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- PDB-9isf: Crystal structure of nanobody 14 in complex with HSV-2 gD -

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Basic information

Entry
Database: PDB / ID: 9isf
TitleCrystal structure of nanobody 14 in complex with HSV-2 gD
Components
  • Glycoprotein D
  • Nanobody 14
KeywordsANTIVIRAL PROTEIN / Herpes simplex virus / Nanobody
Function / homologyHerpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / Immunoglobulin-like domain superfamily / viral envelope / virion membrane / membrane / Glycoprotein D
Function and homology information
Biological speciesHuman alphaherpesvirus 2
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.72 Å
AuthorsHu, J. / Jin, T.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82272301 China
CitationJournal: Nat Commun / Year: 2025
Title: A potent protective bispecific nanobody targeting Herpes simplex virus gD reveals vulnerable epitope for neutralizing.
Authors: Hu, J. / Tan, H. / Wang, M. / Deng, S. / Liu, M. / Zheng, P. / Wang, A. / Guo, M. / Wang, J. / Li, J. / Qiu, H. / Yao, C. / Zhu, Z. / Hasi, C. / Pan, D. / He, H. / Huang, C. / Shang, Y. / Zhu, S. / Jin, T.
History
DepositionJul 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein D
B: Nanobody 14


Theoretical massNumber of molelcules
Total (without water)44,9242
Polymers44,9242
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)107.605, 107.605, 129.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein Glycoprotein D


Mass: 30911.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 2 / Gene: US6 / Production host: Homo sapiens (human) / References: UniProt: A0A1W6QD44
#2: Antibody Nanobody 14


Mass: 14012.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / 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: 4.19 Å3/Da / Density % sol: 74.16 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: 0.2 M Ammonium citrate dibasic (pH 5.1) 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.72→107.61 Å / Num. obs: 8197 / % possible obs: 96.6 % / Redundancy: 13.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.425 / Rpim(I) all: 0.12 / Rrim(I) all: 0.442 / Χ2: 0.99 / Net I/σ(I): 6.5 / Num. measured all: 108508
Reflection shellResolution: 3.72→3.93 Å / % possible obs: 89.4 % / Redundancy: 13.2 % / Rmerge(I) obs: 1.779 / Num. measured all: 14243 / Num. unique obs: 1081 / CC1/2: 0.836 / Rpim(I) all: 0.503 / Rrim(I) all: 1.851 / Χ2: 0.94 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.72→48.12 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3474 420 5.16 %
Rwork0.3006 --
obs0.3031 8136 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.72→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 0 0 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d5.725386
X-RAY DIFFRACTIONf_chiral_restr0.066416
X-RAY DIFFRACTIONf_plane_restr0.01482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.72-4.260.40741270.33662466X-RAY DIFFRACTION95
4.26-5.370.32031430.29192625X-RAY DIFFRACTION99
5.37-48.120.34041500.2912625X-RAY DIFFRACTION94

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