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- PDB-9nw5: 3H4v31 anti-HLA-E-VL9 Fab -

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Basic information

Entry
Database: PDB / ID: 9nw5
Title3H4v31 anti-HLA-E-VL9 Fab
Components
  • 3H4v31 heavy chain
  • 3H4v31 light chain
KeywordsIMMUNE SYSTEM / HLA-E / antibody / NKG2a / CD94
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWrapp, D. / Hwang, J.K. / Marston, D.J. / Haynes, B.F. / Azoitei, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI164567 United States
CitationJournal: To Be Published
Title: HLA-E-VL9 antibodies mediate NKG2A+ NK cell and CD8+ T cell killing of HIV-infected CD4+ T cells
Authors: Hwang, J.K. / Marston, D.J. / Tuyishime, M. / Yang, H. / Wrapp, D. / Li, D. / Brackenridge, S. / Frazier, M. / Rhodes, B. / Harris, C. / Quastel, M. / Kapingidza, A.B. / Gater, J. / Borrow, ...Authors: Hwang, J.K. / Marston, D.J. / Tuyishime, M. / Yang, H. / Wrapp, D. / Li, D. / Brackenridge, S. / Frazier, M. / Rhodes, B. / Harris, C. / Quastel, M. / Kapingidza, A.B. / Gater, J. / Borrow, P. / Gillespie, G.M. / Ferrari, G. / McMichael, A.J. / Haynes, B.F. / Azoitei, M.L.
History
DepositionMar 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 3H4v31 heavy chain
L: 3H4v31 light chain


Theoretical massNumber of molelcules
Total (without water)48,8122
Polymers48,8122
Non-polymers00
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-25 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.480, 82.811, 94.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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: Antibody 3H4v31 heavy chain


Mass: 25364.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 3H4v31 light chain


Mass: 23448.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20.1% PEG 1500, 2.01% MPD, 0.2 M magnesium sulfate, 0.1 M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.05→62.34 Å / Num. obs: 36913 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 18.35 Å2 / CC1/2: 0.94 / Net I/σ(I): 12.5
Reflection shellResolution: 2.05→2.11 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2836 / CC1/2: 0.886

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Processing

Software
NameVersionClassification
PHENIXdev_3758refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→62.34 Å / SU ML: 0.3143 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2442 1796 5.1 %
Rwork0.2152 33388 -
obs0.2167 35184 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.51 Å2
Refinement stepCycle: LAST / Resolution: 2.05→62.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 0 483 3822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523417
X-RAY DIFFRACTIONf_angle_d0.77384647
X-RAY DIFFRACTIONf_chiral_restr0.05522
X-RAY DIFFRACTIONf_plane_restr0.0052591
X-RAY DIFFRACTIONf_dihedral_angle_d23.09451231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.54441370.55422345X-RAY DIFFRACTION88.58
2.11-2.170.25251380.26552641X-RAY DIFFRACTION99.82
2.17-2.240.31141290.30222153X-RAY DIFFRACTION81.47
2.24-2.320.3972900.3231917X-RAY DIFFRACTION71.68
2.32-2.410.23791430.21882670X-RAY DIFFRACTION100
2.41-2.520.2681330.21352692X-RAY DIFFRACTION100
2.52-2.650.3081470.22262653X-RAY DIFFRACTION99.64
2.65-2.820.241400.21572656X-RAY DIFFRACTION99.43
2.82-3.040.25511460.19852680X-RAY DIFFRACTION99.75
3.04-3.340.2251490.19592710X-RAY DIFFRACTION99.97
3.34-3.830.2011530.17772664X-RAY DIFFRACTION98.43
3.83-4.820.17621410.14632727X-RAY DIFFRACTION98.9
4.82-62.340.19031500.18262880X-RAY DIFFRACTION99.97

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