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- PDB-9zgb: Crystal structure of VRC42.01 Fab in complex with HIV-1 gp41 MPER... -

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Basic information

Entry
Database: PDB / ID: 9zgb
TitleCrystal structure of VRC42.01 Fab in complex with HIV-1 gp41 MPER peptide and phosphatidic acid (06:0 PA)
Components
  • Antibody VRC42.01 Fab heavy chain
  • Antibody VRC42.01 Fab light chain
  • 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 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 VRC42.01 Fab heavy chain
B: Antibody VRC42.01 Fab light chain
C: Transmembrane protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6415
Polymers49,9043
Non-polymers7372
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-31 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.401, 128.375, 207.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody Antibody VRC42.01 Fab heavy chain


Mass: 24051.127 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 VRC42.01 Fab light chain


Mass: 23249.666 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: 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
#4: 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
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: 4.96 Å3/Da / Density % sol: 75.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG200, CAPS, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.44→50 Å / Num. obs: 13274 / % possible obs: 98.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 60.69 Å2 / CC1/2: 0.978 / Net I/σ(I): 8.2
Reflection shellResolution: 3.44→3.5 Å / Num. unique obs: 650 / CC1/2: 0.628

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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: 3.45→35.01 Å / SU ML: 0.487 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2692 668 5.05 %
Rwork0.2267 12565 -
obs0.229 13233 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.66 Å2
Refinement stepCycle: LAST / Resolution: 3.45→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 21 0 3396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01533480
X-RAY DIFFRACTIONf_angle_d1.62724740
X-RAY DIFFRACTIONf_chiral_restr0.0683525
X-RAY DIFFRACTIONf_plane_restr0.0134607
X-RAY DIFFRACTIONf_dihedral_angle_d17.09581220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.710.37231170.29992475X-RAY DIFFRACTION97.85
3.71-4.090.28451370.25512450X-RAY DIFFRACTION97.84
4.09-4.680.24711260.2052483X-RAY DIFFRACTION97.86
4.68-5.890.25811200.20722566X-RAY DIFFRACTION99.44
5.89-35.010.24121680.2032591X-RAY DIFFRACTION97.77

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