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- PDB-6vbo: Crystal structure of anti-HIV-1 antibody DH813 bound to gp120 V2 ... -

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Basic information

Entry
Database: PDB / ID: 6vbo
TitleCrystal structure of anti-HIV-1 antibody DH813 bound to gp120 V2 peptide
Components
  • DH813 heavy chain
  • DH813 light chain
  • Envelope glycoprotein gp160
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Antibody / GP120 V2 / RV305/RV144 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / 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 perturbation of host defense response / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 1.683 Å
AuthorsJanus, B.M. / Ofek, G.
CitationJournal: JCI Insight / Year: 2020
Title: HIV vaccine delayed boosting increases Env variable region 2-specific antibody effector functions.
Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Janus, B. / Gohain, N. / Williams, L.D. / Tay, M.Z. / Monroe, A. / Peachman, K. / Choe, M. / Min, S. / Lusso, P. / Zhang, P. / Go, E.P. / Desaire, H. ...Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Janus, B. / Gohain, N. / Williams, L.D. / Tay, M.Z. / Monroe, A. / Peachman, K. / Choe, M. / Min, S. / Lusso, P. / Zhang, P. / Go, E.P. / Desaire, H. / Bonsignori, M. / Hwang, K.K. / Beck, C. / Kakalis, M. / O'Connell, R.J. / Vasan, S. / Kim, J.H. / Michael, N.L. / Excler, J.L. / Robb, M.L. / Rerks-Ngarm, S. / Kaewkungwal, J. / Pitisuttithum, P. / Nitayaphan, S. / Sinangil, F. / Tartaglia, J. / Phogat, S. / Wiehe, K. / Saunders, K.O. / Montefiori, D.C. / Tomaras, G.D. / Moody, M.A. / Arthos, J. / Rao, M. / Joyce, M.G. / Ofek, G.A. / Ferrari, G. / Haynes, B.F.
History
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: DH813 light chain
H: DH813 heavy chain
C: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)50,1343
Polymers50,1343
Non-polymers00
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-29 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.570, 63.920, 70.580
Angle α, β, γ (deg.)90.000, 92.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody DH813 light chain


Mass: 23957.439 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 DH813 heavy chain


Mass: 23501.447 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 Envelope glycoprotein gp160 / Env polyprotein


Mass: 2675.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: I2E6B7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% 2-propanol, 15% PEG 8000 and 0.1M imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 52264 / % possible obs: 93.3 % / Redundancy: 4.1 % / Rpim(I) all: 0.061 / Net I/σ(I): 10.1
Reflection shellResolution: 1.68→1.72 Å / Mean I/σ(I) obs: 1.76 / Num. unique obs: 3994 / Rpim(I) all: 0.061

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3228phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVE

1fve


Resolution: 1.683→27.748 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.46
RfactorNum. reflection% reflection
Rfree0.2081 1982 3.79 %
Rwork0.1746 --
obs0.1759 52264 93.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.49 Å2 / Biso mean: 33.5968 Å2 / Biso min: 13.42 Å2
Refinement stepCycle: final / Resolution: 1.683→27.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 0 532 3918
Biso mean---39.33 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6834-1.72550.2846960.2427251265
1.7255-1.77210.31291310.2404343690
1.7721-1.82430.27321440.2271354293
1.8243-1.88310.27941390.226361894
1.8831-1.95040.26781430.2099362095
1.9504-2.02850.25381350.2029368996
2.0285-2.12080.24281560.1912370096
2.1208-2.23250.18731430.1821367496
2.2325-2.37230.22841510.1806370297
2.3723-2.55540.23391450.1844373496
2.5554-2.81230.21421470.1815370896
2.8123-3.21880.21341520.1729373797
3.2188-4.05330.18781470.1524375097
4.0533-27.7480.16361530.1512386098

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