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

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Basic information

Entry
Database: PDB / ID: 9zga
TitleCrystal structure of DH511.12P Fab in complex with HIV-1 gp41 MPER peptide and phosphatidic acid (06:0 PA); double-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 / PHOSPHATE ION / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9989
Polymers51,8483
Non-polymers1,1506
Water6,774376
1
A: Antibody DH511.12P Fab heavy chain
B: Antibody DH511.12P Fab light chain
C: Transmembrane protein gp41
hetero molecules

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)105,99718
Polymers103,6976
Non-polymers2,30012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area14710 Å2
ΔGint-83 kcal/mol
Surface area40990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.527, 73.527, 230.411
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-558-

HOH

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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 DH511.12P Fab heavy chain


Mass: 25396.617 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 DH511.12P Fab light chain


Mass: 23848.539 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 , 4 types, 382 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate


Mass: 368.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H29O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 3.47 Å3/Da / Density % sol: 64.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, potassium iodide

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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: 1.97→32.9 Å / Num. obs: 52310 / % possible obs: 99.7 % / Redundancy: 20.4 % / Biso Wilson estimate: 28.3 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.4
Reflection shellResolution: 1.97→2 Å / Num. unique obs: 2553 / CC1/2: 0.354

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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: 1.97→32.88 Å / SU ML: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2643 2488 4.76 %
Rwork0.2259 49810 -
obs0.2277 52298 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.29 Å2
Refinement stepCycle: LAST / Resolution: 1.97→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 62 376 4025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01123732
X-RAY DIFFRACTIONf_angle_d1.12655071
X-RAY DIFFRACTIONf_chiral_restr0.0641566
X-RAY DIFFRACTIONf_plane_restr0.0085636
X-RAY DIFFRACTIONf_dihedral_angle_d16.12051341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-20.34281540.31372670X-RAY DIFFRACTION99.16
2-2.040.35991550.29552721X-RAY DIFFRACTION99.21
2.04-2.090.29751290.27572705X-RAY DIFFRACTION99.16
2.09-2.140.28931370.26922703X-RAY DIFFRACTION99.23
2.14-2.190.28631320.25882716X-RAY DIFFRACTION99.58
2.19-2.250.3091530.25212716X-RAY DIFFRACTION99.55
2.25-2.320.30151500.24882728X-RAY DIFFRACTION99.45
2.32-2.390.28591100.23952759X-RAY DIFFRACTION99.55
2.39-2.480.28291370.24762712X-RAY DIFFRACTION99.65
2.48-2.580.29671370.23522756X-RAY DIFFRACTION99.72
2.58-2.690.28891140.25192782X-RAY DIFFRACTION99.69
2.69-2.830.26541360.2362784X-RAY DIFFRACTION99.86
2.84-3.010.28091350.24012759X-RAY DIFFRACTION99.9
3.01-3.240.2741510.22412774X-RAY DIFFRACTION99.93
3.25-3.570.26771150.2122821X-RAY DIFFRACTION99.93
3.57-4.090.2381590.18672832X-RAY DIFFRACTION100
4.09-5.150.2131350.1692850X-RAY DIFFRACTION99.97
5.15-32.880.23731490.24373022X-RAY DIFFRACTION100

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