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- PDB-8zgu: Crystal structural of HTNV Gn and AH100 Fab -

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Basic information

Entry
Database: PDB / ID: 8zgu
TitleCrystal structural of HTNV Gn and AH100 Fab
Components
  • AH100 heavy chain
  • AH100 light chain
  • Envelopment polyprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HTNV Gn / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / virus-mediated perturbation of host defense response / virion membrane / signal transduction / membrane / metal ion binding
Similarity search - Function
: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal ...: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesOrthohantavirus hantanense
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsWang, F.R. / Wu, Y. / Gao, F.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303402 China
National Natural Science Foundation of China (NSFC)32090014 China
National Natural Science Foundation of China (NSFC)82022042 China
CitationJournal: To Be Published
Title: Crystal structural of HTNV Gn and AH100 Fab
Authors: Wang, F.R. / Wu, Y. / Gao, F.
History
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelopment polyprotein
H: AH100 heavy chain
L: AH100 light chain


Theoretical massNumber of molelcules
Total (without water)85,0973
Polymers85,0973
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.380, 170.380, 117.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 38604.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthohantavirus hantanense / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A077D153
#2: Antibody AH100 heavy chain


Mass: 23832.586 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 AH100 light chain


Mass: 22659.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium citrate, pH5.5, 50% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.00389 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00389 Å / Relative weight: 1
ReflectionResolution: 3.51→50 Å / Num. obs: 20660 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellResolution: 3.51→3.72 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 10 / CC1/2: 0.856

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.51→48.26 Å / SU ML: 0.6447 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.3357
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.295 555 5 %
Rwork0.2525 10535 -
obs0.2548 11090 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 189.4 Å2
Refinement stepCycle: LAST / Resolution: 3.51→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5823 0 0 0 5823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00355968
X-RAY DIFFRACTIONf_angle_d0.70578136
X-RAY DIFFRACTIONf_chiral_restr0.0486930
X-RAY DIFFRACTIONf_plane_restr0.00611031
X-RAY DIFFRACTIONf_dihedral_angle_d6.3404815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.51-3.860.40671350.33722572X-RAY DIFFRACTION99.63
3.86-4.420.33891370.31442596X-RAY DIFFRACTION100
4.42-5.560.28431380.2522621X-RAY DIFFRACTION99.96
5.57-48.260.26581450.20992746X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: 45.8566885518 Å / Origin y: 16.1207774466 Å / Origin z: 45.4897522119 Å
111213212223313233
T0.95377926987 Å20.17845369211 Å20.377381472958 Å2-1.01096927812 Å20.36007133016 Å2--1.1463238304 Å2
L2.7797266525 °21.11331914028 °2-0.353548310211 °2-3.07227812528 °2-0.33009347448 °2--3.21358537223 °2
S-0.306271286382 Å °-0.546789266821 Å °-0.807088486521 Å °-0.100440490943 Å °-0.320909940443 Å °-0.259291759702 Å °1.06054127442 Å °0.787957838548 Å °0.26464767617 Å °
Refinement TLS groupSelection details: all

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