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- PDB-9ish: Crystal structure of nanobody 32 in complex with HSV-2 gD -

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Basic information

Entry
Database: PDB / ID: 9ish
TitleCrystal structure of nanobody 32 in complex with HSV-2 gD
Components
  • Glycoprotein D
  • Nanobody 32
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: 2.88 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

Downloads & links

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Assembly

Deposited unit
C: Glycoprotein D
D: Nanobody 32
A: Glycoprotein D
B: Nanobody 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0718
Polymers90,1864
Non-polymers8854
Water00
1
C: Glycoprotein D
D: Nanobody 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5354
Polymers45,0932
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycoprotein D
B: Nanobody 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5354
Polymers45,0932
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.639, 136.217, 136.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glycoprotein D


Mass: 30911.258 Da / Num. of mol.: 2
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 32


Mass: 14181.700 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)
#3: 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.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
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
Has ligand of interestN
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: 2.86 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: 0.1 M MES monohydrate (pH 6.0) 14% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.88→96.36 Å / Num. obs: 24241 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.05 / Rrim(I) all: 0.174 / Χ2: 1 / Net I/σ(I): 14.6 / Num. measured all: 281242
Reflection shellResolution: 2.88→3.04 Å / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 1.023 / Num. measured all: 35344 / Num. unique obs: 3490 / CC1/2: 0.815 / Rpim(I) all: 0.33 / Rrim(I) all: 1.076 / Χ2: 0.96 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→19.28 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 1991 8.27 %
Rwork0.2163 --
obs0.2213 24077 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→19.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 56 0 4782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d8.377712
X-RAY DIFFRACTIONf_chiral_restr0.073733
X-RAY DIFFRACTIONf_plane_restr0.012866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.950.3731430.31911554X-RAY DIFFRACTION100
2.95-3.030.36151430.28991558X-RAY DIFFRACTION100
3.03-3.120.30781370.27571529X-RAY DIFFRACTION100
3.12-3.220.31511400.26691552X-RAY DIFFRACTION100
3.22-3.340.33321420.24041558X-RAY DIFFRACTION100
3.34-3.470.25321430.23271577X-RAY DIFFRACTION100
3.47-3.630.28971370.22841526X-RAY DIFFRACTION100
3.63-3.820.35171450.22931574X-RAY DIFFRACTION100
3.82-4.050.30761380.21981564X-RAY DIFFRACTION100
4.05-4.360.23341430.18891597X-RAY DIFFRACTION100
4.36-4.790.21561380.15891585X-RAY DIFFRACTION100
4.8-5.470.22731400.18061593X-RAY DIFFRACTION100
5.48-6.840.28221460.21321624X-RAY DIFFRACTION100
6.85-19.280.24571560.21231695X-RAY DIFFRACTION100

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