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- PDB-9zg9: Crystal structure of DH511.12P Fab in complex with HIV-1 gp41 MPE... -

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Basic information

Entry
Database: PDB / ID: 9zg9
TitleCrystal structure of DH511.12P Fab in complex with HIV-1 gp41 MPER peptide and phosphatidic acid (06:0 PA); single-lipid form
Components
  • (Antibody DH511.12P 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: 2.21 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

Downloads & links

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Assembly

Deposited unit
A: Antibody DH511.12P Fab heavy chain
B: Antibody DH511.12P Fab light chain
C: Transmembrane protein gp41
D: Antibody DH511.12P Fab heavy chain
E: Antibody DH511.12P Fab light chain
F: Transmembrane protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,73410
Polymers103,5226
Non-polymers1,2114
Water8,125451
1
A: Antibody DH511.12P Fab heavy chain
B: Antibody DH511.12P Fab light chain
C: Transmembrane protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6046
Polymers51,7613
Non-polymers8433
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-29 kcal/mol
Surface area21360 Å2
MethodPISA
2
D: Antibody DH511.12P Fab heavy chain
E: Antibody DH511.12P Fab light chain
F: Transmembrane protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1304
Polymers51,7613
Non-polymers3681
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-32 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.095, 63.382, 121.398
Angle α, β, γ (deg.)90.000, 97.278, 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

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Protein/peptide , 1 types, 2 molecules CF

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


Mass: 2603.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q73372

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Antibody , 2 types, 4 molecules ADBE

#1: Antibody Antibody DH511.12P Fab heavy chain


Mass: 25396.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody DH511.12P Fab light chain


Mass: 23761.459 Da / Num. of mol.: 2
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, 455 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.: 3 / 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.: 451 / 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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG10000, HEPES, ethylene glycol

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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: 2.21→33.91 Å / Num. obs: 57869 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 29.3 Å2 / CC1/2: 0.988 / Net I/σ(I): 6.4
Reflection shellResolution: 2.21→2.25 Å / Num. unique obs: 2906 / CC1/2: 0.32

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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: 2.21→33.91 Å / SU ML: 0.2888 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2402 2882 4.98 %
Rwork0.1904 54951 -
obs0.193 57833 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.54 Å2
Refinement stepCycle: LAST / Resolution: 2.21→33.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7110 0 37 451 7598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01167319
X-RAY DIFFRACTIONf_angle_d1.14319960
X-RAY DIFFRACTIONf_chiral_restr0.06071114
X-RAY DIFFRACTIONf_plane_restr0.01111256
X-RAY DIFFRACTIONf_dihedral_angle_d15.73622597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.250.35751530.29372598X-RAY DIFFRACTION99.57
2.25-2.280.28551300.27262571X-RAY DIFFRACTION99.74
2.28-2.330.32591210.25862614X-RAY DIFFRACTION99.85
2.33-2.370.33781450.24932600X-RAY DIFFRACTION99.93
2.37-2.420.3151280.25282586X-RAY DIFFRACTION99.93
2.42-2.470.33511350.23972601X-RAY DIFFRACTION99.96
2.47-2.530.32631270.24072649X-RAY DIFFRACTION99.93
2.53-2.590.31281490.23412541X-RAY DIFFRACTION100
2.59-2.660.29381320.23442622X-RAY DIFFRACTION99.96
2.66-2.740.28861420.21962614X-RAY DIFFRACTION100
2.74-2.830.30241540.21942575X-RAY DIFFRACTION100
2.83-2.930.291380.21292624X-RAY DIFFRACTION100
2.93-3.050.26621550.2072585X-RAY DIFFRACTION100
3.05-3.190.22961300.2022629X-RAY DIFFRACTION100
3.19-3.350.29421330.18872613X-RAY DIFFRACTION100
3.35-3.560.20531340.1762611X-RAY DIFFRACTION100
3.56-3.840.20651370.17062627X-RAY DIFFRACTION100
3.84-4.220.20571330.15012663X-RAY DIFFRACTION100
4.22-4.830.12961450.12222621X-RAY DIFFRACTION100
4.83-6.080.18681230.14182666X-RAY DIFFRACTION100
6.08-33.910.19021380.17572741X-RAY DIFFRACTION99.9

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