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- PDB-9zgd: Crystal structure of VRC42.01 Fab in the presence of HIV-1 gp41 M... -

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Basic information

Entry
Database: PDB / ID: 9zgd
TitleCrystal structure of VRC42.01 Fab in the presence of HIV-1 gp41 MPER peptide and phosphatidic acid (06:0 PA); unliganded form
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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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

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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


Theoretical massNumber of molelcules
Total (without water)49,9043
Polymers49,9043
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-35 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.443, 73.524, 44.214
Angle α, β, γ (deg.)90.000, 99.430, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG6000, citric acid, lithium chloride

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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: 3.1→50 Å / Num. obs: 11021 / % possible obs: 97.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 53.14 Å2 / CC1/2: 0.943 / Net I/σ(I): 10
Reflection shellResolution: 3.14→3.19 Å / Num. unique obs: 537 / CC1/2: 0.536

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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: 3.1→35.66 Å / SU ML: 0.342 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2441 533 4.85 %
Rwork0.2086 10464 -
obs0.2103 10997 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.35 Å2
Refinement stepCycle: LAST / Resolution: 3.1→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 0 14 3444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00483516
X-RAY DIFFRACTIONf_angle_d0.65984783
X-RAY DIFFRACTIONf_chiral_restr0.0458530
X-RAY DIFFRACTIONf_plane_restr0.0057613
X-RAY DIFFRACTIONf_dihedral_angle_d14.21191247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.410.31091350.27212361X-RAY DIFFRACTION86.76
3.41-3.910.27381490.24632620X-RAY DIFFRACTION96.55
3.91-4.920.21731230.19262738X-RAY DIFFRACTION99
4.92-35.660.20841260.17482745X-RAY DIFFRACTION97.65

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