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- PDB-8xk5: SNB1G11 Fab bound to SFTSV glycoprotein Gn -

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Basic information

Entry
Database: PDB / ID: 8xk5
TitleSNB1G11 Fab bound to SFTSV glycoprotein Gn
Components
  • Envelopment polyprotein
  • mAb SNB1G11 Fab heavy chain
  • mAb SNB1G11 Fab light chain
KeywordsVIRAL PROTEIN / glycoprotein / Gn / Fab
Function / homology
Function and homology information


host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / 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 speciesMus musculus (house mouse)
Severe fever with thrombocytopenia syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsDeng, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: A broadly protective antibody targeting glycoprotein Gn inhibits severe fever with thrombocytopenia syndrome virus infection.
Authors: Ren, X. / Sun, J. / Kuang, W. / Yu, F. / Wang, B. / Wang, Y. / Deng, W. / Xu, Z. / Yang, S. / Wang, H. / Hu, Y. / Deng, Z. / Ning, Y.J. / Zhao, H.
History
DepositionDec 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
Revision 1.2Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mAb SNB1G11 Fab heavy chain
B: mAb SNB1G11 Fab light chain
E: Envelopment polyprotein
C: mAb SNB1G11 Fab heavy chain
D: mAb SNB1G11 Fab light chain
F: Envelopment polyprotein
I: mAb SNB1G11 Fab heavy chain
J: mAb SNB1G11 Fab light chain
K: Envelopment polyprotein
N: mAb SNB1G11 Fab heavy chain
O: mAb SNB1G11 Fab light chain
R: Envelopment polyprotein
G: mAb SNB1G11 Fab heavy chain
H: mAb SNB1G11 Fab light chain
L: Envelopment polyprotein


Theoretical massNumber of molelcules
Total (without water)464,51915
Polymers464,51915
Non-polymers00
Water00
1
A: mAb SNB1G11 Fab heavy chain
B: mAb SNB1G11 Fab light chain
E: Envelopment polyprotein


Theoretical massNumber of molelcules
Total (without water)92,9043
Polymers92,9043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: mAb SNB1G11 Fab heavy chain
D: mAb SNB1G11 Fab light chain
F: Envelopment polyprotein


Theoretical massNumber of molelcules
Total (without water)92,9043
Polymers92,9043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: mAb SNB1G11 Fab heavy chain
J: mAb SNB1G11 Fab light chain
K: Envelopment polyprotein


Theoretical massNumber of molelcules
Total (without water)92,9043
Polymers92,9043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
N: mAb SNB1G11 Fab heavy chain
O: mAb SNB1G11 Fab light chain
R: Envelopment polyprotein


Theoretical massNumber of molelcules
Total (without water)92,9043
Polymers92,9043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
G: mAb SNB1G11 Fab heavy chain
H: mAb SNB1G11 Fab light chain
L: Envelopment polyprotein


Theoretical massNumber of molelcules
Total (without water)92,9043
Polymers92,9043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.670, 180.960, 263.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody
mAb SNB1G11 Fab heavy chain


Mass: 27999.414 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fab heavy chain / Production host: Homo sapiens (human)
#2: Antibody
mAb SNB1G11 Fab light chain


Mass: 25380.344 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fab light chain / Production host: Homo sapiens (human)
#3: Protein
Envelopment polyprotein / M polyprotein


Mass: 39523.969 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe fever with thrombocytopenia syndrome virus
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4V2Q5
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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20 % (w/v) Jeffamine ED2003, 0.1M HEPES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. obs: 79582 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.997 / Net I/σ(I): 8.5
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 5.1 % / Num. unique obs: 5119 / CC1/2: 0.543

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→29.97 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.281 5276 5.08 %
Rwork0.215 --
obs0.2184 79582 76.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27019 0 0 0 27019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01227669
X-RAY DIFFRACTIONf_angle_d1.45837457
X-RAY DIFFRACTIONf_dihedral_angle_d6.5293800
X-RAY DIFFRACTIONf_chiral_restr0.0744035
X-RAY DIFFRACTIONf_plane_restr0.0124794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.090.4054240.2912438X-RAY DIFFRACTION13
3.09-3.120.3105470.2673745X-RAY DIFFRACTION22
3.12-3.160.3834560.27891019X-RAY DIFFRACTION30
3.16-3.20.3459610.26411169X-RAY DIFFRACTION35
3.2-3.250.4092710.26661423X-RAY DIFFRACTION42
3.25-3.290.343680.26661537X-RAY DIFFRACTION45
3.29-3.340.32471000.2751724X-RAY DIFFRACTION51
3.34-3.40.3104980.26551840X-RAY DIFFRACTION55
3.4-3.450.32991230.26542025X-RAY DIFFRACTION60
3.45-3.510.34051170.25572183X-RAY DIFFRACTION65
3.51-3.570.31211200.25012360X-RAY DIFFRACTION70
3.57-3.640.32971380.2412509X-RAY DIFFRACTION74
3.64-3.720.28451360.23642671X-RAY DIFFRACTION79
3.72-3.80.31541380.22972888X-RAY DIFFRACTION84
3.8-3.890.32261630.23513060X-RAY DIFFRACTION90
3.89-3.980.31861890.22173217X-RAY DIFFRACTION95
3.98-4.090.25851860.21693392X-RAY DIFFRACTION100
4.09-4.210.29631710.18783438X-RAY DIFFRACTION100
4.21-4.350.27091930.18463352X-RAY DIFFRACTION100
4.35-4.50.23621600.17593422X-RAY DIFFRACTION100
4.5-4.680.22571950.17653396X-RAY DIFFRACTION100
4.68-4.890.24621870.18373411X-RAY DIFFRACTION100
4.89-5.150.24321690.17653449X-RAY DIFFRACTION100
5.15-5.470.26521960.19893423X-RAY DIFFRACTION100
5.47-5.890.2642080.20533397X-RAY DIFFRACTION100
5.89-6.480.28371620.22473491X-RAY DIFFRACTION100
6.48-7.40.28771900.2253474X-RAY DIFFRACTION100
7.4-9.280.24621870.2023501X-RAY DIFFRACTION100
9.28-29.970.25021930.22043582X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -51.3935 Å / Origin y: 2.4523 Å / Origin z: -33.5303 Å
111213212223313233
T0.0245 Å20.0107 Å20.0529 Å2-0.0309 Å20.12 Å2--0.0253 Å2
L0.015 °2-0.0075 °2-0.0182 °2-0.0221 °2-0.0091 °2--0.0279 °2
S0.0461 Å °0.0124 Å °0.0585 Å °0.0248 Å °-0.0178 Å °0.0186 Å °0.028 Å °0.0213 Å °0 Å °
Refinement TLS groupSelection details: all

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