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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: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis of membrane engagement and polyreactivity control in HIV-1 MPER broadly neutralizing antibodies.
Authors: So Yeon Cho / Kimmo Rantalainen / Gabriel Ozorowski / Danny Lu / Ryan Tingle / Wen-Hsin Lee / Andrew B Ward / William R Schief / Ian A Wilson /
Abstract: The membrane-proximal external region (MPER) of HIV-1 Env represents a critical target for broadly neutralizing antibodies (bnAbs) due to its conservation and functional importance. However, MPER- ...The membrane-proximal external region (MPER) of HIV-1 Env represents a critical target for broadly neutralizing antibodies (bnAbs) due to its conservation and functional importance. However, MPER-targeting bnAbs recognize composite epitopes comprising peptide and viral membrane lipid components, creating an inherent tension between viral neutralization efficacy and polyreactivity. 10E8-class antibodies exhibit high neutralization potency with low polyreactivity, whereas 4E10-class antibodies show comparably broad neutralization but higher polyreactivity, underscoring the need to understand the structural basis of this distinction. We therefore determined crystal structures of DH511.1 (memory B cell-derived), DH511.12P (plasma cell-derived), and VRC42.01 in complex with MPER peptide and phosphatidic acid, along with a cryo-EM reconstruction of DH511.2 bound to membrane-embedded Env. Through integrative analysis taking into account previously determined structures of other MPER bnAbs, we reveal two distinct lipid recognition strategies. Groove-mediated binders, including 10E8 and DH511, engage lipids through antibody-membrane interface grooves with distinct geometries and angular approaches to the membrane. In contrast, heavy chain-mediated binders, including 4E10, PGZL1, and VRC42, utilize positively charged CDR H1 patches for direct lipid headgroup recognition. Importantly, DH511 lineage members exhibited differential cardiolipin polyreactivity linked to their maturation stage. PGZL1 and VRC42.01 employ weaker positive patches at lipid-binding sites than 4E10, and PGZL1 additionally introduces a CDR H3-mediated negative patch that creates electrostatic repulsion with negatively charged lipid headgroups, thereby limiting nonspecific interactions. These findings provide a structural framework for understanding how MPER bnAbs balance lipid binding with specificity and inform immunogen design for inducing safe and effective neutralizing responses.
History
DepositionDec 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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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