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- PDB-4nug: Crystal structure of HIV-1 broadly neutralizing antibody PGT151 -

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Basic information

Entry
Database: PDB / ID: 4nug
TitleCrystal structure of HIV-1 broadly neutralizing antibody PGT151
Components
  • PGT151 heavy chain
  • PGT151 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / Fab fragment / HIV Envelope
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8617 Å
AuthorsBlattner, C. / Wilson, I.A.
CitationJournal: Immunity / Year: 2014
Title: Structural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers.
Authors: Claudia Blattner / Jeong Hyun Lee / Kwinten Sliepen / Ronald Derking / Emilia Falkowska / Alba Torrents de la Peña / Albert Cupo / Jean-Philippe Julien / Marit van Gils / Peter S Lee / ...Authors: Claudia Blattner / Jeong Hyun Lee / Kwinten Sliepen / Ronald Derking / Emilia Falkowska / Alba Torrents de la Peña / Albert Cupo / Jean-Philippe Julien / Marit van Gils / Peter S Lee / Wenjie Peng / James C Paulson / Pascal Poignard / Dennis R Burton / John P Moore / Rogier W Sanders / Ian A Wilson / Andrew B Ward /
Abstract: All previously characterized broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) target one of four major sites of vulnerability. Here, we define and structurally characterize a ...All previously characterized broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) target one of four major sites of vulnerability. Here, we define and structurally characterize a unique epitope on Env that is recognized by a recently discovered family of human monoclonal antibodies (PGT151-PGT158). The PGT151 epitope is comprised of residues and glycans at the interface of gp41 and gp120 within a single protomer and glycans from both subunits of a second protomer and represents a neutralizing epitope that is dependent on both gp120 and gp41. Because PGT151 binds only to properly formed, cleaved trimers, this distinctive property, and its ability to stabilize Env trimers, has enabled the successful purification of mature, cleaved Env trimers from the cell surface as a complex with PGT151. Here we compare the structural and functional properties of membrane-extracted Env trimers from several clades with those of the soluble, cleaved SOSIP gp140 trimer.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PGT151 light chain
H: PGT151 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7104
Polymers50,1452
Non-polymers5652
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-25 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.645, 66.977, 84.552
Angle α, β, γ (deg.)90.00, 133.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PGT151 light chain


Mass: 24057.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#2: Antibody PGT151 heavy chain


Mass: 26087.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: S6BAM6
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 4.2
Details: 40% PEG 3350, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 11, 2012
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→33.5 Å / Num. all: 39140 / Num. obs: 39140 / % possible obs: 97.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.08 / Net I/σ(I): 29.2
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 74.5 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.35

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FX7

2fx7


Resolution: 1.8617→33.489 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 1957 5 %RANDOM
Rwork0.1589 ---
obs0.1613 39127 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8617→33.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 32 485 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063635
X-RAY DIFFRACTIONf_angle_d1.0954923
X-RAY DIFFRACTIONf_dihedral_angle_d12.8161333
X-RAY DIFFRACTIONf_chiral_restr0.075542
X-RAY DIFFRACTIONf_plane_restr0.004631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8617-1.90820.28861230.18652338X-RAY DIFFRACTION87
1.9082-1.95980.21931390.16832622X-RAY DIFFRACTION97
1.9598-2.01750.20021390.15642648X-RAY DIFFRACTION98
2.0175-2.08260.19331390.15472638X-RAY DIFFRACTION98
2.0826-2.1570.23071400.15342664X-RAY DIFFRACTION98
2.157-2.24330.23951400.17232667X-RAY DIFFRACTION98
2.2433-2.34540.23271400.16482654X-RAY DIFFRACTION98
2.3454-2.4690.24251400.16852659X-RAY DIFFRACTION98
2.469-2.62370.26731410.17312692X-RAY DIFFRACTION99
2.6237-2.82610.21081420.17542680X-RAY DIFFRACTION99
2.8261-3.11040.20621420.16912701X-RAY DIFFRACTION99
3.1104-3.560.19321420.15452714X-RAY DIFFRACTION99
3.56-4.48350.15861440.1342716X-RAY DIFFRACTION99
4.4835-33.49390.19721460.1562777X-RAY DIFFRACTION99
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)
10.6563-0.3157-0.02850.50080.08180.45130.1006-0.1879-0.2276-0.0411-0.03510.0407-0.02530.03790.04640.1329-0.0213-0.02280.19770.04520.16742.7534-33.70225.041
20.44560.28530.00480.2211-0.05530.08840.1725-0.127-0.22370.0257-0.1419-0.0472-0.07050.07560.01680.1348-0.01710.00490.17570.01390.1226.7443-27.789623.2006
32.0090.56610.18132.53670.34990.5324-0.0534-0.09270.1356-0.04840.04240.1107-0.04940.0509-0.00790.13440.01470.00140.1587-0.00110.13636.1389-25.214318.3121
43.4081.61330.21684.0838-0.28961.12310.0057-0.1160.01130.165-0.0686-0.1387-0.07950.17240.06660.15010.00570.01750.177-0.02210.099740.5676-25.004719.6178
50.25010.0157-0.09930.3256-0.27050.38920.0065-0.03640.012-0.08290.0320.0442-0.0459-0.07610.00630.10370.0025-0.0070.09450.00570.1078-0.5029-12.980213.4998
60.0553-0.06310.06380.2628-0.17780.1270.0652-0.04260.150.04730.04010.13550.0152-0.0570.01320.1558-0.02870.03660.1329-0.00140.17-4.1486-15.485218.1375
70.28710.138-0.09510.2617-0.03190.03150.06470.0375-0.0341-0.0508-0.0480.0006-0.01260.021400.14120.0204-0.01210.1133-0.01230.11934.5452-23.73534.4911
80.02280.07120.01990.22360.06230.01660.07720.0102-0.0494-0.3174-0.0116-0.169-0.08260.1724-0.00570.20140.05360.020.24080.03280.151936.8978-18.1066-2.3124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resseq 1:80)
2X-RAY DIFFRACTION2chain 'L' and (resseq 81:106)
3X-RAY DIFFRACTION3chain 'L' and (resseq 107:166)
4X-RAY DIFFRACTION4chain 'L' and (resseq 167:213)
5X-RAY DIFFRACTION5chain 'H' and (resseq 1:99)
6X-RAY DIFFRACTION6chain 'H' and (resseq 100:119)
7X-RAY DIFFRACTION7chain 'H' and (resseq 120:213)
8X-RAY DIFFRACTION8chain 'H' and (resseq 214:228)

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