921600.21662941X-RAY DIFFRACTION99.94
3.81-4.040.25561580.20282957X-RAY DIFFRACTION100
4.04-4.360.20261580.17832957X-RAY DIFFRACTION99.94
4.36-4.790.2141500.16122953X-RAY DIFFRACTION99.87
4.79-5.490.19351620.17322989X-RAY DIFFRACTION99.9
5.49-6.910.19281740.20432970X-RAY DIFFRACTION99.9
6.91-45.920.19321660.21143005X-RAY DIFFRACTION98.51
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)
10.285846637623-0.04808301270.127391410090.558338592124-0.200875440610.7733731861-0.05177770446350.0254241363210.06552863570670.2394713957540.0526563878973-0.03308829487760.0140918844832-0.08639089611850.007375392612470.328538831080.06195957976850.02275638326010.202211600726-0.008442840815050.178173830344-27.078734481520.707595733-15.5159138512
20.2677549714150.03438140908310.1852906660950.2133002106910.05288162635430.6786265595640.189301890103-0.0574612922645-0.06637853048120.24286829696-0.1020210041060.007320431477870.226434368561-0.03056342655480.05592707004120.437112864475-0.0731494929271-0.04652476905020.2439432110060.03577269997010.22548466797219.242101352825.2361693123-7.00849587935
30.1538429031140.1961857981260.04829694659060.5892409059280.1849717369590.176700833198-0.09481704005910.0678430297796-0.07707556063220.03579879590210.134923575773-0.1642716657090.258549048466-0.0836041365591-0.002392042548410.164122706072-0.03782169010730.03687425710010.289838097121-0.03958816797480.28786067550718.116153977717.6832280604-59.6237240213
40.6535043466810.28491394151-0.2266482709261.0461067267-0.1665327253730.159758862258-0.3284305614380.09680409246240.0266876681325-0.1587997170480.3133723917570.0588596956618-0.0235340016942-0.0363886930935-0.002593448528930.129221472707-0.171633530341-0.003790276589170.26544213934-0.004838352505720.22150546580924.860836296834.3138009782-65.2807883282
50.2282324437390.0725751740065-0.04695404528070.6314396913670.3713354394830.250965965754-0.197024701815-0.01373211237090.238679406095-0.2036264672620.1550640022880.187850827605-0.3359275794640.0121066078342-0.02009126837960.129799944217-0.093248492929-0.05275048400780.1219154721970.09666683759060.208194629841-21.284683970128.341212116-67.4829944477
60.581164249920.3220023354060.4104286402860.8870225842530.4299142214370.335449705267-0.2328685145830.133144508213-0.00546072987697-0.2463193407570.15165770037-0.0779552599686-0.2087976573940.105601179393-0.08285166128060.172408390912-0.09579790465220.02203861433360.2150978545790.003791866416150.236776634429-18.510504721810.1517275831-72.2864764507
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA - F21 - 3491
22chain BBI - M21 - 3481
33chain CCN1 - 2231 - 214
44chain DDO1 - 2111 - 211
55chain HHG1 - 2231 - 214
66chain LLH1 - 2111 - 211

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