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- PDB-7ri2: Crystal structure of anti-HIV llama VHH antibody A12 in complex w... -

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Basic information

Entry
Database: PDB / ID: 7ri2
TitleCrystal structure of anti-HIV llama VHH antibody A12 in complex with HIV-1 C1086 gp120
Components
  • Glycoprotein 120
  • anti-HIV llama VHH antibody A12
KeywordsIMMUNE SYSTEM / Llama / antibody / VHH / HIV-1 / gp120
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Database references / Category: citation / citation_author
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
Revision 1.2Oct 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
A: Glycoprotein 120
B: anti-HIV llama VHH antibody A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,98310
Polymers58,2132
Non-polymers1,7708
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint22 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.596, 66.596, 266.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: R4GRV3
#2: Antibody anti-HIV llama VHH antibody A12


Mass: 15888.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): HEK293F / 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / 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
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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 50 mM of KH2PO4, 24.2% PEG 8000, pH 7.8

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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 225 mm CCD / Detector: CCD / Date: Apr 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15260 / % possible obs: 77.7 % / Redundancy: 11.3 % / Biso Wilson estimate: 79.93 Å2 / Rmerge(I) obs: 0.124 / Χ2: 1.518 / Net I/σ(I): 9 / Num. measured all: 172947
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.6-2.6950.4457580.916139.8
2.69-2.86.20.4138860.967146.4
2.8-2.937.60.3419131.092147.6
2.93-3.088.20.29611381.228160
3.08-3.289.60.29516471.071185.5
3.28-3.53120.26419071.105197.8
3.53-3.88140.20119461.466199.6
3.88-4.45140.15219731.801199.5
4.45-5.613.70.13119992.009199.8
5.6-5012.50.08920931.766195.4

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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: 2.8→23.55 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 45.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3296 623 4.67 %
Rwork0.2732 12728 -
obs0.2759 13351 85.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 313.93 Å2 / Biso mean: 151.4488 Å2 / Biso min: 66.75 Å2
Refinement stepCycle: final / Resolution: 2.8→23.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 112 0 3399
Biso mean--173.87 --
Num. residues----420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-3.080.4546980.38941922202053
3.08-3.530.39341530.36623313346690
3.53-4.440.34811870.29633633382098
4.44-23.550.29981850.2353860404598
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)
16.9907-2.1163.14838.3299-0.20839.05040.5859-0.5131.06580.4713-0.6408-0.5101-1.0739-1.9160.3951.59610.18990.33911.73390.15080.84798.301831.2811-34.4147
23.95290.7122-0.99754.1553-2.03491.5690.24490.58120.552-0.60550.13150.686-1.0565-2.1497-0.37621.57690.48050.16742.2880.31540.88972.865422.9363-36.8647
30.7879-0.8173-0.43131.39520.10631.4244-0.07530.5449-0.0392-1.22110.45220.41550.6647-2.9114-0.20061.44110.012-0.01523.02080.29330.9126-6.069316.0985-33.4494
44.9421.20370.18373.5177-0.08813.21770.14271.3405-0.0367-0.3289-0.14350.6076-0.21-3.1755-0.03941.1270.16720.17543.6105-0.02831.0864-15.042216.3579-20.5603
56.05884.83961.38375.07650.89061.56410.32250.75291.23320.8839-0.83131.51480.0302-2.1434-1.20621.55490.06920.58973.55280.00150.9303-11.448820.97-13.3056
64.09460.28660.11844.49891.42880.63170.97870.27470.90270.4222-1.15271.1183-0.1162-2.39450.10761.57110.21990.20683.531-0.05880.9958-14.882318.9203-16.3874
72.7659-0.0959-0.293.45711.87420.9769-0.01881.3499-0.4006-0.5926-0.39580.64640.7095-2.5418-0.09830.7425-0.2232-0.06082.63570.22930.6301-2.81213.652-29.4466
83.05540.5033-0.78925.1153.02572.2141-0.2158-0.14580.01250.30030.13280.03470.36050.2580.10892.08910.45980.21722.1371-0.30470.782510.466213.5242-55.9908
96.3193-3.2675-1.13748.52113.97464.92890.19111.195-0.2334-0.38820.2937-0.94660.96751.1481-0.1781.0578-0.35890.0661.6205-0.16660.567423.72961.9379-15.3739
106.7925-4.68611.12367.75492.39774.11050.93191.11.3995-0.0149-0.2651-1.37810.1787-0.3781-0.00450.7394-0.54950.20641.46850.00160.44817.672411.438-15.3981
113.757-1.8975-0.04211.35010.38394.98230.09190.4291-1.3049-1.18780.83380.52671.0882-0.595-0.33661.2577-0.72820.01461.56750.08190.363610.7651.321-12.3398
125.4698-2.8044-3.70254.23014.34114.7867-0.33480.9238-0.07450.50570.4576-0.00771.0516-0.89730.00381.4383-0.31070.19171.4985-0.10280.687214.06169.0443-3.8624
133.9081-2.6318-1.67366.79911.45175.83450.1054-0.20320.38241.1714-0.7673-1.09131.5250.79590.14340.97-0.6037-0.16491.3168-0.18010.304721.76086.0336-8.3704
147.10623.2822-1.31911.76740.59096.64171.19221.4329-0.4318-0.03310.4902-0.30710.0648-0.80.49240.5246-0.79820.1591.7113-0.06060.338713.48437.4221-17.0819
155.578-3.624.27817.9947-4.99097.07940.28931.6541-0.04250.2721-0.38810.6913-0.7025-0.55770.31721.1906-0.29720.3511.7078-0.00640.67675.612219.4141-9.0507
165.5318-4.42040.27054.23240.63197.5911-0.22290.9174-0.08540.3971-0.170.78630.3358-1.14480.19181.1629-0.54-0.03131.45460.0080.507114.43992.7153-16.538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 73 )A45 - 73
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 235 )A74 - 235
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 283 )A236 - 283
4X-RAY DIFFRACTION4chain 'A' and (resid 284 through 378 )A284 - 378
5X-RAY DIFFRACTION5chain 'A' and (resid 379 through 395 )A379 - 395
6X-RAY DIFFRACTION6chain 'A' and (resid 396 through 457 )A396 - 457
7X-RAY DIFFRACTION7chain 'A' and (resid 458 through 491 )A458 - 491
8X-RAY DIFFRACTION8chain 'A' and (resid 492 through 492 )A492
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 17 )B1 - 17
10X-RAY DIFFRACTION10chain 'B' and (resid 18 through 39 )B18 - 39
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 52 )B40 - 52
12X-RAY DIFFRACTION12chain 'B' and (resid 52A through 66 )B52
13X-RAY DIFFRACTION13chain 'B' and (resid 67 through 87 )B67 - 87
14X-RAY DIFFRACTION14chain 'B' and (resid 88 through 96 )B88 - 96
15X-RAY DIFFRACTION15chain 'B' and (resid 97 through 100F)B97 - 100
16X-RAY DIFFRACTION16chain 'B' and (resid 100G through 113 )B100

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