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- PDB-7n0x: Rhesusized RV144 DH827 Fab bound to HIV-1 Env V2 peptide -

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Basic information

Entry
Database: PDB / ID: 7n0x
TitleRhesusized RV144 DH827 Fab bound to HIV-1 Env V2 peptide
Components
  • Glycoprotein 120
  • Rhesusized RV144 DH827 heavy chain Fab fragment
  • Rhesusized RV144 DH827 light chain
KeywordsIMMUNE SYSTEM / DH827 / HIV-1 Env V2 peptide / RV144 / Rhesusized antibody
Function / homologystimulatory C-type lectin receptor signaling pathway / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / DI(HYDROXYETHYL)ETHER / Envelope glycoprotein V1V2 region
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: Front Immunol / Year: 2021
Title: Structure and Fc-Effector Function of Rhesusized Variants of Human Anti-HIV-1 IgG1s.
Authors: Tolbert, W.D. / Nguyen, D.N. / Tuyishime, M. / Crowley, A.R. / Chen, Y. / Jha, S. / Goodman, D. / Bekker, V. / Mudrak, S.V. / DeVico, A.L. / Lewis, G.K. / Theis, J.F. / Pinter, A. / Moody, M. ...Authors: Tolbert, W.D. / Nguyen, D.N. / Tuyishime, M. / Crowley, A.R. / Chen, Y. / Jha, S. / Goodman, D. / Bekker, V. / Mudrak, S.V. / DeVico, A.L. / Lewis, G.K. / Theis, J.F. / Pinter, A. / Moody, M.A. / Easterhoff, D. / Wiehe, K. / Pollara, J. / Saunders, K.O. / Tomaras, G.D. / Ackerman, M. / Ferrari, G. / Pazgier, M.
History
DepositionMay 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Rhesusized RV144 DH827 heavy chain Fab fragment
L: Rhesusized RV144 DH827 light chain
G: Glycoprotein 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2124
Polymers49,1063
Non-polymers1061
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-34 kcal/mol
Surface area20410 Å2
Unit cell
Length a, b, c (Å)81.512, 71.865, 87.740
Angle α, β, γ (deg.)90.00, 111.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-498-

HOH

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Components

#1: Antibody Rhesusized RV144 DH827 heavy chain Fab fragment


Mass: 24208.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody Rhesusized RV144 DH827 light chain


Mass: 22737.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Protein/peptide Glycoprotein 120


Mass: 2160.619 Da / Num. of mol.: 1 / Fragment: UNP Residues 56-73 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q70992
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 16.75% PEG 3350 10.05% isopropanol 0.2 M ammonium citrate/citric acid pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.99→81.66 Å / Num. obs: 61001 / % possible obs: 99.5 % / Redundancy: 4 % / CC1/2: 0.995 / Rpim(I) all: 0.053 / Rsym value: 0.095 / Net I/σ(I): 5.3
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4384 / CC1/2: 0.807 / Rpim(I) all: 0.265 / Rsym value: 0.474 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FCU

5fcu


Resolution: 2→52.18 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 2995 4.91 %
Rwork0.1809 --
obs0.1823 61001 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→52.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 7 273 3641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073454
X-RAY DIFFRACTIONf_angle_d0.8864700
X-RAY DIFFRACTIONf_dihedral_angle_d6.448479
X-RAY DIFFRACTIONf_chiral_restr0.057529
X-RAY DIFFRACTIONf_plane_restr0.006598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.030.37631370.28532625X-RAY DIFFRACTION93
2.03-2.060.2911140.26962781X-RAY DIFFRACTION96
2.06-2.10.30181540.24992761X-RAY DIFFRACTION96
2.1-2.140.3141310.24682767X-RAY DIFFRACTION98
2.14-2.180.32431480.23432824X-RAY DIFFRACTION97
2.18-2.230.25451230.23392710X-RAY DIFFRACTION97
2.23-2.280.26681560.22172749X-RAY DIFFRACTION96
2.28-2.340.2711600.21332790X-RAY DIFFRACTION97
2.34-2.40.26131410.23062744X-RAY DIFFRACTION96
2.4-2.470.28861500.22842759X-RAY DIFFRACTION97
2.47-2.550.25021280.21482742X-RAY DIFFRACTION96
2.55-2.650.25161500.21012733X-RAY DIFFRACTION96
2.65-2.750.25521670.20462767X-RAY DIFFRACTION97
2.75-2.880.28251540.19442789X-RAY DIFFRACTION97
2.88-3.030.20841270.19772790X-RAY DIFFRACTION97
3.03-3.220.23071400.18042787X-RAY DIFFRACTION98
3.22-3.470.1951240.16982725X-RAY DIFFRACTION95
3.47-3.820.17911230.15532769X-RAY DIFFRACTION97
3.82-4.370.14281460.12792826X-RAY DIFFRACTION98
4.37-5.50.14271550.12692832X-RAY DIFFRACTION99
5.51-52.180.15361670.1632736X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1280.07022.66991.21720.81734.9019-0.1188-0.08120.24370.0207-0.15420.2109-0.1043-0.18290.2660.2113-0.00390.05410.127-0.00420.2674-10.16637.562817.0285
21.21910.46822.52370.58060.93886.420.0563-0.0651-0.07720.10650.0010.01310.134-0.192-0.06330.17520.02280.05270.15430.00810.2177-5.440120.076113.6551
38.75-3.39260.51878.92380.85833.813-0.2172-0.86760.20051.03390.2507-0.4268-0.06770.1726-0.03910.5262-0.0174-0.06820.3614-0.03110.23969.00635.861145.619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'H' and resid 1 through 213)
2X-RAY DIFFRACTION2(chain 'L' and resid 1 through 210)
3X-RAY DIFFRACTION3(chain 'G' and resid 167 through 184)

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