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- PDB-9zg8: Crystal structure of DH511.1 Fab crystallized in the presence of ... -

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Basic information

Entry
Database: PDB / ID: 9zg8
TitleCrystal structure of DH511.1 Fab crystallized in the presence of HIV-1 gp41 MPER peptide and phosphatidic acid (06:0 PA); unbound form
Components
  • Antibody DH511.1 Fab heavy chain
  • Antibody DH511.1 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsCho, S.Y. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144462 United States
Bill & Melinda Gates FoundationINV-007522 United States
Bill & Melinda Gates FoundationINV-008813 United States
CitationJournal: To Be Published
Title: Structural basis of membrane engagement and polyreactivity control in HIV-1 MPER broadly neutralizing antibodies
Authors: Cho, S.Y. / Wilson, I.A.
History
DepositionDec 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody DH511.1 Fab heavy chain
B: Antibody DH511.1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0353
Polymers48,9402
Non-polymers951
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-30 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.220, 72.745, 93.013
Angle α, β, γ (deg.)90.000, 100.036, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Antibody DH511.1 Fab heavy chain


Mass: 25532.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody DH511.1 Fab light chain


Mass: 23406.984 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG8000, phosphate citrate, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92019 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 1.66→34.11 Å / Num. obs: 60983 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 17.51 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.4
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 3056 / CC1/2: 0.312

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→34.11 Å / SU ML: 0.1876 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.208 2974 4.88 %
Rwork0.1732 57988 -
obs0.1748 60962 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.06 Å2
Refinement stepCycle: LAST / Resolution: 1.66→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 5 672 4040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873446
X-RAY DIFFRACTIONf_angle_d0.99514690
X-RAY DIFFRACTIONf_chiral_restr0.0643526
X-RAY DIFFRACTIONf_plane_restr0.0088600
X-RAY DIFFRACTIONf_dihedral_angle_d13.02691221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.690.30621460.29062745X-RAY DIFFRACTION99.48
1.69-1.710.31211450.27932706X-RAY DIFFRACTION99.79
1.71-1.750.26411510.25422741X-RAY DIFFRACTION99.9
1.75-1.780.29061080.24672829X-RAY DIFFRACTION99.97
1.78-1.820.2891220.22972743X-RAY DIFFRACTION100
1.82-1.860.27011350.22612743X-RAY DIFFRACTION100
1.86-1.90.25421830.22062700X-RAY DIFFRACTION99.97
1.9-1.950.23941500.19252762X-RAY DIFFRACTION100
1.95-20.2171110.18772746X-RAY DIFFRACTION100
2-2.060.2371330.18282823X-RAY DIFFRACTION100
2.06-2.120.2091500.17642726X-RAY DIFFRACTION100
2.12-2.20.21650.17032741X-RAY DIFFRACTION100
2.2-2.290.2191760.16852707X-RAY DIFFRACTION100
2.29-2.390.23451310.17222745X-RAY DIFFRACTION100
2.39-2.520.20341370.17162782X-RAY DIFFRACTION100
2.52-2.680.21961530.17112754X-RAY DIFFRACTION100
2.68-2.880.20471580.16782753X-RAY DIFFRACTION100
2.88-3.170.18791370.16372789X-RAY DIFFRACTION100
3.17-3.630.19261460.14772768X-RAY DIFFRACTION100
3.63-4.570.14271320.12942813X-RAY DIFFRACTION100
4.57-34.110.17121050.15992872X-RAY DIFFRACTION99.77

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