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- PDB-8xk8: N1D10 Fab bound to SFTSV glycoprotein-Gn -

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Basic information

Entry
Database: PDB / ID: 8xk8
TitleN1D10 Fab bound to SFTSV glycoprotein-Gn
Components
  • Envelopment polyprotein
  • mAb N1D10 Fab heavy chain
  • mAb N1D10 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 speciesSevere fever with thrombocytopenia syndrome virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å
AuthorsZhao, H. / Deng, 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 6, 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: Envelopment polyprotein
B: Envelopment polyprotein
H: mAb N1D10 Fab heavy chain
L: mAb N1D10 Fab light chain
C: mAb N1D10 Fab heavy chain
D: mAb N1D10 Fab light chain


Theoretical massNumber of molelcules
Total (without water)183,8266
Polymers183,8266
Non-polymers00
Water00
1
A: Envelopment polyprotein
H: mAb N1D10 Fab heavy chain
L: mAb N1D10 Fab light chain


Theoretical massNumber of molelcules
Total (without water)91,9133
Polymers91,9133
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-35 kcal/mol
Surface area30340 Å2
MethodPISA
2
B: Envelopment polyprotein
C: mAb N1D10 Fab heavy chain
D: mAb N1D10 Fab light chain


Theoretical massNumber of molelcules
Total (without water)91,9133
Polymers91,9133
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-35 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.124, 111.909, 87.856
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 39523.969 Da / Num. of mol.: 2
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
#2: Antibody mAb N1D10 Fab heavy chain


Mass: 26368.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fab heavy chain / Production host: Homo sapiens (human)
#3: Antibody mAb N1D10 Fab light chain


Mass: 26020.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.095 M tri-Sodium citrate pH 5.6, 19 %(v/v) Isopropanol, 19 %(w/v) PEG 4000, 5 %(v/v) glycerol

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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: Nov 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.52→47.16 Å / Num. obs: 20028 / % possible obs: 98.5 % / Redundancy: 2.7 % / CC1/2: 0.758 / Net I/σ(I): 3.4
Reflection shellResolution: 3.52→3.85 Å / Redundancy: 2.6 % / Num. unique obs: 4658 / CC1/2: 0.626

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.53→20.69 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3239 1086 5.49 %
Rwork0.2499 --
obs0.2539 19778 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.53→20.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11394 0 0 0 11394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411672
X-RAY DIFFRACTIONf_angle_d0.79915820
X-RAY DIFFRACTIONf_dihedral_angle_d5.8421602
X-RAY DIFFRACTIONf_chiral_restr0.0481726
X-RAY DIFFRACTIONf_plane_restr0.0062026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.53-3.690.34081330.26832301X-RAY DIFFRACTION99
3.69-3.880.36591100.28022330X-RAY DIFFRACTION98
3.88-4.120.39271170.26612333X-RAY DIFFRACTION99
4.12-4.440.3391250.24082370X-RAY DIFFRACTION100
4.44-4.880.30061220.23052358X-RAY DIFFRACTION99
4.88-5.580.32921650.23592319X-RAY DIFFRACTION99
5.58-6.980.30971470.26172328X-RAY DIFFRACTION99
6.98-20.690.22291670.21142353X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 36.627 Å / Origin y: -24.1179 Å / Origin z: 22.921 Å
111213212223313233
T0.0893 Å2-0.0058 Å2-0.0131 Å2-0.0914 Å2-0.005 Å2--0.0801 Å2
L0.0689 °20.0514 °20.0144 °2-0.0188 °2-0.0222 °2--0.0443 °2
S0.0067 Å °-0.0154 Å °-0.0044 Å °0.0457 Å °-0.0001 Å °-0.0384 Å °-0.0181 Å °-0.0188 Å °0.0462 Å °
Refinement TLS groupSelection details: all

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