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- PDB-9zg7: Crystal structure of DH511.1 Fab in complex with HIV-1 gp41 MPER ... -

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Basic information

Entry
Database: PDB / ID: 9zg7
TitleCrystal structure of DH511.1 Fab in complex with HIV-1 gp41 MPER peptide and phosphatidic acid (06:0 PA)
Components
  • (Antibody DH511.1 Fab ...) x 2
  • Transmembrane protein gp41
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host complement activation by recruitment of complement control protein / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated suppression of host complement activation by recruitment of complement control protein / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / DI(HYDROXYETHYL)ETHER / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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

Downloads & links

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Assembly

Deposited unit
A: Antibody DH511.1 Fab heavy chain
B: Antibody DH511.1 Fab light chain
C: Transmembrane protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0175
Polymers51,5433
Non-polymers4742
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-28 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.329, 73.089, 142.540
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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


Mass: 2603.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q73372

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Antibody , 2 types, 2 molecules AB

#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)

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Non-polymers , 3 types, 361 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate


Mass: 368.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H29O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG400, sodium citrate

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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: 0.92015 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92015 Å / Relative weight: 1
ReflectionResolution: 2.06→33.5 Å / Num. obs: 31389 / % possible obs: 99.7 % / Redundancy: 13.6 % / Biso Wilson estimate: 21.78 Å2 / CC1/2: 0.99 / Net I/σ(I): 6
Reflection shellResolution: 2.06→2.09 Å / Num. unique obs: 1500 / CC1/2: 0.36

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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: 2.06→32.52 Å / SU ML: 0.2579 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2472 1569 5 %
Rwork0.211 29814 -
obs0.2128 31383 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.36 Å2
Refinement stepCycle: LAST / Resolution: 2.06→32.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 25 359 3923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443647
X-RAY DIFFRACTIONf_angle_d0.72714956
X-RAY DIFFRACTIONf_chiral_restr0.0453551
X-RAY DIFFRACTIONf_plane_restr0.0066628
X-RAY DIFFRACTIONf_dihedral_angle_d14.751304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.120.33281420.29532627X-RAY DIFFRACTION99.43
2.12-2.20.30681360.28162648X-RAY DIFFRACTION99.46
2.2-2.290.33251570.26722661X-RAY DIFFRACTION99.23
2.29-2.390.31821440.24912661X-RAY DIFFRACTION99.72
2.39-2.520.29671280.24142701X-RAY DIFFRACTION99.65
2.52-2.680.28841440.23222672X-RAY DIFFRACTION99.75
2.68-2.880.21251360.20762712X-RAY DIFFRACTION99.79
2.88-3.170.2811410.21382721X-RAY DIFFRACTION99.86
3.17-3.630.20671440.17932754X-RAY DIFFRACTION99.93
3.63-4.570.19651540.15462743X-RAY DIFFRACTION99.97
4.57-32.520.2041430.19752914X-RAY DIFFRACTION99.93

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