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- PDB-7ri1: Crystal structure of anti-HIV llama VHH antibody J3 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7ri1
TitleCrystal structure of anti-HIV llama VHH antibody J3 in complex with HIV-1 C1086 gp120
Components
  • Glycoprotein 120
  • Lamma VHH antibody J3
KeywordsIMMUNE SYSTEM / Llama / antibody / VHH / HIV-1 / gp120
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhou, T. / Kwong, P.D.
CitationJournal: Structure / Year: 2022
Title: Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site.
Authors: Tongqing Zhou / Lei Chen / Jason Gorman / Shuishu Wang / Young D Kwon / Bob C Lin / Mark K Louder / Reda Rawi / Erik-Stephane D Stancofski / Yongping Yang / Baoshan Zhang / Anna Forsman ...Authors: Tongqing Zhou / Lei Chen / Jason Gorman / Shuishu Wang / Young D Kwon / Bob C Lin / Mark K Louder / Reda Rawi / Erik-Stephane D Stancofski / Yongping Yang / Baoshan Zhang / Anna Forsman Quigley / Laura E McCoy / Lucy Rutten / Theo Verrips / Robin A Weiss / / Nicole A Doria-Rose / Lawrence Shapiro / Peter D Kwong /
Abstract: Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies ...Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies (J3, A12, C8, and D7), all of which targeted the CD4-binding site, in complex with the HIV-1 envelope (Env) gp120 core, and determined a cryoelectron microscopy (cryo-EM) structure of J3 with the Env trimer. Crystal and cryo-EM structures of J3 complexes revealed this nanobody to mimic binding to the prefusion-closed trimer for the primary site of CD4 recognition as well as a secondary quaternary site. In contrast, crystal structures of A12, C8, and D7 with gp120 revealed epitopes that included portions of the gp120 inner domain, inaccessible on the prefusion-closed trimer. Overall, these structures explain the broad and potent neutralization of J3 and limited neutralization of A12, C8, and D7, which utilized binding modes incompatible with the neutralization-targeted prefusion-closed conformation of Env.
History
DepositionJul 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Advisory / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_database_PDB_obs_spr / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Feb 1, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein 120
B: Lamma VHH antibody J3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,84314
Polymers56,8142
Non-polymers2,02912
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-59 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.090, 119.090, 110.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-694-

HOH

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Components

#1: Protein Glycoprotein 120


Mass: 42324.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: plasmid / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: R4GRV3
#2: Protein Lamma VHH antibody J3


Mass: 14489.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: plasmid / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M OF HEPES BUFFER PH 7.5 AND 1 M OF LITHIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31504 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 40.07 Å2 / Rmerge(I) obs: 0.102 / Χ2: 1.037 / Net I/σ(I): 9.7 / Num. measured all: 209127
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.4-2.447.20.83515500.854199.8
2.44-2.497.20.73715520.945199.7
2.49-2.537.30.6115640.924199.6
2.53-2.597.20.52815580.96199.7
2.59-2.647.30.47615460.967199.7
2.64-2.77.20.38615540.976199.8
2.7-2.777.20.31615691.016199.9
2.77-2.857.20.28815680.994199.9
2.85-2.937.20.22615681.0181100
2.93-3.027.10.18115661.071199.9
3.02-3.1370.14615841.145199.8
3.13-3.266.80.11515711.237199.7
3.26-3.416.70.09415791.137199.9
3.41-3.586.30.07515751.197199.3
3.58-3.8160.06315861.079199.1
3.81-4.15.80.05415881.03199.2
4.1-4.525.70.04515841.079198.7
4.52-5.175.60.04115941.007197.9
5.17-6.515.50.04216061.033197
6.51-505.30.03516421.165193

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Processing

Software
NameVersionClassification
PHENIX1.19-4092refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGB

3ngb


Resolution: 2.55→46.2 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 1316 5.1 %
Rwork0.1763 24479 -
obs0.1787 25795 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.68 Å2 / Biso mean: 50.7382 Å2 / Biso min: 22.11 Å2
Refinement stepCycle: final / Resolution: 2.55→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3659 0 123 134 3916
Biso mean--60.07 43.39 -
Num. residues----469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.650.26211140.20712525263992
2.65-2.770.26621380.20182612275095
2.77-2.920.26581480.21382647279596
2.92-3.10.25251570.2082662281998
3.1-3.340.23451480.18852734288299
3.34-3.680.23181520.17452756290899
3.68-4.210.20451600.15462774293499
4.21-5.30.19031650.14322796296199
5.3-46.20.22861340.18312973310799
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)
13.84530.54890.34815.5507-1.0361.5569-0.19290.15370.72960.1450.2434-0.3099-0.43130.6144-0.06890.6304-0.3381-0.03890.62480.00210.393820.7478-34.12927.3611
22.03771.99840.08391.95310.0860.0009-0.1519-0.01670.5224-0.26830.3524-0.0675-0.98740.8456-0.17430.7418-0.3607-0.0250.608-0.0420.562123.9081-29.916112.5112
34.0733.73390.3995.1880.74382.4786-0.46620.33290.4429-0.8520.53140.3994-0.45950.2694-0.09140.3655-0.0893-0.03550.31060.06930.24977.5021-44.339312.5257
41.5687-0.127-0.27841.5150.31440.3854-0.12070.06980.5237-0.22560.0683-0.1889-0.63080.5627-0.03960.5852-0.4048-0.06050.55640.00050.476322.7001-34.057216.4011
52.38560.86160.10162.19630.09012.67320.1417-0.37740.02090.5218-0.1284-0.4346-0.20060.8108-0.08020.3446-0.1462-0.08980.4852-0.01750.285920.2626-48.352632.1953
64.19282.1865-0.75874.638-0.55973.52410.0118-0.01570.54650.2355-0.1635-0.1262-0.82460.31840.14170.5199-0.2355-0.02680.4317-0.05080.422118.0504-30.646319.8187
72.0855-0.128-1.10170.9049-0.09831.81920.51850.18680.5765-0.1909-0.14970.4474-1.0625-0.413-0.33720.71560.14540.09160.34160.0520.442-10.8931-37.714331.4595
87.1652-2.4589-4.94646.13053.2427.0909-0.3606-0.67650.22690.56920.2445-0.0328-0.03170.59670.11180.35430.0366-0.00160.15530.03190.3037-3.5644-44.32138.9221
94.99831.1977-1.90447.2304-3.88947.49770.28340.4272-0.152-0.07760.09240.6928-0.1794-0.5172-0.30570.28740.12550.04830.208-0.02220.2821-10.533-47.015832.572
103.6302-0.827-2.15241.42120.18363.66010.1875-0.26530.1960.05770.09990.0754-0.781-0.0164-0.30390.4281-0.00670.01450.203-0.04140.2366-5.6997-40.809739.2738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 64 )A45 - 64
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 98 )A65 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 202 )A99 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 258 )A203 - 258
5X-RAY DIFFRACTION5chain 'A' and (resid 259 through 470 )A259 - 470
6X-RAY DIFFRACTION6chain 'A' and (resid 471 through 492 )A471 - 492
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 33 )B1 - 33
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 57 )B34 - 57
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 80 )B58 - 80
10X-RAY DIFFRACTION10chain 'B' and (resid 81 through 122 )B81 - 122

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